littler/0000755000176200001440000000000014577647212011750 5ustar liggesuserslittler/NAMESPACE0000644000176200001440000000024413351700132013143 0ustar liggesusers## (almost) emtpty file as we ## do not need a dynamic library ## do not import from other packages ## only export one small helper (by request) export("r") littler/ChangeLog0000644000176200001440000015024314577617312013525 0ustar liggesusers2024-03-23 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.20 * configure.ac: Idem * configure: Idem 2024-03-17 Dirk Eddelbuettel * inst/examples/ciw.r: Correct one documentation label 2024-03-14 Dirk Eddelbuettel * inst/examples/doi2bib.r: Allow multiple DOIs, check packages 2024-03-13 Dirk Eddelbuettel * inst/examples/doi2bib.r: New wrapper for DOI request for bibtex entry 2024-03-11 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll micro version and date 2024-03-10 Dirk Eddelbuettel * R/init.R: Tweaks to generalized message * src/littler.c: In non-vanilla mode, rerun temp. dir initialization after local configuration files to allow for non-standard temp. file 2024-03-10 Berwin A Turlach * R/init.R: Generalize message to reflect ${R_ARCH} (if set) 2024-03-06 Dirk Eddelbuettel * inst/examples/ciw.r: Add connectivity check, tweak lines display 2024-03-05 Dirk Eddelbuettel * inst/examples/tttf.r: Support devtools::load_all() option 2024-03-02 Dirk Eddelbuettel * inst/examples/ciw.r: Several small tweaks 2024-02-29 Dirk Eddelbuettel * inst/examples/ciw.r: New wrapper around ciw::incoming() 2024-02-28 Dirk Eddelbuettel * inst/examples/tttf.r: Use env -S r -t for per-session temp dir, support command-line argument -c | --ci to set env.var CI 2024-02-25 Dirk Eddelbuettel * DESCRIPTION (Suggests): Removed package used in only one example 2024-02-22 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll micro version and date * inst/examples/tt.r: Fill in "inst/tinytest" if `-d | --dir` but the target directory was omitted, and exists 2024-02-20 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll micro version and date * inst/examples/tt.r: Use env -S r -t for per-session temp dir, support command-line argument -c | --ci to set env.var CI 2024-02-16 Dirk Eddelbuettel * .github/workflows/ci.yaml (jobs): Update to actions/checkout@v4, add r-ci-setup actions 2024-01-18 Dirk Eddelbuettel * inst/examples/tttl.r: Use env -S r -t for per-session temp dir 2024-01-16 Dirk Eddelbuettel * inst/examples/rcc.r (rccwrapper): Use env -S r -t to switch to using a per-session temporary directory as R does 2024-01-03 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll micro version and date * inst/examples/installDeps2.r: Add simpler, dependency-free second variant of 'install dependencies found in DESCRIPTION' 2023-12-17 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.19 * configure.ac: Idem * configure: Idem 2023-12-12 Dirk Eddelbuettel * inst/examples/installRSPM.r: Update to p3m, install as installP3M.r 2023-12-01 Dirk Eddelbuettel * inst/examples/r2u.r: Add new --compile flag, small edits * inst/examples/installDeps.r: Small edit for --help text 2023-11-03 Dirk Eddelbuettel * inst/examples/installGithub.r: Add usage example for installation from repository sub-directory 2023-10-09 Dirk Eddelbuettel * inst/examples/r2u.r: Add --dryrun argument for (single) package build 2023-10-03 Dirk Eddelbuettel * inst/examples/tt.r: Switch the default value for 'effects' from FALSE to TRUE which, while a breaking change, is the better default. 2023-09-25 Dirk Eddelbuettel * inst/examples/installRub.r: Also allow 'package@universe' format 2023-09-20 Dirk Eddelbuettel * inst/examples/r2u.r: Another posit.co URL update 2023-09-19 Dirk Eddelbuettel * inst/examples/tttf.r: Extend --library to several arguments 2023-09-16 Dirk Eddelbuettel * inst/examples/installRSPM.r: Edits to help text, also show default distribution 2023-09-02 Dirk Eddelbuettel * inst/examples/r2u.r: Support BioConductor updates 2023-09-01 Dirk Eddelbuettel * inst/examples/tttf.r: Add --source argument 2023-08-21 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll micro version and date * README.md: Add r-universe badge 2023-08-20 Dirk Eddelbuettel * inst/examples/installRSPM.r: Minor edits for coexistence, update base url to new corporate name and URL * inst/examples/installPPM.r: Install as hard link to installRSPM.r 2023-08-09 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll micro version and date * inst/examples/r2u.r: Add two more options for modifying the Debian version of a package being built * inst/examples/tttf.r: Very initial version of a single file testthat runner (aka 'testthat::test_file()' 2023-07-15 Dirk Eddelbuettel * inst/examples/installDeps.r: Support dependencies argument * inst/examples/check.r: Correct one line in help text 2023-06-01 Dirk Eddelbuettel * README.md: Note more prominently that this does not build on Windows 2023-05-15 Dirk Eddelbuettel * inst/examples/tttl.r: Expanded usage text 2023-05-11 Dirk Eddelbuettel * inst/examples/r2u.r: Micro-edit to displayed text 2023-03-25 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.18 * configure.ac: Idem * configure: Idem 2023-03-23 SHIMA Tatsuya * inst/examples/install2.r (capture): Update error message pattern used to detect failure to change in R 4.3.* 2023-03-23 Dirk Eddelbuettel * inst/examples/install2.r (capture): Small generalisation for somewhat fragile error capture 2023-03-22 Dirk Eddelbuettel * inst/examples/tttl.r: Small usability enhancement 2023-03-21 Dirk Eddelbuettel * inst/examples/installRub.r: Small extensions * inst/examples/r2u.r: Correction on suffix use 2023-03-20 Dirk Eddelbuettel * inst/examples/installRub.r: Initial version of r-universe binary installer 2023-03-10 Dirk Eddelbuettel * inst/examples/tttl.r: Very simple wrapper to testthat::test_local() * inst/examples/tt.r: Remove extra library(), change to https url 2023-02-22 Dirk Eddelbuettel * inst/examples/r2u.r: Extend with --suffix option 2023-02-14 Dirk Eddelbuettel * inst/examples/installGithub.r: Offer a type option and set it * inst/examples/install2.r: Ditto 2023-02-13 Dirk Eddelbuettel * inst/examples/getRStudioDesktop.r: Updated default file * inst/examples/getRStudioServer.r: Idem 2022-12-31 Dirk Eddelbuettel * inst/examples/roxy.r: Added --libpath LIB option 2022-10-29 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.17 * configure.ac: Idem * configure: Idem 2022-10-28 Dirk Eddelbuettel * src/littler.c: Turn several functions into proper prototypes to make clang-15 happier * .github/workflows/ci.yaml (jobs): Update to actions/checkout@v3 2022-09-03 Dirk Eddelbuettel * inst/examples/installBioc.r (capture): Update error message pattern used to detect failure to change in R 4.3.* 2022-09-03 SHIMA Tatsuya * inst/examples/install2.r (capture): Update error message pattern used to detect failure to change in R 4.3.* 2022-08-28 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.16 * configure.ac: Idem * configure: Idem * inst/examples/installBioc.r: Small polish 2022-08-24 Pieter Moris * inst/examples/installBioc.r: Generalization, extension and extra features similar to how install2.r generalizes install2.r 2022-07-16 Dirk Eddelbuettel * inst/examples/r2u.r: Add simple r2u.r frontend 2022-04-03 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll minor version and date * src/littler.c (init_rand): Update to current seeding version in R, add stdint.h header for uint_least64_t 2022-04-02 Dirk Eddelbuettel * configure.ac: Add two more header function checks * configure: Regenerated * src/config.h.in: Regenerated from expanded configure.ac 2022-02-25 Dirk Eddelbuettel * inst/examples/install2.r: Default installation directory is now the first element in .libPaths() which can reflect R_LIBS_USER etc 2022-02-22 Dirk Eddelbuettel * inst/examples/rcc.r: Add -v | --valgrind option 2022-01-21 Dirk Eddelbuettel * inst/examples/install2.r: Correct typo (thanks, @jds485) 2022-01-16 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll minor version and date 2022-01-16 SHIMA Tatsuya * inst/examples/install2.r: Generalize -r option use 2021-12-21 Dirk Eddelbuettel * inst/examples/getPandoc.r: Add Pandoc .deb downloader 2021-12-15 Dirk Eddelbuettel * inst/examples/cowu.r: Add Windows UCRT checker 2021-12-03 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.15 * configure.ac: Idem * configure: Idem 2021-12-02 Dirk Eddelbuettel * inst/examples/mdweave2html.r: Add caller for simplermarkdown 2021-11-17 Dirk Eddelbuettel * README.md: Remove Travis badge * .travis.yml: Remove Travis YAML config 2021-10-27 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll minor version and date, (Suggests): Use simplermarkdown not knitr, rmarkdown, minidown * vignettes/littler-faq.md: Converted to simplermarkdown vignette * vignettes/littler-examples.md: Idem * vignettes/water.css: Added 2021-10-26 Dirk Eddelbuettel * inst/examples/build.r: Set --compact-vignettes to both * inst/examples/getRStudioDesktop.r: Updated to changed urls * inst/examples/getRStudioServer.r: Idem 2021-10-23 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll minor version and date 2021-10-22 Gergely Daroczi * inst/examples/install2.r: Check failure from parallel installs 2021-10-20 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll minor version and date 2021-10-20 Gergely Daroczi * inst/examples/install2.r: Support download methods argument 2021-10-18 John Kerl * README.md: Fix three typos 2021-10-05 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.14 * configure.ac: Idem * configure: Idem * configure.ac: Updated via 'autoupdate' and 'autoreconf --warnings=obsolete' followed by light edit * src/config.h.in: Idem 2021-10-03 Dirk Eddelbuettel * DESCRIPTION (URL): Add documentation site to URL entry 2021-09-18 Dirk Eddelbuettel * inst/examples/getQuartoCli.r: Add simple convenience downloader for Quarto command-line .deb package parsing GitHub release result 2021-09-14 Dirk Eddelbuettel * inst/examples/roxy.r: Add -m | --minimal variant for namespace and rd roclets using the cached older version 2021-08-31 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll minor version and date 2021-08-30 Dirk Eddelbuettel * inst/examples/getRStudioDesktop.r: Updated to changed names * inst/examples/getRStudioServer.r: Idem 2021-07-24 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.13 * configure.ac: Idem * configure: Idem * tests/simpleTests.R: Slightly extended * R/test.R (test): Minor tweak * vignettes/littler-faq.Rmd (vignette): Update one URL * vignettes/littler-faq.html: Re-rendered * vignettes/littler-examples.html: Idem * .editorconfig: Added * .Rbuildignore: Added .editorconfig 2021-07-21 Dirk Eddelbuettel * inst/NEWS.Rd: Added entries for several changes since last release 2021-07-19 Dirk Eddelbuettel * inst/examples/kitten.r: Note bunny and puppy only work with plain 2021-07-09 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll minor version and date * inst/examples/kitten.r: Correct calls for arma and eigen 2021-06-28 Dirk Eddelbuettel * inst/examples/cranIncoming.r: Corrected message 2021-06-28 Aaron Wolen * inst/examples/tt.r: Correct two typos 2021-04-04 Dirk Eddelbuettel * DESCRIPTION (URL): Add repo URL 2021-03-28 Dirk Eddelbuettel * docs/mkdmt-src/: Moved mkdocs-material input 2021-03-24 Dirk Eddelbuettel * vignettes/littler-faq.Rmd (vignette): Add %\Vignette{Encoding,Package} * vignettes/littler-examples.Rmd (vignette): Idem 2021-03-12 Dirk Eddelbuettel * inst/examples/kitten.r: Allow calling Rcpp{,Arma,Eigen}.package.skeleton * inst/examples/roxy.r: Expand roclets example and argument test 2021-03-10 Dirk Eddelbuettel * inst/examples/getRStudioDesktop.r: Updated to cope with rvest change * inst/examples/getRStudioServer.r: Idem 2021-03-01 Dirk Eddelbuettel * docs-src/: Updated reflecting current files * docs/: Ditto 2021-02-22 Dirk Eddelbuettel * inst/examples/kitten.r: Add bunny option for kitten() 2021-02-20 Dirk Eddelbuettel * inst/examples/kitten.r: Pass puppy option on to kitten() call 2021-01-31 Dirk Eddelbuettel * inst/examples/silenceTwitterAccount.r: Check for updated version of rtweet with post_silence function 2021-01-30 Dirk Eddelbuettel * inst/examples/installRSPM.r: Correct -c | --code argument use 2021-01-29 Dirk Eddelbuettel * inst/examples/silenceTwitterAccount.r: Wrapper for rtweet 2021-01-17 Dirk Eddelbuettel * inst/examples/compiledDeps.r: Add -n | --nonrecursive option 2021-01-16 Dirk Eddelbuettel * inst/examples/compiledDeps.r: New script to show which dependencies of a package are in fact native i.e. compiled 2020-12-27 Dirk Eddelbuettel * .github/workflows/ci.yaml: Add CI runner using r-ci * README.md: Add new CI badge * tests/simpleTests.R: Update for GitHub Actions 2020-10-04 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.12 * configure: Idem 2020-10-03 Dirk Eddelbuettel * vignettes/littler-faq.Rmd: Switch to minidown::mini_document and 'framework: water' to dramatically reduce vignettes size * vignettes/littler-examples.Rmd: Idem * inst/examples/urlUpdate.r: Add -c | --check-only option 2020-10-02 Dirk Eddelbuettel * inst/examples/urlUpdate.r: New script to update URLs 2020-09-25 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * inst/examples/cranIncoming.r: New script 2020-09-21 Dirk Eddelbuettel * inst/examples/installBSPM.r: Initial version of BSPM installer 2020-09-20 Iñaki Úcar * inst/examples/installRSPM.r: Add RH/CentOS/Fedora support 2020-09-20 Dirk Eddelbuettel * .travis.yml (install): Switch to BSPM use for Travis * docs/: Added package website * docs-src/: Added package website inputs 2020-09-19 Dirk Eddelbuettel * inst/examples/installRSPM.r: First rough version of an RSPM installer which 'works for me' on Ubuntu but needs other tests 2020-09-13 Dirk Eddelbuettel * inst/examples/check.r: New option '-n | --no-manvig' replacing earlier attempt and implementing '--no-manual --no-vignettes' 2020-09-07 Dirk Eddelbuettel * README.md: Added 'last commit' badge 2020-09-01 Dirk Eddelbuettel * inst/examples/installDeps.r: Added initial version 2020-08-15 Dirk Eddelbuettel * inst/examples/tt.r: For n=1 enforce serial mode 2020-07-26 Dirk Eddelbuettel * inst/examples/cos.r: Support pre-built tar.gz as well 2020-07-24 Dirk Eddelbuettel * inst/examples/cow.r: Support pre-built tar.gz as well 2020-07-23 Dirk Eddelbuettel * inst/examples/c4c.r: Support pre-built tar.gz as well 2020-07-07 Dirk Eddelbuettel * inst/examples/com.r: Add 'check_on_macos' wrapper 2020-06-28 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * inst/examples/check.r: Add options --no-manual and --no-vignettes 2020-06-26 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Release 0.3.11 * configure: Idem 2020-06-25 Dirk Eddelbuettel * inst/examples/check.r: Accomodate recent docopt change for quoted arguments simplifying the use script use * inst/examples/rcc.r: Idem * inst/examples/roxy.r: Idem, add new option -f --full to select --nocache and all roclets * inst/examples/installGithub.r: Minor help text edit 2020-06-17 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version 2020-06-16 Dirk Eddelbuettel * vignettes/littler-faq.Rmd (vignette): Mention zsh builtin again * vignettes/littler-examples.Rmd (vignette): Add short note too 2020-06-03 Dirk Eddelbuettel * src/littler.c: Update copyright year to 2020 in two places 2020-06-02 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Release 0.3.10 * configure.ac: Idem * configure: Idem 2020-06-01 Dirk Eddelbuettel * inst/examples/roxy.r: Added docopt, support nocache and roclets * .travis.yml: Switch to bionic and R 4.0.0 2020-04-11 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version 2020-04-09 Sergio Oller * inst/examples/install2.r: Generalize --error behaviour by ignoring two more possible sources of error 2020-03-20 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * inst/examples/installBioc.r: Ensure .libPaths() is set 2020-02-23 Dirk Eddelbuettel * inst/examples/installBioc.r: New helper script for BioConductor 2019-12-27 Dirk Eddelbuettel * inst/examples/update.r: Set _R_SHLIB_STRIP_ to 'true' 2019-12-23 Dirk Eddelbuettel * inst/examples/install.r: Set _R_SHLIB_STRIP_ to 'true' * inst/examples/install2.r: Idem * inst/examples/installGitHub: Idem * inst/examples/installRepo: Idem 2019-12-01 Dirk Eddelbuettel * inst/examples/tt.r: Correct ncpu fallback setting 2019-11-16 Dirk Eddelbuettel * inst/examples/rcc.r: Set _R_CHECK_TESTS_NLINES_=0 for full logs 2019-10-28 Dirk Eddelbuettel * inst/examples/update.r: Now only considers writeable directories 2019-10-27 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Release 0.3.9 * configure.ac: Idem * configure: Idem 2019-10-26 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * inst/examples/kitten.r: Now with puppy love for tinytest * inst/examples/pkg2bibtex.r: New helper for bibtex package records * inst/examples/sweave.r: New helper script to sweave (and compact) * inst/examples/render.r: Add pdf compacting option * inst/examples/compactpdf.r: Slightly improved file logic * inst/examples/kitten.r: Add tinytest::puppy support via '-p' option 2019-10-25 Dirk Eddelbuettel * inst/examples/sweave.r: New helper to 'Sweave' Rnw files, with automatic call to compactPDF (and option to suppress this) * inst/examples/render.r: Add support for compactPDF, and option not to 2019-09-26 Dirk Eddelbuettel * inst/examples/update.r: Correct libloc help text and default value * inst/examples/rcc.r: Use max(all rc values) as status return 2019-09-25 Dirk Eddelbuettel * inst/examples/rcc.r: Support exit status return, accept new option '--erroron' to pass to error_on option of rcmdcheck 2019-08-29 Dirk Eddelbuettel * inst/examples/tt.r: Support tinytest side effects and npus 2019-08-25 Dirk Eddelbuettel * inst/examples/compactpdf.r: New simple helper script * inst/examples/build.r: Add '--compact-vignettes --resave-data' 2019-07-24 Dirk Eddelbuettel * inst/examples/cos.r: New 'rhub: check on Solaris' helper 2019-06-23 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version 2019-06-21 Stefan Widgren * inst/examples/dratInsert.r: Correct use of call. in stop() * inst/examples/render.r: Idem * vignettes/littler-examples.Rmd: Idem 2019-06-09 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.8 * configure.ac: Idem * configure: Idem * inst/examples/c4c.r: Set check_args="--no-manual --no-vignettes" as we cannot assume rhub to have functioning latex infrastructure * inst/examples/cow.r: Ditto * inst/examples/rchk.r: Ditto 2019-06-08 Dirk Eddelbuettel * inst/examples/tt.r: Initial steps towards a tinytest wrapper 2019-06-03 Dirk Eddelbuettel * inst/examples/install2.r: Extend to optional parallel installation 2019-05-22 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * inst/examples/install.r: Extend to optional parallel installation as tested in installedParallel.r * inst/examples/installParallel.r: Removed now redundant file 2019-05-13 Dirk Eddelbuettel * inst/examples/installParallel.r: Potential replacement for install.r which can install external repos in parallel 2019-04-30 Dirk Eddelbuettel * inst/examples/install.r: Usage help display update 2019-03-23 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * vignettes/littler-faq.Rmd (vignette): New section on adding r to PATH * src/Makevars.in: Reference new littler-faq entry in help display * R/init.R (.onAttach): If 'r' ('lr') is not in path, displayed message also references new entry in littler-faq vignette 2019-03-15 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.7 * configure.ac: Idem * configure: Idem 2019-03-14 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * configure.ac: Correct use of AC_DEFINE * configure: Idem 2019-01-31 Gergely Daroczi * inst/examples/install2.r: Fix warning on multiple repos * inst/examples/installGithub.r: Add -r | --repos option like in install2.r 2019-01-27 Dirk Eddelbuettel * src/littler.c: Update copyright year to 2019 * vignettes/littler-examples.Rmd (date): Correct typo in date 2019-01-26 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.6 * configure.ac: Idem * configure: Idem * inst/examples/install.r (installArg): Use explicit argument repos 2019-01-14 Dirk Eddelbuettel * README.md: Add dependency badge 2019-01-06 Dirk Eddelbuettel * vignettes/littler-faq.Rmd: Adding a short FAQ vignette * R/init.R (.onAttach): Mention new FAQ vignette in message 2018-12-31 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * inst/examples/update.r: Add -n | --ncpus support 2018-12-30 Colin Gillespie * inst/examples/install2.r: Add -n (Ncpus) argument 2018-10-30 Dirk Eddelbuettel * inst/examples/install.r: Add "." if no argument given but DESCRIPTION and NAMESPACE in current directory * inst/examples/install2.r: Idem 2018-10-27 Dirk Eddelbuettel * inst/examples/install.r: Use "." to install from current directory * inst/examples/install2.r: Idem 2018-10-04 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.5 * configure.ac: Idem * configgure: Idem 2018-09-23 Dirk Eddelbuettel * inst/examples/rchk.r: Minimal wrapper for rchk 2018-09-21 Dirk Eddelbuettel * inst/examples/rcc.r (rccwrapper): Insert a wrapper to set arguments explicitly now that the command order was changed in rcmdcheck 1.3.0 2018-09-12 Dirk Eddelbuettel * inst/examples/roxy.r: Overcome roxygen2 6.1.0 breakage by loading a build of, eg, roxygen2 6.0.1 if found at ~/.R/cache/roxygen2 2018-09-02 Dirk Eddelbuettel * .travis.yml: Switch Travis CI to R 3.5 repo 2018-08-24 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.4 * configure.ac: Idem * configgure: Idem * README.md: Updated 2018-08-23 Dirk Eddelbuettel * inst/examples/check.r: Use is.null(), other docopt simplifications 2018-08-09 Dirk Eddelbuettel * inst/examples/rcc.r: Use is.null() to test for empty arguments 2018-08-03 Dirk Eddelbuettel * update.r: No longer need suppressMessages() around library() * shiny.r: Idem * rcc.r: Idem * install2.r: Idem * check.r: Idem * build.r: Idem * render.r: Idem * testInstalled.r: Idem * rd2md.r: Idem 2018-07-31 Dirk Eddelbuettel * inst/examples/getRStudioDesktop.r: More defensive use of URL while curl (OS-level) library packages have is more fragile * inst/examples/getRStudioServer.r: Idem 2018-07-29 Dirk Eddelbuettel * inst/examples/getRStudioDesktop.r: URLs updated * inst/examples/getRStudioServer.r: Idem 2018-05-25 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * inst/examples/update.r: Added docopt support 2018-05-24 Dirk Eddelbuettel * vignettes/littler-examples.Rmd: Updated and extended * inst/examples/render.r: Minor tweak 2018-05-23 Dirk Eddelbuettel * inst/examples/rcc.r: Correct args for '--fast' call 2018-05-12 Dirk Eddelbuettel * inst/examples/install2.r: New option -s to skip installed packages * inst/examples/installIfNew.R: Removed as now redundant * inst/examples/getRStudioServer.r: Update URL to trusty 2018-05-06 Brandon Bertelsen * inst/examples/installIfNew.R: New example to only install new packages not already installed 2018-02-26 Dirk Eddelbuettel * inst/examples/getRStudioDesktop.r: Source URL update 2018-01-02 Dirk Eddelbuettel * inst/examples/kitten.r: New script to call pkgKitten::kitten() * inst/examples/compAttr.r: Use '#!/usr/bin/env r' as shebang line * inst/examples/fsizes.r: Idem * inst/examples/getRStudioDesktop.r: Idem * getRStudioServer.r: Idem * highlightsweave.r: Idem * inst/examples/knit.r: Idem * inst/examples/pnrrs.r: Idem * inst/examples/roxy.r: Idem 2017-12-18 Dirk Eddelbuettel * inst/examples/check.r: Remove second docopt() parse * inst/examples/dratInsert.r: Idem * inst/examples/install2.r: Idem * inst/examples/installGithub.r: Idem * inst/examples/installRepo.r: Idem * inst/examples/rd2md.r: Idem 2017-12-17 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.3 * README.md: Updated 2017-12-10 Dirk Eddelbuettel * vignettes/littler-examples.Rmd: Expanded and updated 2017-11-30 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * inst/examples/getRStudioServer.r: Rewritten using rvest * inst/examples/getRStudioDesktop.r: Idem 2017-11-10 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * inst/examples/build.r: Use current directory if none given 2017-09-05 Dirk Eddelbuettel * vignettes/littler-examples.Rmd (vignette): Expanded 2017-09-04 Dirk Eddelbuettel * inst/examples/dratInsert.r: Combine suppressMessages() calls * inst/examples/installGithub.r: Idem * inst/examples/installRepo.r: Idem * inst/examples/rd2md.r: Idem * inst/examples/testInstalled.r: Idem 2017-08-13 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version * inst/examples/build.r: New option --fast skipping vignettes and manual * inst/examples/rcc.r: Ditto 2017-08-10 Dirk Eddelbuettel * inst/examples/runit.r: Updated docopt usage 2017-07-12 Dirk Eddelbuettel * inst/examples/c4c.r: Use #!/usr/bin/env r instead * inst/examples/cow.r: Idem 2017-06-22 Dirk Eddelbuettel * inst/examples/cow.r: Added simple rhub::check_on_windows() wrapper * .travis.yml (group): Added as required by Travis CI 2017-05-01 Carl Boettiger * inst/examples/install2.r: More robust error handling 2017-04-23 Dirk Eddelbuettel * inst/examples/pnrrs.r: Added 'pnrrs.r' helper calling tools::package_native_routine_registration_skeleton() available in R 3.4.0 and later 2017-04-04 Carl Boettiger * inst/examples/installGithub.r: Correct argument to upgrade 2017-02-18 Dirk Eddelbuettel * .travis.yml (before_install): Use https 2017-02-14 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.2 * src/scripts/littler.R: Also skip R_USER 2017-02-13 Dirk Eddelbuettel * inst/examples/build.r: New script calling R CMD build 2017-02-05 Dirk Eddelbuettel * inst/examples/c4c.r: New script calling rhub::check4cran() * inst/examples/getRStudioDesktop.r: New script * inst/examples/getRStudioServer.r: New script 2016-12-02 Dirk Eddelbuettel * R/init.R: Additional #nocov tags * R/test.R: Idem 2016-11-17 Dirk Eddelbuettel * R/rd2md.r: New script 2016-11-17 Dirk Eddelbuettel * inst/examples/installGithub.r: Use remotes instead of devtools * inst/examples/installRepo.r: Ditto * vignettes/littler-examples.Rmd: Ditto * inst/examples/check.r: Small correction for .libPaths() management 2016-10-01 Dirk Eddelbuettel * inst/examples/rd2md.r: Convert Rd to markdown (for use in posts) 2016-08-13 Dirk Eddelbuettel * configure (PACKAGE_VERSION): Re-ran autoconf to set version to 0.3.1 2016-08-06 Dirk Eddelbuettel * DESCRIPTION: Release 0.3.1 * DESCRIPTION: Added URL and BugReports: * R/test.R (r): New helper function r() to return path to binary * man/r.rd: Documentation * man/littler.rd: Removed alias to 'r' * NAMESPACE: Export r * inst/examples/rcc.r: New example wrapping rcmdcheck::rcmdcheck() * inst/examples/render.r: New (still very simple) example to call rmarkdown::render() * inst/examples/check.r: Extended help and usage now via '-x' * inst/examples/dratInsert.r: Idem * inst/examples/install2.r: Idem * inst/examples/installGithub.r: Idem * inst/examples/installRepo.r: Idem * .travis.yml: Switch to using run.sh for Travis CI * tests/simpleTests.R: Make tests conditional on Linux 2016-06-05 Dirk Eddelbuettel * inst/examples/roxy.r: Minor correction to documentation 2016-03-28 Dirk Eddelbuettel * inst/examples/check.r: Add support for rcmdcheck * DESCRIPTION: Add Suggests: rcmdcheck 2016-03-21 Brandon Bertelsen * vignettes/littler-examples.Rmd: Correct installGithub.r example 2016-02-26 Dirk Eddelbuettel * src/littler.c (showVersionAndExit): Updated copyright * src/scripts/littler.R: Added copyright header, reindented * src/scripts/autoloads.R: Idem * src/scripts/ldflags.R: Idem 2016-02-21 Mattias Ellert * configure.ac: Add support for AM_LDFLAGS * src/scripts/littler.R: Exclude three more variables reflecting the (optional) installation directory 2015-11-20 Dirk Eddelbuettel * inst/examples/rhome.r: New script to call R.home(...) 2015-11-18 Dirk Eddelbuettel * DESCRIPTION: Add Suggests: docopt * .travis.yml: Add r-cran-docopt (via our PPA) 2015-11-17 Steven Pav * inst/examples/install2.r: Support options past '--' which are passed on to R CMD INSTALL as INSTALL_opts 2015-11-04 Dirk Eddelbuettel * DESCRIPTION: Add 'SystemRequirements: libR' per discussion with CRAN 2015-10-30 Dirk Eddelbuettel * NAMESPACE: Added some comments explaining empty content 2015-10-29 Dirk Eddelbuettel * DESCRIPTION: Release 0.3.0 * inst/NEWS.Rd: Added NEWS.Rd file * inst/script-tests/*: Set (old) scripts to #!/usr/bin/env r shebang 2015-10-28 Dirk Eddelbuettel * vignettes/littler-examples.Rmd: Added vignette * configure.ac: Detect if built in git repo * src/gitversion.h.in: Reflect git version if built from repo * src/littler.c: Small tweaks to --version output * .travis.yml: Install knitr for Travis 2015-10-27 Dirk Eddelbuettel * R/test.R: Generalized binary for other OS types, switched to simpler and more predictable default command * tests/simpleTests.R: Renamed from run-all.R, simpler default test, added new test calling an R 'state' variable * deprecated/tools: Moved from tools as no longer needed under rewritten configure.ac * man/littler.Rd: Added manual page 2015-10-26 Jeroen Oooms * R/tests.R: Added wrapper to call 'r' from tests/ directory * tests/run-all.R: Added simple test 2015-10-26 Dirk Eddelbuettel * configure.ac: Also respect 'R CMD config CFLAGS' in build * src/littler.c: Suppress pedantic warnings on fopen results * src/gitversion.h: Define compiletime and compiledate only if VERBOSE_BUILD is set 2015-10-25 Dirk Eddelbuettel * DESCRIPTION: Added, as part of conversion to package * NAMESPACE: Ditto * R/init.R: Ditto * src/littler.c: Moved from top-level * src/config.h.in: Ditto * src/Makevars.in: Moved, and adapted from Makefile.am * src/config-const.h: Added with some (so far) const values * src/scripts/autoloads.R: Moved from top-level * src/scripts/littler.R: Ditto * cleanup: Adapted to new layout * .gitignore: Ditto * .Rbuildignore: Added * inst/script-tests/: Moved from top-level tests/ * inst/examples/: Moved from top-level examples/ * inst/man-page/r.1: Moved from top-level r.1 * .travis.yml: Adapted to work on R package * deprecated/: Added to hold some no-longer used files * README.md: Updated 2015-10-02 Dirk Eddelbuettel * examples/installRepo.r: New script wrapping GitHub, Bitbucket, Subversion (via http) and generic URL access. * examples/check.r: Expanded --help thanks to docopt * examples/installGithub.r: Ditto * examples/install2.r: Ditto * examples/dratInsert.r: Ditto 2015-09-30 Dirk Eddelbuettel * examples/installGithub.r: Simplify, correct and extend script (with thanks to Alexios for the bug report) 2015-09-20 Dirk Eddelbuettel * examples/check.r: Added new option to support 'kitchen sink' installation of Depends, Imports, LinkingTo and Suggests (cf #30) 2015-08-27 Dirk Eddelbuettel * examples/install2.r: Better testing of opt$repos values 2015-07-09 Dirk Eddelbuettel * littler.c (main): Add verbosity argument to parse_eval() which allows for more silent initial operations to set library paths, load libraries and load data -- addresses wish of GitHub ticket #26 2015-05-07 Dirk Eddelbuettel * littler.c: Invert #ifdef on REPRODUCIBLE_BUILD to VERBOSE_BUILD: by default we no longer encode the timestamp of the builds * bootstrap: Ditto: Unless VERBOSE_BUILD is define do not place timestamps in to gitversion.h * littler.c: Also source $R_HOME/etc/Rprofile.site and ~/.Rprofile if present, and document this via --usage flag output. 2015-03-22 Dirk Eddelbuettel * examples/dratInsert.r: Changed to support a commit message * examples/installGithub.r: Remove support -l which no longer works with the current version of devtools (but .libLoc() is respected) 2015-03-14 Dirk Eddelbuettel * configure.ac: Mark as release 0.2.3 2015-03-09 Dirk Eddelbuettel * littler.c (showVersionAndExit): If REPRODUCIBLE_BUILD is defined, do not display built time and date to ensure binary reproducibility * bootstrap: If REPRODUCIBLE_BUILD is defined, do not insert __TIME__ and __DATE__ compile time macros into generated header gitversion.h 2015-03-06 Dirk Eddelbuettel * littler.c (showUsageAndExit): Add link to examples web page. 2015-03-05 Dirk Eddelbuettel * r.1: Updated with recent command additions. 2015-02-27 Dirk Eddelbuettel * examples/dratInsert.r: New script to insert package into drat 2015-02-26 Dirk Eddelbuettel * examples/check.r: New option '--deb-pkgs PKGS' to install .deb packages prior to running the check (in one-command Docker use) 2015-02-19 Dirk Eddelbuettel * littler.c: New command-line argument -L|--libpath to add a directory to the `.libPaths()` 2015-02-17 Carl Boettiger * examples/install2.r: Permit multiple -r|--repos arguments 2015-02-08 Dirk Eddelbuettel * examples/install.r: Set the default value of repos to getOption("repos") as we can now set values in the littler dotfile * examples/install2.r: Ditto * examples/update.r: Ditto 2015-02-03 Dirk Eddelbuettel * littler.c (showVersionAndExit): Update copyright to 2015 here too 2015-01-29 Dirk Eddelbuettel * configure.ac: Mark as release 0.2.2 2015-01-18 Dirk Eddelbuettel * examples/check.r: Add --setwd dir option to change directories 2015-01-17 Dirk Eddelbuettel * examples/check.r: Add a script which wrap R CMD check; with optional support for prior installation of dependencies * examples/shiny.r: Add simple wrapper for shiny::runApp() 2015-01-12 Dirk Eddelbuettel * littler.c: Test for both /etc/littler.r and ~/.littler.r and source if found (but not if -v|--vanilla was given) 2014-12-31 Dirk Eddelbuettel * examples/install2.r: Smarter use of arguments: files with matching extension are installed directly; also clean up temp files 2014-12-28 Dirk Eddelbuettel * examples/install.r: Smarter use of arguments: files with matching extension are installed directly; also expanded help text 2014-12-22 Dirk Eddelbuettel * littler.R: Do not include R_LIBS_USER in list of variables 2014-12-21 Dirk Eddelbuettel * examples/install.r: Reflect value of REPOS and LIBLOC in addition to the [unchanged] default values for either * examples/install2.r: If 'repos' is set to (string) NULL, set it to the actual NULL symbol (so that installation from file proceeds) 2014-10-19 Dirk Eddelbuettel * configure.ac: Mark as release 0.2.1 * littler.c: Minor whitespace changes for 'r --version' * examples/*.r: Add proper copyright and license header for remaining files 2014-10-13 Dirk Eddelbuettel * examples/install.r: Remove temporary rds files matching libloc or repos containing info about installed and available packages * examples/update.r: Add proper copyright and license header * examples/update.r: Ditto * examples/install2.r: Ditto 2014-10-11 Dirk Eddelbuettel * examples/install2.r: Minor polishing 2014-10-10 Carl Boettiger * examples/install2.r: Expanded coverage of '--depends' argument 2014-10-08 Dirk Eddelbuettel * INSTALL: Updated, made distinction between installing from a tarball and installing from git [via './bootstrap'] more clear * README: Brief update, still needs more thorough rewrite 2014-10-04 Dirk Eddelbuettel * examples/testInstalled.r: Renamed from test.r, minor edits 2014-10-03 Carl Boettiger * examples/test.r: Contributed new test script 2014-09-29 Dirk Eddelbuettel * examples/install2.r: Minor edits * examples/installGitHub.r: Ditto 2014-09-29 Carl Boettiger * examples/install2.r: Fix return code, and add new option --deps * examples/installGitHub.r: New example to install from GitHub 2014-09-01 Dirk Eddelbuettel * configure.ac: Mark as release 0.2.0 2014-08-31 Dirk Eddelbuettel * examples/fsizes.r: Use explicit 'file("stdin")' with 'readLines()' 2014-08-26 Dirk Eddelbuettel * examples/install2.r: Using docopt (>= 0.3) using stripped names 2014-08-25 Dirk Eddelbuettel * examples/fileOps.r: Really simple example on vectorised file operations -- but more as an illustration 2014-08-22 Dirk Eddelbuettel * littler.c (main): Minor correction for help text 2014-08-20 Dirk Eddelbuettel * examples/runit.r: New example file 'runit.r' (using docopt) * examples/install2.r: Simplified by using docopt 2014-07-27 Dirk Eddelbuettel * r.1: Update manual page about new -d option * littler.c: Store read.csv() result in 'X', not 'dat' 2014-07-26 Dirk Eddelbuettel * littler.c: New command-line option '-d|--datastdin' which triggers execution of 'dat <- read.csv(file("stdin", stringsAsFactors=FALSE)' 2014-07-23 Dirk Eddelbuettel * examples/install2.r: Updated throughout * cleanup: Also remove .deps 2014-07-17 Dirk Eddelbuettel * examples/highlightsweave.r: New example for a highlight sweave driver (as eg needed for Rcpp vignettes) helper script 2014-07-14 Dirk Eddelbuettel * examples/roxy.r: Expanded similar to compAttr.r 2014-07-13 Dirk Eddelbuettel * examples/compAttr.r: Added new example script to call compileAttributes() from the Rcpp package 2014-06-07 Dirk Eddelbuettel * examples/roxy.r: Added new example script 2014-05-23 Dirk Eddelbuettel * tools/compile: Added, based on current automake version 2014-05-08 Dirk Eddelbuettel * examples/install.r: Updated to currently used version containing the faster RStudio CDN as the default CRAN mirror * examples/update.r: Ditto 2014-04-23 Dirk Eddelbuettel * tools/missing: Updated to current version from libtool on Ubuntu * tools/install.sh: Idem * tools/config.guess: Updated to current version from autotools-dev * tools/config.sub: Idem * Makefile.am: Explicitly expand ldflags.txt to a Makefile variable * Makefile.am: Removed use of .PHONY again * .travis.yml: Added a very simple .travis.yml * .travis.yml: Ensure we end 'script' section on error code 0 * littler.c: Ensure --help and --version end with exit(0) * Makefile.am (CFLAGS): Add CFLAGS 2014-02-07 Dirk Eddelbuettel * configure.ac: Mark as release 0.1.6 [though never released as 0.1.6] * configure.ac: Renamed from configure.in * bootstrap: Autogenerate header gitversion.h instead of svnversion.h * littler.c: Use gitversion.h, also whitespace / indentation update * Makefile.am: Use gitversiob.h * cleanup: Ditto 2013-10-29 Dirk Eddelbuettel * littler.c: Correction to display of '--version' 2012-10-06 Dirk Eddelbuettel * ldflags.R: Applied patch by Jonas Rauch to correctly compute -rpath linker flags on Linux, squashing a really old bug 2012-09-03 Dirk Eddelbuettel * examples/update.r: Minor tweak 2011-09-17 Dirk Eddelbuettel * configure.in: Mark as release 0.1.5 * littler.c (littler_CleanUp): Remove call to Rf_KillAllDevices() 2011-09-15 Dirk Eddelbuettel * configure.in: Mark as release 0.1.4 * Makefile.am: Applied patch by Mathias Klose to prevent FTBFS with 'ld --as-needed', cf LP bug 770980. * littler.c: A few small tweaks suggested by 'gcc -Wall' * examples/install2.r: Added a second R package installer example * examples/update.r: Switch to '/usr/bin/r -t' as shebang line * examples/fsizes.r: Dito * littler.c: Update copyrights to 2011 * README: Idem 2010-01-05 Dirk Eddelbuettel * configure.in: Mark as release 0.1.3 * littler.c: Update copyrights to 2010 * README: Idem * bootstrap: Added tests to not re-generate svnversion.h when information about revision number and date cannot be had retrieved * ldflags.R: Ensure no 'empty string' entries get expanded as this triggered a Debian lintian error related to rpath usage * tools/config.{guess,sub}: Updated 2010-01-04 Dirk Eddelbuettel * littler.c: Set up littler so that 'interactive()' is false, and add new flag -i|--interactive to activate the previous behaviour * r.1: Document the new flag 2009-12-12 Dirk Eddelbuettel * littler.c: Expand the littler_CleanUp function to be closer to the example clean up function in section 8.1.2 'Setting R callbacks' in the R Extensions manual * tests/dotLast.r: simple test of .Last() which we now reach * examples/install.r: Do not call install.packages with dependencies=TRUE as this leads to too many auxilliary pkgs * examples/update.r: Small fix to clearCache() 2009-03-23 Dirk Eddelbuettel * r.1: Added two missing \ to protect \n inside quotes 2009-01-13 Dirk Eddelbuettel * configure.in: Mark as release 0.1.2 * littler.c,r.1: Added -q|--quick switch to skip autoload with thanks to Simon Urbanek for the suggestion. * littler.c: Updated copyright to 2009 2009-01-10 Dirk Eddelbuettel * Makefile.am: Tweaked flow and logic a little, updated copyright 2008-08-28 Jeffrey Horner * littler.c: added -t|--rtemp to use R's temp dir strategy with thanks to Paul Gilbert for the suggestion. 2008-08-27 Dirk Eddelbuettel * Release 0.1.1 2008-08-18 Dirk Eddelbuettel * tests/exitstatus.sh: Added test script for new exit status feature 2008-08-18 Jeffrey Horner * littler.c: now exits with status provided by call to q(). 2008-06-09 Dirk Eddelbuettel * r.1: Applied patch by Seb which adds more examples. Thanks! 2008-04-30 Dirk Eddelbuettel * README: added entry about getopt 2008-03-12 Dirk Eddelbuettel * examples/update.r: simplified clearCache 2008-01-14 Dirk Eddelbuettel * Release 0.1.0 * littler.c: Added new option -l|--packages to load R packages * littler.c: Small change to optional argument handling * littler.c: Also use --no-restore argument on startup * littler.c: Small additions to --help output * r.1: Documented new option -l | --packages * README: Updated as well * autoloads.R: No longer suppress autoload of package datasets * bootstrap: Two small fixes for non-bash sh use * examples/update.r: rewritten cache clearing part * tests/timing*.sh: added Rscript for comparison 2007-04-13 Dirk Eddelbuettel * Release 0.0.11 * Makefile.am: Removed use of one GNU extension to Make to facilitate builds on non-GNU systems * examples/update.r: Fix by Jeff for file caching issues 2007-02-20 Dirk Eddelbuettel * Release 0.0.10 2007-02-19 Jeffrey Horner * README: Updated FAQ entry regarding Rscript with 'hello world!' example. * littler.c: Added R version checking to support R 2.4 and 2.5 * tests/*: Convened on ../r as path to r. 2007-02-18 Dirk Eddelbuettel * configure.in: Tag it as release 0.0.10 * README: Added FAQ entry regarding Rscript * README, littler.c: Rolled copyright into 2007 2007-02-16 Jeffrey Horner * configure.in: added --with-java-libs and --with-tcltk-libs for conditionally linking littler against respective libraries. 2007-02-15 Jeffrey Horner * littler.R: added more R_* environment variables to output. * configure.in: added R CMD *_LIBS output to ld linker flags * INSTALL: Added minimal recipe to build GNU R with --enable-R-shlib 2007-02-08 Jeffrey Horner * littler.c: added function init_rand to set initial seed values for the R function tempfile. * configure.in: added checks for existence of gettimeofday and time to support init_rand. 2007-01-04 Dirk Eddelbuettel * configure.in: Tag it as release 0.0.9 2007-01-04 Jeffrey Horner * littler.c: added call to R_ReplDLLinit to initialize console buffers 2006-11-22 Jeffrey Horner * examples/updates.r: always regenerate package cache 2006-10-28 Dirk Eddelbuettel * update.r: Switched repos to to cran.r-project.org 2006-10-25 Dirk Eddelbuettel * configure.in: Tag it as release 0.0.8 * examples/install.r, examples/update.r: Two new examples * Makefile.am: Some small cleanups and fixes * INSTALL: Clarified need for R as shared library, reformatted 2006-10-09 Dirk Eddelbuettel * Makefile, bootstrap: Added .PHONY targets, have bootstrap optionally create svnversion.h * FAQ: document clash of 'r' with the zsh builtin 2006-10-06 Jeffrey Horner * configure.in, littler.c, Makefile.am, littler.R: make littler set all R_* environment variables. * configure.in: unconditionally create littler.h, autoloads.h, and ldflags.txt during configure. 2006-10-05 Jeffrey Horner * Release 0.0.7 * Makefile.am: added ldflags.R to dist 2006-10-04 Dirk Eddelbuettel * Release 0.0.6 2006-10-03 Dirk Eddelbuettel * README, INSTALL: Some more polishing 2006-10-03 Jeffrey Horner * README: added FAQ answer to use the configure flags --program-prefix and/or --program-suffix for renaming r binary. 2006-10-02 Dirk Eddelbuettel * configure.in: Added check for R version >= 2.3.1 2006-09-29 Dirk Eddelbuettel * littler.c: support svnrevision/date in --version * bootstrap, svnversion.h: call svn and do some awk'ing borrowed from R's Makefiles to auto-create svnversion.h * configure.in, Makefile.am: updated accordingly 2006-09-29 Jeffrey Horner * README: Added 'Implementation' section. 2006-09-28 Jeffrey Horner * littler.c: parse_eval(), the REP loop for stdin and '-e', now use R_tryEval() instead of eval(). * configure.in, Makefile.am, ldflags.R: For linux, we add all paths set by RHOME/etc/ldpaths to r's RPATH. 2006-09-26 Dirk Eddelbuettel * Release 0.0.5 made and announced by Jeff * rinterp.c, rinterp.1: renamed to littler.c, littler.1 * Makefile.am, configure.in: Many changes to accomodate that * autoloads.R: code generator to aid in autoload()ing functions from default packages. 2006-09-05 Jeffrey Horner * Release 0.0.4: * rinterp.c: Bug fix: forgot to reset membuf_t.buf after a call to resize_membuf() * rinterp.c: After R init, we delete R_SESSION_TMPDIR and point it to one of TMPDIR, TMP, TEMP, or "/tmp". We also turn off R's signal handlers. 2006-08-15 Jeffrey Horner * Release 0.0.3: * configure.in: Added Dirk's patch to configure.in to automatically find R in search path and to use --rpath linker option. * rinterp.c: Read commands from stdin when no file is given on cmdline. (feature request from Dirk Eddelbuettel ) 2006-08-09 Jeffrey Horner * Release 0.0.2: * rinterp.c: Added argv support. (feature request from Juha Vierine ) 2006-07-14 Jeffrey Horner * Release 0.0.1: * Initial release of Rinterp: hashbang support for R littler/README.md0000644000176200001440000001140514471021241013205 0ustar liggesusers## littler: A scripting and command-line front-end for GNU R [![CI](https://github.com/eddelbuettel/littler/workflows/ci/badge.svg)](https://github.com/eddelbuettel/littler/actions?query=workflow%3Aci) [![License](https://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](https://www.gnu.org/licenses/gpl-2.0.html) [![CRAN](https://www.r-pkg.org/badges/version/littler)](https://cran.r-project.org/package=littler) [![r-universe](https://eddelbuettel.r-universe.dev/badges/littler)](https://eddelbuettel.r-universe.dev/littler) [![Dependencies](https://tinyverse.netlify.com/badge/littler)](https://cran.r-project.org/package=littler) [![Downloads](https://cranlogs.r-pkg.org/badges/littler?color=brightgreen)](https://www.r-pkg.org/pkg/littler) [![Last Commit](https://img.shields.io/github/last-commit/eddelbuettel/littler)](https://github.com/eddelbuettel/littler) [![Documentation](https://img.shields.io/badge/documentation-is_here-blue)](https://eddelbuettel.github.io/littler/) ### So What Is It For? ```r #!/usr/bin/env r ## for use in scripts other input | r ## for use in pipes r somefile.R ## for running files r -e 'expr' ## for evaluating expressions r --help ## to show a quick synopsis ``` ### Examples? Plenty. See the [examples vignette](https://cran.r-project.org/package=littler/vignettes/littler-examples.html) for a full set of introductory examples. Also see the [examples/ directory](https://github.com/eddelbuettel/littler/tree/master/inst/examples) for a full 28 example scripts, as well as maybe the [older tests directory](https://github.com/eddelbuettel/littler/tree/master/inst/script-tests) both of which are installed with the package. Some scripts I use daily or near daily (in alphabetical order): ``` build.r ## builds from the current directory c4c.r ## submits current directory to winbuilder compAttr.r ## run compileAttributes() for a Rcpp package dratInstert.r 1.2-3.tar.gz -r /srv ## inserts package into drat repo install.r abc def ## installs packages abc and def install.r abc_1.2-3.tar.gz ## installs given tarball install2.r -l /tmp/lib abc def ## installs abc and def into /tmp/lib rcc.r abc_1.2-3.tar.gz ## run's R CMD check via Gabor's rcmdcheck render.r foo.Rmd ## calls rmarkdown::render() roxy.r ## run roxygenize() for a package (only Rd creation) update.r ## updates any currently installed packages ``` ### Installation #### Version 0.3.0 or later The package resides on the CRAN network and can be installed via ``` install.packages("littler") ``` Note that the package states `OS_type: unix`. It works great on all Linux variants, with a naming caveat on macOS (see below and the [FAQ vignettes](https://github.com/eddelbuettel/littler/blob/master/vignettes/littler-faq.md)) and not at all on Windows (but could be ported just like [RInside](https://github.com/eddelbuettel/rinside) has been--the two show architectural similarities). #### Previous Versions up to 0.2.3 In general, simply running the script `bootstrap` will configure and build the executable. Running `make install` (possibly as `sudo make install`) will install the resulting binary. On Linux systems, ensure you have the `autotools-dev` package (or its equivalent on non-Debian/Ubuntu systems). On OS X, you may need to run `brew install automake autoconf` to get all the tools. #### Alternate Naming On some operating systems such as OS X, `r` is not different from `R`. As this risks confusing the main binary `R` for the R system with our smaller scripting frontend `r`, we suggest to consider running `configure --program-prefix="l"` which this leads to installation of a binary `lr` instead of `r`. #### Alternate R Version As littler uses autoconf its `AC_PATH_PROG()` macro to find `R`, one can simply adjust the `PATH` when calling `configure` (or, rather, `bootstrap`) to have another version of R used. For example, on a server with R-devel in this location, the following builds littler using this R-devel version: `PATH="/usr/local/lib/R-devel/bin/:$PATH" ./bootstrap`. ### More Information For more information about littler, please see * [Dirk's littler page](https://dirk.eddelbuettel.com/code/littler.html) * [Dirk's page with littler examples](https://dirk.eddelbuettel.com/code/littler.examples.html) (but note that the latter now overlaps with the [example vignette](https://cran.r-project.org/package=littler/vignettes/littler-examples.html)). ### Authors Jeff Horner (2006 to 2008) and Dirk Eddelbuettel (since 2006) ### License GPL (>= 2) littler/man/0000755000176200001440000000000012751400225012502 5ustar liggesuserslittler/man/littler.Rd0000644000176200001440000000413312751376620014464 0ustar liggesusers\name{littler} \alias{littler} \title{Command-line and scripting front-end for R} \description{ The \code{r} \emph{binary} provides a convenient and powerful front-end. By embedding R, it permits four distinct ways to leverage the power of R at the shell prompt: scripting, filename execution, piping and direct expression evaluation. } \details{ The \code{r} front-end was written with four distinct usage modes in mind. First, it allow to write so-called \sQuote{shebang} scripts starting with \code{#!/usr/bin/env r}. These \sQuote{shebang} scripts are perfectly suited for automation and execution via e.g. via \code{cron}. Second, we can use \code{r somefile.R} to quickly execute the name R source file. This is useful as \code{r} is both easy to type---and quicker to start that either \code{R} itself, or its scripting tool \code{Rscript}, while still loading the \code{methods} package. Third, \code{r} can be used in \sQuote{pipes} which are very common in Unix. A simple and trivial example is \code{echo 'cat(2+2)' | r} illustrating that the standard output of one program can be used as the standard input of another program. Fourth, \code{r} can be used as a calculator by supplying expressions after the \code{-e} or \code{--eval} options. } \value{ Common with other shell tools and programs, \code{r} returns its exit code where a value of zero indicates success. } \note{ On OS X one may have to link the binary to, say, \code{lr} instead. As OS X insists that files named \code{R} and \code{r} are the same, we cannot use the latter. } \author{ Jeff Horner and Dirk Eddelbuettel wrote \code{littler} from 2006 to today, with contributions from several others. Dirk Eddelbuettel \email{edd@debian.org} is the maintainer. } \examples{ \dontrun{ #!/usr/bin/env r ## for use in scripts other input | r ## for use in pipes r somefile.R ## for running files r -e 'expr' ## for evaluating expressions r --help ## to show a quick synopsis } } \keyword{package} littler/man/r.Rd0000644000176200001440000000116112751400225013231 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/test.R \name{r} \alias{r} \title{Return Path to \code{r} Binary} \usage{ r(usecat = FALSE) } \arguments{ \item{usecat}{Optional toggle to request output to stdout (useful in Makefiles)} } \value{ The path is returned as character variable. If the \code{usecat} option is set the character variable is displayed via \code{\link{cat}} instead. } \description{ Return the path of the install \code{r} binary. } \details{ The test for Windows is of course superfluous as we have no binary for Windows. Maybe one day... } \author{ Dirk Eddelbuettel } littler/DESCRIPTION0000644000176200001440000000226314577647212013461 0ustar liggesusersPackage: littler Type: Package Title: R at the Command-Line via 'r' Version: 0.3.20 Date: 2024-03-23 Author: Dirk Eddelbuettel and Jeff Horner (2006-2008) Maintainer: Dirk Eddelbuettel Description: A scripting and command-line front-end is provided by 'r' (aka 'littler') as a lightweight binary wrapper around the GNU R language and environment for statistical computing and graphics. While R can be used in batch mode, the r binary adds full support for both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path expression as the first line in scripts) as well as command-line use in standard Unix pipelines. In other words, r provides the R language without the environment. URL: https://github.com/eddelbuettel/littler, https://dirk.eddelbuettel.com/code/littler.html, https://eddelbuettel.github.io/littler/ BugReports: https://github.com/eddelbuettel/littler/issues License: GPL (>= 2) OS_type: unix SystemRequirements: libR Suggests: simplermarkdown, docopt, rcmdcheck VignetteBuilder: simplermarkdown RoxygenNote: 5.0.1 NeedsCompilation: yes Packaged: 2024-03-23 18:27:34 UTC; edd Repository: CRAN Date/Publication: 2024-03-23 21:50:02 UTC littler/build/0000755000176200001440000000000014577617425013052 5ustar liggesuserslittler/build/vignette.rds0000644000176200001440000000033614577617425015413 0ustar liggesusersuA0EErd 5.6R"I MН'h `\3>Y 1F -v2-G&TEB0m偔VJ ɳC}l^%_(#gCpuB7Qz4ƄCV4$Q5݀O/["GS}Ip%-d*lj*V@q 0_Llittler/tests/0000755000176200001440000000000014077011474013100 5ustar liggesuserslittler/tests/simpleTests.R0000644000176200001440000000123414077011474015537 0ustar liggesusers ## These tests were suggested by a user on OS X (in 2015), and then ## promptly failed on OS X per CRAN -- so we now make this conditional ## on Linux where it is known to work ## ## Until it doesn't as it appears to (in 2020) fail on Travis CI if (unname(Sys.info()["sysname"]) == "Linux" && Sys.getenv("TRAVIS", "false") != "true" && Sys.getenv("CI", "false") != "true") { stopifnot(file.exists(littler:::r())) stopifnot(length(system2(littler:::r(), "--version", stdout=TRUE)) > 10) # 14 lines stopifnot(identical(littler:::test(), "4")) # default test is cat(2+2) stopifnot(as.numeric(littler:::test('cat(R.version$year)')) >= 2015) } littler/configure.ac0000644000176200001440000001337414577616224014245 0ustar liggesusers# -*- mode: Autoconf; tab-width: 4; -*- # Process this file with autoconf to produce a configure script. # require at least autoconf 2.69 AC_PREREQ([2.69]) # Every other copy of the package version number gets its value from here # The m4_esyscmd_s invocation is due to an excellent StackOverflow answer. # Sadly it breaks under Debian package builds (likely due to a missing component) AC_INIT([littler],[0.3.20],[edd@debian.org]) # Look for ancillary configure tools in tools dnl AC_CONFIG_AUX_DIR(tools) # Ensure R_HOME is set yet respect a previously set value : ${R_HOME=`R RHOME`} if test -z "${R_HOME}"; then AC_MSG_ERROR([Could not determine R_HOME.]) fi RPROG=${R_HOME}/bin/R CC=`${RPROG} CMD config CC` AM_CFLAGS=`${RPROG} CMD config CFLAGS` AM_LDFLAGS=`${RPROG} CMD config LDFLAGS` dnl # Options for Automake dnl # dnl # no-texinfo.tex - obviously means don't include the big texinfo.tex file dnl # in the dist. dnl # foreign - treats our package as non-gnu, essentially excudluding strict dnl # checks for certain files like ChangeLog, NEWS, README, etc dnl # dnl AM_INIT_AUTOMAKE( no-texinfo.tex foreign ) # create a config.h file AC_CONFIG_HEADERS(src/config.h) AC_SUBST(VERSION) # commenting this out relieves us from requiring tools/ with all the scripts dnl AC_CANONICAL_HOST # Checks for programs. dnl AC_PROG_INSTALL AC_PROG_CC # Checks for libraries. # Checks for header files. dnl AC_CHECK_HEADERS( stdio.h string.h errno.h stdlib.h sys/types.h sys/stat.h unistd.h) AC_CHECK_HEADER([getopt.h], [AC_DEFINE([HAVE_GETOPT_H], 1, [Define to 1 if you have .])], [AC_MSG_ERROR([littler needs getopt support to run. Please find and install it.])]) AC_HEADER_MAJOR # Checks for library functions. AC_CHECK_FUNC(setenv,AC_DEFINE(HAVE_SETENV,1,[Define if you have the setenv function.])) AC_CHECK_FUNC(clock_gettime,AC_DEFINE(HAVE_CLOCK_GETTIME,1,[Define if you have clock_gettime.])) AC_CHECK_FUNC(realtime,AC_DEFINE(HAVE_REALTIME,1,[Define if you have realtime.])) AC_CHECK_FUNC(gettimeofday,AC_DEFINE(HAVE_GETTIMEOFDAY,1,[Define if you have the gettimeofday function.])) AC_CHECK_FUNC(time,AC_DEFINE(HAVE_TIME,1,[Define if you have the time function.])) # Checks for typedefs, structures, and compiler characteristics. # Test the R version for shared library AC_DEFUN([R_PROG],[ AC_MSG_CHECKING([if R was built as a shared library]) # Unset any user defined notion of R_HOME export R_HOME # First test if R was found if test "${RPROG}" = ""; then echo echo "R not found. Please update your PATH variable to include the R bin directory" echo AC_MSG_ERROR( aborting! ) fi # Now make sure that a well known include file exists # and the libR.so if ${RPROG} CMD config --ldflags 2>/dev/null | grep -v 'R was not built as a shared library' >/dev/null; then AM_CFLAGS="${AM_CFLAGS} `${RPROG} CMD config --cppflags`" AM_LDFLAGS="${AM_LDFLAGS} `${RPROG} CMD config --ldflags`" # Now add the various libraries for linking AM_LDFLAGS="${AM_LDFLAGS} `${RPROG} CMD config BLAS_LIBS | grep -v ERROR`" AM_LDFLAGS="${AM_LDFLAGS} `${RPROG} CMD config LAPACK_LIBS | grep -v ERROR`" # are we on apple or not if test "$build_vendor" != "apple"; then RUN_NAMETOOL="" fi AC_MSG_RESULT([yes]) else echo echo "R was not built as a shared library" echo echo "Either build it with one, or use another install of R" echo AC_MSG_ERROR( aborting! ) fi ]) R_PROG ## Check for .git directory if test -d ".git/"; then GITREVISION=`git log --format=fuller | head -6 | awk '/^commit / {print substr($2,1,7)}'` GITDATE=`git log --format=fuller | head -6 | awk '/^CommitDate: / {print $2, $3, $4, $5, $6, $7}'` AC_DEFINE([VERBOSE_BUILD],[1],[Verbose build with git revision and date information]) else GITREVISION="" GITDATE="" fi # Now check if certain libraries should be linked in # Java AC_ARG_WITH([java-libs], [AS_HELP_STRING([--with-java-libs],[Link littler to R's java libraries])], [if test x$"$withval" != xno; then AM_LDFLAGS="${AM_LDFLAGS} `${RPROG} CMD config JAVA_LIBS | grep -v ERROR`" fi], ) dnl # Tcl/TK dnl AC_ARG_WITH([tcltk-libs], dnl [AS_HELP_STRING([--with-tcltk-libs],[dnl Link littler to R's tcltk libraries])], dnl [ dnl if test x$"$withval" != xno; then dnl AM_LDFLAGS="${AM_LDFLAGS} `${RPROG} CMD config TCLTK_LIBS | grep -v ERROR`" dnl fi dnl ], dnl ) dnl # R version check dnl # Note that this may fail really old versions of R as the string wasn't always "R version x.y.z ..." dnl r_version=`${RPROG} --version | head -1 | cut -f3 -d" " ` dnl case ${r_version} in dnl 1.*.*|2.0.*|2.1.*|2.2.*|2.3.0) dnl AC_MSG_ERROR([R version ${r_version} is too old. Please upgrade to a more recent version.]) dnl ;; dnl esac #AC_MSG_RESULT([AM_LDFLAGS is now: ${AM_LDFLAGS}]) # get other linker flags for rpath EXTRA_LDFLAGS=`${RPROG} --silent --vanilla --slave --file=src/scripts/ldflags.R` #AC_MSG_RESULT([EXTRA_LDFLAGS is now: ${EXTRA_LDFLAGS}]) #AM_LDFLAGS="${AM_LDFLAGS} ${EXTRA_LDFLAGS}" #AC_MSG_RESULT([AM_LDFLAGS is now: ${AM_LDFLAGS}]) # Are we building for Mac OS X? this program will exist if so. AC_PATH_PROG(NAMETOOL, install_name_tool) AC_DEFUN([NAMETOOL_FUN],[ if test "${NAMETOOL}" != ""; then RUN_NAMETOOL="${NAMETOOL} -change libR.dylib `${RPROG} RHOME`/lib/libR.dylib r" fi ]) NAMETOOL_FUN AC_SUBST(RPROG) AC_SUBST(CC) AC_SUBST(AM_CFLAGS) AC_SUBST(AM_LDFLAGS) AC_SUBST(EXTRA_LDFLAGS) AC_SUBST(RUN_NAMETOOL) AC_SUBST(GITREVISION) AC_SUBST(GITDATE) AC_CONFIG_FILES([src/Makevars src/gitversion.h]) AC_OUTPUT littler/src/0000755000176200001440000000000014577617426012543 5ustar liggesuserslittler/src/littler.c0000644000176200001440000006204714573456172014372 0ustar liggesusers/* * littler - Provides hash-bang (#!) capability for R (www.r-project.org) * * Copyright (C) 2006 - 2024 Jeffrey Horner and Dirk Eddelbuettel * * littler is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * */ #include #include #include #include #include #include #include #include #include #include #include "config.h" /*#include "config-const.h"*/ #include "gitversion.h" #include "autoloads.h" #include "littler.h" #include #include #include #include #define R_INTERFACE_PTRS #include #include #include int verbose = 0; /* should we be verbose? default no, use -p */ /* PACKAGE, VERSION, ... are being filled by autoconf and friends via config.h */ const char *programName = PACKAGE_NAME; const char *binaryName = "r"; #ifndef HAVE_SETENV int setenv(char *name, char *value, int clobber){ char *cp; if (clobber == 0 && getenv(name) != 0) return (0); if ((cp = malloc(strlen(name) + strlen(value) + 2)) == 0) return (1); sprintf(cp, "%s=%s", name, value); return (putenv(cp)); } #endif int source(char *file){ SEXP expr, s, f, p; int errorOccurred; /* Find source function */ s = Rf_findFun(Rf_install("source"), R_GlobalEnv); PROTECT(s); /* Make file argument */ PROTECT(f = NEW_CHARACTER(1)); SET_STRING_ELT(f, 0, COPY_TO_USER_STRING(file)); /* Make print.eval argument */ PROTECT(p = NEW_LOGICAL(1)); LOGICAL_DATA(p)[0] = (verbose)? TRUE : FALSE; /* expression source(f,print.eval=p) */ PROTECT(expr = allocVector(LANGSXP,3)); SETCAR(expr,s); SETCAR(CDR(expr),f); SETCAR(CDR(CDR(expr)), p); SET_TAG(CDR(CDR(expr)), Rf_install("print.eval")); errorOccurred=0; R_tryEval(expr,NULL,&errorOccurred); UNPROTECT(4); return errorOccurred; } /* Autoload default packages and names from autoloads.h * * This function behaves in almost every way like * R's autoload: * function (name, package, reset = FALSE, ...) * { * if (!reset && exists(name, envir = .GlobalEnv, inherits = FALSE)) * stop("an object with that name already exists") * m <- match.call() * m[[1]] <- as.name("list") * newcall <- eval(m, parent.frame()) * newcall <- as.call(c(as.name("autoloader"), newcall)) * newcall$reset <- NULL * if (is.na(match(package, .Autoloaded))) * assign(".Autoloaded", c(package, .Autoloaded), env = .AutoloadEnv) * do.call("delayedAssign", list(name, newcall, .GlobalEnv, * .AutoloadEnv)) * invisible() * } * * What's missing is the updating of the string vector .Autoloaded with the list * of packages, which by my code analysis is useless and only for informational * purposes. * */ void autoloads(void){ SEXP da, dacall, al, alcall, AutoloadEnv, name, package; int i,j, idx=0, errorOccurred, ptct; /* delayedAssign call*/ PROTECT(da = Rf_findFun(Rf_install("delayedAssign"), R_GlobalEnv)); PROTECT(AutoloadEnv = Rf_findVar(Rf_install(".AutoloadEnv"), R_GlobalEnv)); if (AutoloadEnv == R_NilValue){ fprintf(stderr,"%s: Cannot find .AutoloadEnv!\n", programName); exit(1); } PROTECT(dacall = allocVector(LANGSXP,5)); SETCAR(dacall,da); /* SETCAR(CDR(dacall),name); */ /* arg1: assigned in loop */ /* SETCAR(CDR(CDR(dacall)),alcall); */ /* arg2: assigned in loop */ SETCAR(CDR(CDR(CDR(dacall))),R_GlobalEnv); /* arg3 */ SETCAR(CDR(CDR(CDR(CDR(dacall)))),AutoloadEnv); /* arg3 */ /* autoloader call */ PROTECT(al = Rf_findFun(Rf_install("autoloader"), R_GlobalEnv)); PROTECT(alcall = allocVector(LANGSXP,3)); SET_TAG(alcall, R_NilValue); /* just like do_ascall() does */ SETCAR(alcall,al); /* SETCAR(CDR(alcall),name); */ /* arg1: assigned in loop */ /* SETCAR(CDR(CDR(alcall)),package); */ /* arg2: assigned in loop */ ptct = 5; for(i = 0; i < packc; i++){ idx += (i != 0)? packobjc[i-1] : 0; for (j = 0; j < packobjc[i]; j++){ /*printf("autload(%s,%s)\n",packobj[idx+j],pack[i]);*/ PROTECT(name = NEW_CHARACTER(1)); PROTECT(package = NEW_CHARACTER(1)); SET_STRING_ELT(name, 0, COPY_TO_USER_STRING(packobj[idx+j])); SET_STRING_ELT(package, 0, COPY_TO_USER_STRING(pack[i])); /* Set up autoloader call */ PROTECT(alcall = allocVector(LANGSXP,3)); SET_TAG(alcall, R_NilValue); /* just like do_ascall() does */ SETCAR(alcall,al); SETCAR(CDR(alcall),name); SETCAR(CDR(CDR(alcall)),package); /* Setup delayedAssign call */ SETCAR(CDR(dacall),name); SETCAR(CDR(CDR(dacall)),alcall); R_tryEval(dacall,R_GlobalEnv,&errorOccurred); if (errorOccurred){ fprintf(stderr,"%s: Error calling delayedAssign!\n", programName); exit(1); } ptct += 3; } } UNPROTECT(ptct); } /* Line reading code */ typedef struct membuf_st { int size; int count; unsigned char *buf; } *membuf_t; membuf_t init_membuf(int sizebytes){ membuf_t lb = malloc(sizebytes+sizeof(struct membuf_st)); if (lb == NULL) { fprintf(stderr,"%s: init_membuf() failed! Exiting!!!\n\n", programName); exit(1); return NULL; /* unreached */ } lb->size = sizebytes; lb->count = 0; lb->buf = (unsigned char *)lb+sizeof(struct membuf_st); return lb; } void destroy_membuf(membuf_t lb){ free(lb); } /* Use power of 2 resizing */ membuf_t resize_membuf(membuf_t *plb){ membuf_t lb = *plb; lb = *plb = realloc(lb,lb->size*2+sizeof(struct membuf_st)); if (lb == NULL) { fprintf(stderr,"%s: init_membuf() failed! Exiting!!!\n\n", programName); exit(1); return NULL; /* unreached */ } lb->size = lb->size * 2; lb->buf = (unsigned char *)lb+sizeof(struct membuf_st); return lb; } membuf_t rewind_membuf(membuf_t *mb){ (*mb)->count = 0; return *mb; } membuf_t add_to_membuf(membuf_t *pmb,char *buf){ membuf_t mb = *pmb; int buflen = strlen(buf); while ((buflen + (mb->count)) >= mb->size){ mb = *pmb = resize_membuf(pmb); } memcpy(mb->buf+mb->count,buf,buflen); mb->buf[mb->count+buflen] = '\0'; mb->count += buflen; return mb; } /* returns 1 on reading another line or until EOF, 0 on EOF */ int readline_stdin(membuf_t *plb){ membuf_t lb = *plb; unsigned int offset=0; char *str; do { lb->buf[lb->size-2] = '\0'; /* mark last char position */ str = fgets((char*)lb->buf+offset,lb->size-offset,stdin); /* EOF or error */ if (str == NULL){ return (offset)? 1 : 0; } /* Did we read a whole line? */ if (lb->buf[lb->size-2] != '\0' && lb->buf[lb->size-2] != '\n'){ /* No. read again. */ offset = lb->size-1; lb = *plb = resize_membuf(plb); } else { /* Yes. return */ return 1; } } while(1); } int parse_eval(membuf_t *pmb, char *line, int lineno, int localverbose){ membuf_t mb = *pmb; ParseStatus status; SEXP cmdSexp, cmdexpr, ans = R_NilValue; int i, errorOccurred; mb = *pmb = add_to_membuf(pmb,line); PROTECT(cmdSexp = allocVector(STRSXP, 1)); SET_STRING_ELT(cmdSexp, 0, mkChar((char*)mb->buf)); /* R_ParseVector gets a new argument in R 2.5.x */ cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilValue)); switch (status){ case PARSE_OK: /* Loop is needed here as EXPSEXP might be of length > 1 */ for(i = 0; i < length(cmdexpr); i++){ ans = R_tryEval(VECTOR_ELT(cmdexpr, i),NULL, &errorOccurred); if (errorOccurred) { UNPROTECT(2); return 1; } if (localverbose) { PrintValue(ans); } } mb = *pmb = rewind_membuf(pmb); break; case PARSE_INCOMPLETE: fprintf(stderr, "%s: Incomplete Line! Need more code! (%d)\n", programName, status); UNPROTECT(2); return 1; break; case PARSE_NULL: fprintf(stderr, "%s: ParseStatus is null (%d)\n", programName, status); UNPROTECT(2); return 1; break; case PARSE_ERROR: fprintf(stderr,"Parse Error line %d: \"%s\"\n", lineno, line); UNPROTECT(2); return 1; break; case PARSE_EOF: fprintf(stderr, "%s: EOF reached (%d)\n", programName, status); break; default: fprintf(stderr, "%s: ParseStatus is not documented %d\n", programName, status); UNPROTECT(2); return 1; break; } UNPROTECT(2); return 0; } extern char *R_TempDir; int perSessionTempDir = FALSE; /* by default, r differs from R and defaults to /tmp unless env.vars set, or flag chosen */ void littler_InitTempDir(void) { char *tmp; if (perSessionTempDir) return; /* use a per-session temporary directory by following R */ tmp = getenv("TMPDIR"); /* set tmp to TMPDIR, or TMP, or TEMP, or "/tmp" */ if (tmp == NULL) { tmp = getenv("TMP"); if (tmp == NULL) { tmp = getenv("TEMP"); if (tmp == NULL) tmp = "/tmp"; } } R_TempDir=tmp; if (setenv("R_SESSION_TMPDIR",tmp,1) != 0){ perror("Fatal Error: couldn't set/replace R_SESSION_TMPDIR!"); exit(1); } } /* littler exit */ void littler_CleanUp(SA_TYPE saveact, int status, int runLast){ R_dot_Last(); R_RunExitFinalizers(); if (perSessionTempDir) R_CleanTempDir(); fpu_setup(FALSE); Rf_endEmbeddedR(0); exit(status); } void showHelpAndExit(void) { printf("\n" "Usage: %s [options] [-|file]" "\n\n" "Launch GNU R to execute the R commands supplied in the specified file, or\n" "from stdin if '-' is used. Suitable for so-called shebang '#!/'-line scripts.\n" "\n" "Options:\n" " -h, --help Give this help list\n" " --usage Give a short usage message\n" " -V, --version Show the version number\n" " -v, --vanilla Pass the '--vanilla' option to R\n" " -t, --rtemp Use per-session temporary directory as R does\n" " -i, --interactive Let interactive() return 'true' rather than 'false'\n" " -q, --quick Skip autoload / delayed assign of default libraries\n" " -p, --verbose Print the value of expressions to the console\n" " -l, --packages list Load the R packages from the comma-separated 'list'\n" " -d, --datastdin Prepend command to load 'X' as csv from stdin\n" " -L, --libpath dir Add directory to library path via '.libPaths(dir)'\n" " -e, --eval expr Let R evaluate 'expr'\n" "\n\n", binaryName); exit(-1); } void showVersionAndExit(void) { char txt[64]; printf("%s ('%s') version %s\n", binaryName, programName, PACKAGE_VERSION); #if defined(VERBOSE_BUILD) printf("\ngit revision %s as of %s\n", gitrevision, gitdate); printf("built at %s on %s\n", compiletime, compiledate); #endif printf("\nusing GNU R "); snprintf(txt, 63, "%d", R_SVN_REVISION); if (strcmp(txt, "unknown")==0) { printf("Version %s.%s %s (%s-%s-%s)", R_MAJOR, R_MINOR, R_STATUS, R_YEAR, R_MONTH, R_DAY); } else { if (strlen(R_STATUS)==0) { printf("Version %s.%s (%s-%s-%s)", R_MAJOR, R_MINOR, R_YEAR, R_MONTH, R_DAY); } else{ printf("Version %s.%s %s (%s-%s-%s r%d)", R_MAJOR, R_MINOR, R_STATUS, R_YEAR, R_MONTH, R_DAY, R_SVN_REVISION); } } printf("\n\nCopyright (C) 2006 - 2021 Jeffrey Horner and Dirk Eddelbuettel\n" "\n" "%s is free software and comes with ABSOLUTELY NO WARRANTY.\n" "You are welcome to redistribute it under the terms of the\n" "GNU General Public License. For more information about\n" "these matters, see http://www.gnu.org/copyleft/gpl.html.\n\n", binaryName); exit(0); } void showUsageAndExit(void) { printf("\n" "%s (aka '%s') can be used in four main modes.\n\n" "The first is via the so-called 'shebang' support it provides for GNU R.\n" "Suppose '%s' is installed in /usr/local/bin/%s. Then the first line of a\n" "script can be written as \"#!/usr/local/bin/%s\" and the rest of the file\n" "can contain standard R commands. By setting executable permissions\n" "on the file, one can now create executable R scripts.\n\n" "The second is to supply a filename with commands that are to be\n" "evaluated.\n\n" "The third use is in standard compound command-line expressions common\n" "under Unix (so called 'command pipes') as '%s' can take arguments\n" "from stdin if the special filename '-' is used to select stdin.\n\n" "The fourth use is in on-the-fly evaluation of R expressions supplied\n" "via the -e or --eval options to provide a quick R expression tester\n" "and calculator.\n\n" "You can provide configuration via file ${R_HOME}/etc/Rprofile.site,\n" "~/.Rprofile, /etc/littler.r or ~/.littler.r all of which are sourced\n" "if present.\n\n" "More documentation is provided in the '%s' manual page and via the\n" "tests directory in the sources.\n\n" "A number of examples are also available at\n" "http://dirk.eddelbuettel.com/code/littler.examples.html.\n\n", binaryName, programName, binaryName, binaryName, binaryName, programName, binaryName); exit(0); } /* set seed for tempfile() updated to R 4.1.0 src/main/times.c and its helper function TimeToSeed() */ void init_rand(void) { unsigned int seed, pid = getpid(); #if defined(HAVE_CLOCK_GETTIME) && defined(CLOCK_REALTIME) { struct timespec tp; clock_gettime(CLOCK_REALTIME, &tp); seed = (unsigned int)(((uint_least64_t) tp.tv_nsec << 16) ^ tp.tv_sec); } #elif defined(HAVE_GETTIMEOFDAY) { struct timeval tv; gettimeofday (&tv, NULL); seed = (unsigned int)(((uint_least64_t) tv.tv_usec << 16) ^ tv.tv_sec); } #else /* C89, so must work */ seed = (Int32) time(NULL); #endif seed ^= (pid <<16); srand(seed); /* also called by R in src/main/main.c */ } int main(int argc, char **argv){ /* R embedded arguments, and optional arguments to be picked via cmdline switches */ char *R_argv[] = {(char*)programName, "--gui=none", "--no-restore", "--no-save", "--no-readline", "--silent", "", ""}; char *R_argv_opt[] = {"--vanilla", "--slave"}; int R_argc = (sizeof(R_argv) - sizeof(R_argv_opt) ) / sizeof(R_argv[0]); int i, nargv, c, optpos=0, vanilla=0, quick=0, interactive=0, datastdin=0; char *evalstr = NULL; char *libstr = NULL; char *libpathstr = NULL; SEXP s_argv; structRstart Rst; char *datastdincmd = "X <- read.csv(file(\"stdin\"), stringsAsFactors=FALSE);"; static struct option optargs[] = { {"help", no_argument, NULL, 'h'}, {"usage", no_argument, 0, 0}, {"version", no_argument, NULL, 'V'}, {"vanilla", no_argument, NULL, 'v'}, {"eval", required_argument, NULL, 'e'}, {"packages", required_argument, NULL, 'l'}, {"verbose", no_argument, NULL, 'p'}, {"rtemp", no_argument, NULL, 't'}, {"quick", no_argument, NULL, 'q'}, {"interactive", no_argument, NULL, 'i'}, {"datastdin", no_argument, NULL, 'd'}, {"libpath", required_argument, NULL, 'L'}, {0, 0, 0, 0} }; while ((c = getopt_long(argc, argv, "+hVve:npl:L:tqid", optargs, &optpos)) != -1) { switch (c) { case 0: /* numeric 0 is code for a long option */ /* printf ("Got option %s %d", optargs[optpos].name, optpos);*/ switch (optpos) { /* so switch on the position in the optargs struct */ /* cases 0, 2, and 3 can't happen as they are covered by the '-h', */ /* '-V', and '-v' equivalences */ case 1: showUsageAndExit(); break; /* never reached */ case 5: verbose = 1; break; default: printf("Uncovered option position '%d'. Try `%s --help' for help\n", optpos, programName); exit(-1); } break; case 'h': /* -h is the sole short option, cf getopt_long() call */ showHelpAndExit(); break; /* never reached */ case 'e': evalstr = optarg; break; case 'l': libstr = optarg; break; case 'v': vanilla=1; break; case 'p': verbose=1; break; case 'V': showVersionAndExit(); break; /* never reached */ case 't': perSessionTempDir=TRUE; break; case 'q': quick=1; break; case 'i': interactive=1; break; case 'd': datastdin=1; break; case 'L': libpathstr = optarg; break; default: printf("Unknown option '%c'. Try `%s --help' for help\n",(char)c, programName); exit(-1); } } if (vanilla) { R_argv[R_argc++] = R_argv_opt[0]; } if (!verbose) { R_argv[R_argc++] = R_argv_opt[1]; } #ifdef DEBUG printf("R_argc %d sizeof(R_argv) \n", R_argc, sizeof(R_argv)); for (i=0; i<7; i++) { printf("R_argv[%d] = %s\n", i, R_argv[i]); } printf("optind %d, argc %d\n", optind, argc); for (i=0; i= 1) { int offset = (evalstr==NULL) + (strcmp(argv[optind],"-") == 0); /* Build string vector */ nargv = argc - optind - offset; PROTECT(s_argv = allocVector(STRSXP,nargv)); for (i = 0; i buf, lineno++, verbose); if (exit_val) break; } destroy_membuf(lb); destroy_membuf(pb); } littler_CleanUp(SA_NOSAVE, exit_val, 0); return(0); /* not reached, but making -Wall happy */ } littler/src/config-const.h0000644000176200001440000000015412613230464015263 0ustar liggesusers /* Name of package */ #define PACKAGE "littler" /* Version number of package */ #define VERSION "0.2.9.1" littler/src/config.h.in0000644000176200001440000000401014222121266014534 0ustar liggesusers/* src/config.h.in. Generated from configure.ac by autoheader. */ /* Define if you have clock_gettime. */ #undef HAVE_CLOCK_GETTIME /* Define if you have realtime. */ #undef HAVE_CLOCK_REALTIME /* Define to 1 if you have . */ #undef HAVE_GETOPT_H /* Define if you have the gettimeofday function. */ #undef HAVE_GETTIMEOFDAY /* Define to 1 if you have the header file. */ #undef HAVE_INTTYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_MEMORY_H /* Define if you have the setenv function. */ #undef HAVE_SETENV /* Define to 1 if you have the header file. */ #undef HAVE_STDINT_H /* Define to 1 if you have the header file. */ #undef HAVE_STDLIB_H /* Define to 1 if you have the header file. */ #undef HAVE_STRINGS_H /* Define to 1 if you have the header file. */ #undef HAVE_STRING_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_STAT_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TYPES_H /* Define if you have the time function. */ #undef HAVE_TIME /* Define to 1 if you have the header file. */ #undef HAVE_UNISTD_H /* Define to 1 if `major', `minor', and `makedev' are declared in . */ #undef MAJOR_IN_MKDEV /* Define to 1 if `major', `minor', and `makedev' are declared in . */ #undef MAJOR_IN_SYSMACROS /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the home page for this package. */ #undef PACKAGE_URL /* Define to the version of this package. */ #undef PACKAGE_VERSION /* Define to 1 if you have the ANSI C header files. */ #undef STDC_HEADERS /* Verbose build with git revision and date information */ #undef VERBOSE_BUILD littler/src/gitversion.h.in0000644000176200001440000000065312614246414015477 0ustar liggesusers /* * gitrevision and gitdate are as reported by git at that point in time, * compiledate and compiletime are being filled gcc at compilation * * verbose_build gets set along with them * */ #if defined(VERBOSE_BUILD) static const char* gitrevision = "@GITREVISION@"; static const char* gitdate = "@GITDATE@"; static const char* compiletime = __TIME__; static const char* compiledate = __DATE__; #endif littler/src/Makevars.in0000644000176200001440000000212414573433440014627 0ustar liggesusers## -*- mode: Makefile; tab-width: 8 -*- ## ## Makevars.in for littler ## Based on older Makefile.am ## ## Copyright (C) 2006 - 2016 Jeffrey Horner and Dirk Eddelbuettel, GNU GPL'ed RPROG=@RPROG@ ROPTS = --silent --vanilla --slave CC=@CC@ PKG_CFLAGS=@AM_CFLAGS@ PKG_LDFLAGS=@AM_LDFLAGS@ @EXTRA_LDFLAGS@ RUN_NAMETOOL=@RUN_NAMETOOL@ SRCS = littler.c TGT = r$(EXEEXT) # By setting OBJECTS to "" we avoid having littler.so built OBJECTS= all: $(SHLIB) $(TGT) prog: littler.c # Main r build rule, with suitable extension where needed (as eg on OS X) $(TGT): $(SRCS) @$(RPROG) $(ROPTS) --file=scripts/autoloads.R > autoloads.h @$(RPROG) $(ROPTS) --file=scripts/littler.R > littler.h $(CC) -o $(TGT) $(PKG_CFLAGS) $(SRCS) $(PKG_LDFLAGS) $(RUN_NAMETOOL) @mkdir -p ../inst/bin$(R_ARCH) @cp -a $(TGT) ../inst/bin$(R_ARCH) @echo "*" @echo "* new binary $(TGT) installed in bin$(R_ARCH)/ subdirectory" @echo "* consider adding a symbolic link from, e.g., /usr/local/bin" @echo "* on OS X, you may have to name this 'lr' instead" @echo "* see the littler-faq vignette for more details" @echo "*" littler/src/scripts/0000755000176200001440000000000013050665612014213 5ustar liggesuserslittler/src/scripts/autoloads.R0000644000176200001440000000313512674112053016330 0ustar liggesusers## ## littler - Provides hash-bang (#!) capability for R (www.r-project.org) ## ## Copyright (C) 2006 - 2016 Jeffrey Horner and Dirk Eddelbuettel ## ## littler is free software; you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation; either version 2 of the License, or ## (at your option) any later version. ## ## This program is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with this program; if not, write to the Free Software ## Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ## dp <- getOption("defaultPackages") #dp <- dp[dp != 'datasets'] ## Rscript loads it too #dp <- dp[dp != 'methods'] ## Rscript (in R 2.6.1) doesn't load methods either # Count of default packages cat("int packc = ",length(dp),";\n",sep='') # List of packages cat("const char *pack[] = {\n",paste('"',dp,'"',sep='',collapse=",\n"),"\n};\n") packobjc <- array(0,dim=length(dp)) packobj <- NULL for (i in 1:length(dp)){ obj = ls(paste("package:",dp[i],sep='')) packobjc[i] = length(obj) packobj = c(packobj,obj) } # List of counts of objects per package cat("int packobjc[] = {\n",paste(packobjc,sep='',collapse=",\n"),"\n};\n") # List of object names cat("const char *packobj[] = {\n",paste('"',packobj,'"',sep='',collapse=",\n"),"\n};\n") littler/src/scripts/littler.R0000644000176200001440000000245513050665612016023 0ustar liggesusers## ## littler - Provides hash-bang (#!) capability for R (www.r-project.org) ## ## Copyright (C) 2006 - 2017 Jeffrey Horner and Dirk Eddelbuettel ## ## littler is free software; you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation; either version 2 of the License, or ## (at your option) any later version. ## ## This program is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with this program; if not, write to the Free Software ## Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ## ExcludeVars <- c("R_SESSION_TMPDIR", "R_HISTFILE", "R_LIBS_USER", "R_LIBRARY_DIR", "R_LIBS", "R_PACKAGE_DIR", "R_USER") IncludeVars <- Sys.getenv() IncludeVars <- IncludeVars[grep("^R_", names(IncludeVars), perl=TRUE)] cat("const char *R_VARS[] = {\n") for (i in 1:length(IncludeVars)){ if (names(IncludeVars)[i] %in% ExcludeVars) next cat('"',names(IncludeVars)[i], '","', IncludeVars[i], '",\n', sep='') } cat("NULL };\n") littler/src/scripts/ldflags.R0000644000176200001440000000207012674112053015746 0ustar liggesusers## ## littler - Provides hash-bang (#!) capability for R (www.r-project.org) ## ## Copyright (C) 2006 - 2016 Jeffrey Horner and Dirk Eddelbuettel ## ## littler is free software; you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation; either version 2 of the License, or ## (at your option) any later version. ## ## This program is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with this program; if not, write to the Free Software ## Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ## s <- Sys.info() if (is.null(s)) q() if (s[1] != "Linux") q() ldp <- strsplit(Sys.getenv('LD_LIBRARY_PATH'),':')[[1]] ldp <- ldp[which(ldp != "")] cat(paste(paste0('-Wl,-rpath,', ldp), collapse=" "), "\n") littler/vignettes/0000755000176200001440000000000014577617425013763 5ustar liggesuserslittler/vignettes/littler-examples.md0000644000176200001440000003054014136370627017571 0ustar liggesusers --- title: "Littler Examples" author: "Dirk Eddelbuettel" date: "Originally written 2015-10-28; Updated 2017-12-10, 2018-05-24, 2019-01-06, 2019-06-09 and 2020-06-16" css: "water.css" --- ## Overview We show and discuss a few of the files included in the `inst/examples/` source directory of [littler](http://dirk.eddelbuettel.com/code/littler.html) (which becomes the `examples/` directory once installed). In a few cases we remove comment lines to keep things more concise on this page. We use `$` to denote a shell (_i.e._ terminal) prompt. Note that some systems (such as macOS) cannot install littler as `r` (as lower-case and upper-case are by default the same; not a great idea). And for example the `zsh` has `r` as a builtin so you would have to use `/usr/bin/r`. See the [littler FAQ](littler-faq.html) for more. ## Simple Direct Command-line Use [littler](http://dirk.eddelbuettel.com/code/littler.html) can be used directly on the command-line just like, say, `bc`, easily consuming standard input from a pipe: ```bash $ echo 'cat(pi^2,"\n")' | r 9.869604 ``` Equivalently, commands that are to be evaluated can be given on the command-line ```bash $ r -e 'cat(pi^2, "\n")' 9.869604 ``` But unlike bc(1), GNU R has a vast number of statistical functions. For example, we can quickly compute a `summary()` and show a stem-and-leaf plot for file sizes in a given directory via ```bash $ ls -l /boot | awk 'BEGIN {print "size"} !/^total/ {print $5}' | \ r -de "print(summary(X[,1])); stem(X[,1])" ``` which produces something like ``` Min. 1st Qu. Median Mean 3rd Qu. Max. 13 512 110100 486900 768400 4735000 The decimal point is 6 digit(s) to the right of the | 0 | 0000001122222279222 2 | 79444 4 | 71888 6 | 8 | 10 | 12 | 14 | 8 16 | 4 18 | 20 | 333 ``` (Note that some systems may not have `/boot` in which case you can try `/sbin` or another directory.) As we saw in the preceding example, the program can also be shortened like using the new `-d` option which reads from stdin and assigns to a `data.frame` named `X`. And, last but not least, this (somewhat unwieldy) expression can be stored in a helper script (where we now switch to using an explicit `readLines()` on `stdin`): ```r #!/usr/bin/env r fsizes <- as.integer(readLines(file("stdin"))) print(summary(fsizes)) stem(fsizes) ``` (where calling `#!/usr/bin/env` is a trick from Python which allows one to forget whether r is installed in `/usr/bin/r`, `/usr/local/bin/r`, `~/bin/r`, ...). ## install.r: Direct CRAN Installation This is one of my favourite [littler](http://dirk.eddelbuettel.com/code/littler.html) scripts which I use frequently to install packages off [CRAN](https://cran.r-project.org). ```r #!/usr/bin/env r if (is.null(argv) | length(argv)<1) { cat("Usage: installr.r pkg1 [pkg2 pkg3 ...]\n") q() } ## adjust as necessary, see help('download.packages') repos <- "https://cran.rstudio.com" ## this makes sense on Debian where no packages touch /usr/local lib.loc <- "/usr/local/lib/R/site-library" install.packages(argv, lib.loc, repos) ``` I invoke it all the time with one, two or more packages to install (or reinstall). ```bash $ install.r digest RcppCNPy ``` It conveniently installs all dependencies, and uses the chosen target directory, all while keeping my R prompt (or prompts with multiple sessions) free to do other things. Also, if used with `options("Ncpu")` set, then (remote CRAN) packages will be installed in parallel. ## install2.r: With Cmdline Parsing Thanks to the fabulous [docopt](https://github.com/edwindj/docopt.R) package, we also have a variant `install2.r` with optional settings of repo and location. It was first installed with [littler 0.2.1](http://dirk.eddelbuettel.com/blog/2014/10/19/). The current (_i.e._, 0.3.3 as of this writing) version is more featureful and longer and included to keep this brief. Some usage examples are ```sh $ install2.r -l /tmp/lib Rcpp BH # install into given library $ install2.r -- --with-keep.source drat # keep the source $ install2.r -- --data-compress=bzip2 stringdist # prefer bz2 compression ``` Another _very_ useful option is `-n N` or `--ncpus N` which will parallelize the installation across `N` processes. This can be set automagically by setting `options("Ncpus")`. ### Installing From Sources Starting with version 0.2.2, `install.r` and `install2.r` now recognise installable source files. So one can also do this: ```bash $ install.r digest_0.6.8.tar.gz ``` and the local source file will the installed via a call to `R CMD INSTALL`. ## check.r: Simple Checker A related use case is to check packages via `check.r`. This script runs `R CMD check`, but also installs package dependencies first as tests may have dependencies not yet satisfied on the test machine. It offers a number of options: ```bash $ check.r -h Usage: check.r [-h] [-x] [--as-cran] [--repo REPO] [--install-deps] [--install-kitchen] [--deb-pkgs PKGS...] [--use-sudo] [--library LIB] [--setwd DIR] [TARGZ ...] -a --as-cran customization similar to CRAN's incoming [default: FALSE] -r --repo REPO repository to use, or NULL for file [default: https://cran.rstudio.com] -i --install-deps also install packages along with their dependencies [default: FALSE] -k --install-kitchen even install packages 'kitchen sink'-style up to suggests [default: FALSE] -l --library LIB when installing use this library [default: /usr/local/lib/R/site-library] -s --setwd DIR change to this directoru before undertaking the test [default: ] -d --deb-pkgs PKGS also install binary .deb packages with their dependencies [default: FALSE] -u --use-sudo use sudo when installing .deb packages [default: TRUE] -h --help show this help text -x --usage show help and short example usage $ ``` ## rcc.r: R CMD check wrapper The script `rcc.r` will also check a source tarball, and offers another set of options: ```bash $ rcc.r -h Usage: rcc.r [-h] [-x] [-c] [-f] [-q] [--args ARGS] [--libpath LIBP] [--repos REPO] [PATH...] -c --as-cran should '--as-cran' be added to ARGS [default: FALSE] -a --args ARGS additional arguments to be passed to 'R CMD CHECK' [default: ] -l --libpath LIBP additional library path to be used by 'R CMD CHECK' [default: ] -r --repos REPO additional repositories to be used by 'R CMD CHECK' [default: ] -f --fast should vignettes and manuals be skipped [default: FALSE] -q --quiet should 'rcmdcheck' be called qietly [default: FALSE] -h --help show this help text -x --usage show help and short example usage $ ``` ## build.r: Building Packages A related script is `build.r` which I often use inside a source repository to quickly build a source tarball. Like `rcc.r`, it has a switch `-f` or `--fast` to omit building of vignettes. ```bash $ build.r # without argument works on current directory $ build.r digest/ # with directory argument builds tar.gz from repo in directory ``` ## installGithub.r: GitHub install Installation directly from [GitHub](https://github.com) is also popular. Here is an example: ```bash $ installGithub.r RcppCore/RcppEigen ``` Installing from github is supported via the following helper script: ```r #!/usr/bin/env r # # A simple example to install one or more packages from GitHub # # Copyright (C) 2014 - 2015 Carl Boettiger and Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt and remotes (or devtools) from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN suppressMessages(library(remotes)) # can use devtools as a fallback ## configuration for docopt doc <- "Usage: installGithub.r [-h] [-d DEPS] REPOS... -d --deps DEPS Install suggested dependencies as well? [default: NA] -h --help show this help text where REPOS... is one or more GitHub repositories. Examples: installGithub.r RcppCore/RcppEigen installGithub.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information. " ## docopt parsing opt <- docopt(doc) if (opt$deps == "TRUE" || opt$deps == "FALSE") { opt$deps <- as.logical(opt$deps) } else if (opt$deps == "NA") { opt$deps <- NA } invisible(sapply(opt$REPOS, function(r) install_github(r, dependencies = opt$deps))) ``` ## update.r: CRAN package update One of the scripts I use the most (interactively) is `update.r` which updates installed packages. An earlier version looked like the following example, the current version is a little longer and has more features: ```r #!/usr/bin/env r # # a simple example to update packages in /usr/local/lib/R/site-library # parameters are easily adjustable ## adjust as necessary, see help('download.packages') repos <- "https://cloud.r-project.org" ## this makes sense on Debian where no package touch /usr/local lib.loc <- "/usr/local/lib/R/site-library" ## r use requires non-interactive use update.packages(repos=repos, ask=FALSE, lib.loc=lib.loc) ``` As above, it has my preferred mirror and library location hard-wired. Another _very_ useful option is `-n N` or `--ncpus N` which will parallelize the upgrade across `N` processes. This can be set automagically by setting `options(Ncpus)`. ## knit.r: Calling knitr Here is another convenience script, `knit.r`, which _knits_ a given file after testing the file actually exists. ```r #!/usr/bin/r # # Simple helper script for knitr # # Dirk Eddelbuettel, May 2013 # # GPL-2 or later if (is.null(argv)) { cat("Need an argument FILE.Rnw\n") q(status=-1) } file <- argv[1] if (!file.exists(file)) { cat("File not found: ", file, "\n") q(status=-1) } require(knitr) knit2pdf(file) ``` ## roxy.r: Running roxygen Similar to the previous example, the script `roxy.r` one uses roxygen to extract documentation from R files -- either in the current directory, or in the given directory or directories. ```r #!/usr/bin/r # # Simple helper script for roxygen2::roxygenize() # # Dirk Eddelbuettel, August 2013 # # GPL-2 or later ## load roxygen library(roxygen2) ## check all command-line arguments (if any are given) for directory status argv <- Filter(function(x) file.info(x)$is.dir, argv) ## loop over all argument, with fallback of the current directory, and ## call compileAttributes() on the given directory sapply(ifelse(length(argv) > 0, argv, "."), FUN=roxygenize, roclets="rd") ``` ## compAttr.r: Compiling Attributes The next script, `compAttr.`, can be used with [Rcpp](http://dirk.eddelbuettel.com/code/rcpp.html), and particularly is powerful _Attributes_ feature, in order to auto-generate helper code. It is similar to the preceding script, but invokes `compileAttributes()` instead. ```r #!/usr/bin/r # # Simple helper script for compileAttributes() # # Dirk Eddelbuettel, July 2014 # # GPL-2 or later ## load Rcpp suppressMessages(library(Rcpp)) ## check all command-line arguments (if any are given) for directory status argv <- Filter(function(x) file.info(x)$is.dir, argv) ## loop over all argument, with fallback of the current directory, and ## call compileAttributes() on the given directory sapply(ifelse(length(argv) > 0, argv, "."), compileAttributes) ``` ## render.r: Render Markdown The `render.r` script generalizes the earlier `knit.r` to convert Markdown into its designated output. ```r #!/usr/bin/env r # # Another example to run a shiny app # # Copyright (C) 2016 Dirk Eddelbuettel # # Released under GPL (>= 2) suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN ## configuration for docopt doc <- "Usage: render.r [-h] [-x] [FILES...] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("Examples: render.r foo.Rmd bar.Rmd # convert two given files render.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } library(rmarkdown) ## helper function renderArg <- function(p) { if (!file.exists(p)) stop("No file '", p, "' found. Aborting.", call.=FALSE) render(p) } ## render files using helper function sapply(opt$FILES, renderArg) ``` littler/vignettes/littler-faq.md0000644000176200001440000000714014136370627016522 0ustar liggesusers --- title: "Littler FAQ" author: "Dirk Eddelbuettel" date: "2019-03-23, updated 2020-06-16" css: "water.css" --- ### Well, why? Glad you asked. When the initial work started, `Rscript` did not exist so there was no scripting tool. We take a small amount of pride into beating `Rscript` narrowly to a first release. Of course, by now, `Rscript` is more widely used as it ships with every R installation but we still have some aspects we like about `r`: it is simpler and shorter, deals (in our biased) view more sanely with command-line arguments via the `argv` vector, always loaded package `methods` (which `Rscript` finally came around to a good decade later) and [still starts faster](http://dirk.eddelbuettel.com/blog/2014/09/02/#littler-faster-at-doing-nothing). And `r` is just to cool a command (in relation to the trusted `R`) so someone had to! ### No Printing In the very beginning of `littler`, we made an executive decision to _not_ echo each command output when we evaluate commands in the read-evaluate-print loop. So `2+2` will be evaluated silently: four will be computed, but not shown. That made sense for scripts we wanted to be silent. The idea is that user will add a `print()` or `cat()` as needed. If you desire each step to printed, add a `-p` or `--verbose` argument. ### No `.Renviron` Another early decision was to make `r` start _faster_ than the alternatives. Our `r` is "just" a small little binary. Whereas `R` and `Rscript` are front-end shell scripts sourcing a number of things and setting them dynamically, we determine values _at compilation time_ and freeze them into the binary. That may seem _risqué_ but worked out just fine. However, while we later added the ability to source `Rprofile` files (which contain R code we can evaluate) there is no way for us to source the `Renviron` files _and to modify the already running process_. So if you want to source `Renviron` you could add an explicit `readEnviron()` to `~/.littler.r` or `/etc/littler/r`. ### Lower-case / upper-case This is mostly an issue on macOS where the brain surgeons behind the OS decided that `r` is the same as `R`. What can we say? On that OS you may need to rename the build to `lr` instead. Please send your complaints to Cupertino, California. ### Adding the binary to your path When the package is installed from source, it displays ``` * * new binary $(TGT) installed in bin/ subdirectory" * consider adding a symbolic link from, e.g., /usr/local/bin" * on OS X, you may have to name this 'lr' instead" * see the littler-faq vignette for more details" * ``` where the variable `$(TGT)` normally expands to `r`. As the text suggests you may want to create a [symbolic link](https://en.wikipedia.org/wiki/Symbolic_link) from a directory in the to make the newly built binary available to users. On Linux you may do ``` cd /usr/local/bin sudo ln -s /usr/local/lib/R/site-library/littler/bin/r . ``` to create a link for `r` in `/usr/local/bin`. On macOS, as suggested, you may want ``` cd /usr/local/bin sudo ln -s /usr/local/lib/R/site-library/littler/bin/r lr ``` to create a command `lr` instead; see the previous question as to why. In either case adjust the source part of the `ln` command to where your binary is -- which R can tell you via `system.file("bin", "r", package="littler")`. Also note that _e.g._ the [zsh](https://zsh.sourceforge.io/) has a builtin command `r` which may conflict, so using the explicit path of, say, `/usr/bin/r` or `/usr/local/bin/r` or ... may provide an alternative. littler/vignettes/water.css0000644000176200001440000000225114136370627015606 0ustar liggesusers/* our addition */ body { max-width: 50rem; margin-left: auto; margin-right: auto; font-family: system-ui; } /* Inline codes */ code { padding: 2px; border-radius: unset; } /* Code blocks */ pre { background-color: unset; border: solid #aaa 1px; padding: 8px; } pre.numberSource { margin: 0; padding-left: 0; } div.sourceCode { overflow: visible; } pre, pre.sourceCode { overflow-x: auto; } pre>code { white-space: pre; overflow: visible; background-color: unset; padding: 0; } pre.sourceCode.numberSource { overflow-x: visible; } pre.sourceCode.numberSource>code { white-space: pre-wrap } pre.sourceCode.numberSource>code>span { left: 8px; text-indent: -4.6em; } /* code folding */ .chunk-summary { text-align: right; } .chunk-summary+pre, .chunk-summary+div.sourceCode { margin-top: 2px; } /* TOC */ nav > ul { border: .0625rem solid #444; border-radius: 4px; margin: 5px; padding: 5px; } nav ul { list-style-type: none; padding-inline-start: 1rem; } nav ul li { padding: 0; } nav ul ul { margin-top: 0; margin-bottom: 0; padding-top: 0; padding-bottom: 0; } nav code { background-color: unset; color: unset; } littler/R/0000755000176200001440000000000014573433440012141 5ustar liggesuserslittler/R/init.R0000644000176200001440000000175414573433440013236 0ustar liggesusers .onAttach <- function(libname, pkgname) { packageStartupMessage("The littler package provides 'r' as a binary.") packageStartupMessage("See 'vignette(\"littler-examples\") for several usage illustrations,") packageStartupMessage("and see 'vignette(\"littler-faq\") for some basic questions.") if (Sys.info()[["sysname"]] %in% c("Linux", "Darwin")) { # nocov start if (unname(Sys.which("r")) == "") { loc <- normalizePath(system.file("bin", .Platform$r_arch, "r", package="littler")) packageStartupMessage("You could link to the 'r' binary installed in\n'", loc, "'\n", "from '/usr/local/bin' in order to use 'r' for scripting.", "See the 'vignette(\"littler-faq\")' for more details.") if (Sys.info()[["sysname"]] == "Darwin") packageStartupMessage("On maxOS, 'r' and 'R' are the same so 'lr' is a possible alternate name for littler.") } # nocov end } } littler/R/test.R0000644000176200001440000000155014077010703013234 0ustar liggesusers## Internal, not exported, function used by unit tests test <- function(src = "cat(2 + 2)") { system2(r(), paste("-e", shQuote(src)), stdout = TRUE) } ##' Return the path of the install \code{r} binary. ##' ##' The test for Windows is of course superfluous as we have no binary for Windows. ##' Maybe one day... ##' @title Return Path to \code{r} Binary ##' @param usecat Optional toggle to request output to stdout (useful in Makefiles) ##' @return The path is returned as character variable. 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000c4df779dbf117342fc63d61aad089 *tests/simpleTests.R 44edae02f3243730584bcf724e8c6872 *vignettes/littler-examples.md c1f981418f8bbfc136bfd85bbe61fa11 *vignettes/littler-faq.md c337c0e0c1e0c0dd67a87649ff442d9f *vignettes/water.css littler/inst/0000755000176200001440000000000014577617425012730 5ustar liggesuserslittler/inst/examples/0000755000176200001440000000000014577617426014547 5ustar liggesuserslittler/inst/examples/cranIncoming.r0000755000176200001440000000204714066355135017334 0ustar liggesusers#!/usr/bin/env r # # A simple example to check the incoming queue at CRAN # # Copyright (C) 2020 - present Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN }) if (!requireNamespace("foghorn", quietly=TRUE)) stop("The 'foghorn' is required. Please install it.", call.=FALSE) ## configuration for docopt doc <- paste0("Usage: cranIncoming.r [-a] [-h] [-x] [ARGS...] -a --all show everything in incoming -h --help show this help text -x --usage show help and short example usage ") opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat(" Basic usage: cranIncoming.r digest binb cranIncoming.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (length(opt$ARGS) == 0) opt$ARGS <- if (opt$all) NULL else character() print(data.frame(foghorn::cran_incoming(opt$ARGS)), row.names=FALSE) littler/inst/examples/rcc.r0000755000176200001440000000646614572067040015502 0ustar liggesusers#!/usr/bin/env -S r -t ## ## Call 'rcmdcheck' on a package ## ## Copyright (C) 2016 - 2024 Dirk Eddelbuettel ## ## Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) ## configuration for docopt doc <- "Usage: rcc.r [-h] [-x] [-c] [-f] [-q] [-v] [--args ARGS] [--libpath LIBP] [--repos REPO] [--erroron ERRON] [PATH...] -c --as-cran should '--as-cran' be added to ARGS [default: FALSE] -a --args ARGS additional arguments to be passed to 'R CMD CHECK' [default: ] -l --libpath LIBP additional library path to be used by 'R CMD CHECK' [default: ] -r --repos REPO additional repositories to be used by 'R CMD CHECK' [default: ] -f --fast should vignettes and manuals be skipped [default: FALSE] -v --valgrind should tests run with 'valgrind' debug tool [default: FALSE] -e --erroron ERRON whether to throw an error on failure [default: never] -q --quiet should 'rcmdcheck' be called quietly [default: FALSE] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("Examples: rcc.r # check repo in current (working) director rcc.r -c # run as R CMD check --as-crn rcc.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } erroron <- switch(opt$erroron, never = "never", error = "error", warning = "warning", note = "note", "badarg") if (erroron=="badarg") stop("Inadmissable argument for '--erroron' option.", call.=FALSE) if (is.null(opt$args)) { # special treatment for --args and -c if (opt$as_cran) { opt$args <- "--as-cran" } else { opt$args <- character() } } else { if (opt$as_cran) { opt$args <- c(opt$args, "--as-cran") } } if (opt$fast) { opt$args <- c(opt$args, "--ignore-vignettes", "--no-manual") } if (opt$valgrind) { opt$args <- c(opt$args, "--use-valgrind") } if (length(opt$PATH) == 0) opt$PATH <- "." # default argument current directory if (is.null(opt$libpath)) opt$libpath <- .libPaths() # default library pathr if (is.null(opt$repos)) opt$repos <- getOption("repos") # default repos if (requireNamespace("rcmdcheck", quietly=TRUE) == FALSE) stop("This command requires the 'rcmdcheck' package.", call. = FALSE) suppressMessages(library(rcmdcheck)) Sys.setenv("_R_CHECK_TESTS_NLINES_"="0") # ensure all errors shown rccwrapper <- function(pa, qu, ar, li, re, eo) { rcmdcheck(path=pa, quiet=qu, args=ar, libpath=li, repos=re, error_on=eo) } rc <- sapply(opt$PATH, # iterate over arguments rccwrapper, # calling 'rcmdcheck()' with arguments opt$quiet, # quiet argument, default false opt$args, # args arguments, possibly with --as-cran opt$libpath, # libpath argument opt$repos, # repos argument erroron, # error_on argument simplify=FALSE) status <- max(sapply(rc, "[[", "status")) q(status=status) littler/inst/examples/sweave.r0000755000176200001440000000231613554700765016222 0ustar liggesusers#!/usr/bin/env r # # Another example to convert from Rnw and also compact # # Copyright (C) 2019 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) ## configuration for docopt doc <- "Usage: sweave.r [-c] [-h] [-x] [FILES...] -c --compact compact pdf file [default: FALSE] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("Examples: sweave.r foo.Rnw bar.Rnw # convert two given files sweave.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } ## helper function sweaveFunction <- function(p) { if (!file.exists(p)) stop("No file '", p, "' found. Aborting.", call.=FALSE) utils::Sweave(p) s <- gsub(".Rnw$", ".tex", p) tools::texi2pdf(s, texi2dvi="pdflatex") tools::texi2pdf(s, texi2dvi="pdflatex") if (opt$compact) { r <- gsub(".Rnw$", ".pdf", p) if (file.exists(r)) tools::compactPDF(r, gs_quality="ebook") } } ## render files using helper function sapply(opt$FILES, sweaveFunction) littler/inst/examples/installRSPM.r0000755000176200001440000000533014536123346017072 0ustar liggesusers#!/usr/bin/env r # # A simple example to install from RSPM/PPM/P3M # # Copyright (C) 2020 - present Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN }) if (Sys.info()[["sysname"]] != "Linux") stop(paste("Currently only supported on Linux.", "Please get in touch if you want to / can help on macOS"), call.=FALSE) code <- "" if (file.exists("/etc/os-release")) { # next block borrowed from my chshli package on GitHub osrel <- read.table("/etc/os-release", sep="=", row.names=1, col.names=c("key","value")) if ("REDHAT_SUPPORT_PRODUCT" %in% rownames(osrel)) { # 'centos7' for CentOS/RHEL 7, 'centos8' for CentOS/RHEL 8 and Fedora ver <- osrel["REDHAT_SUPPORT_PRODUCT_VERSION", "value"] code <- paste0("centos", min(as.numeric(ver), 8)) } else if ("VERSION_CODENAME" %in% rownames(osrel)) { code <- osrel["VERSION_CODENAME", "value"] } } if ((code == "") && (Sys.which("lsb_release") != "")) { code <- system("lsb_release -c | awk '{print $2}'", intern=TRUE) } ## configuration for docopt doc <- paste0("Usage: install(RSPM|PPM|P3M).r [-c code] [-l libloc] [-h] [-x] ARGS... -c --code ARG set code name for distribution [default: ", code, "] -l --libloc ARG location in which to install [default: ", .libPaths()[1], "] -h --help show this help text -x --usage show help and short example usage Note that RSPM/PPM/P3M support may be somewhat experimental. There may not be binaries for every possibly OS, distibution, and R version. Please file issue tickets at the Github repo for littler if you can contribute additional checks and values. As RSPM has been renamed to PPM and then P3M, we now install the script thrice via hardlinks. ") opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n") cat("Basic usage: installRSPM.r digest # install digest for default release '", code, "' installPPM.r -c jammy digest # install digest for Ubuntu 'jammy' installP3M.r -c bookworn digest # install digest for Debian 'bookworm' install(RSPM|PPM|P3M).r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n", sep="") q("no") } if (!is.null(opt$libloc)) .libPaths(opt$libloc) r <- getOption("repos") r["CRAN"] <- paste0("https://p3m.dev/all/__linux__/", opt$code, "/latest") options(repos = r) options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os))) invisible(sapply(opt$ARGS, function(r) install.packages(r))) littler/inst/examples/roxy.r0000755000176200001440000000455314354122012015714 0ustar liggesusers#!/usr/bin/env r # # Simple helper script for roxygen2::roxygenize() # # Dirk Eddelbuettel, 2013 - 2020 # # GPL-2 or later ## load docopt package from CRAN library(docopt) ## configuration for docopt doc <- "Usage: roxy.r [-n] [-f] [-m] [-h] [-x] [-r ROCLETS] [PACKAGES ...] -n --nocache run the current version not the cached version -r --roclets ROCLETS use roclets arguments for roxygenize [default: rd] -f --full implies both '-n' and '-r NULL' -m --minimal implies 'namespace,rd' roclets -l --libpath LIBP additional library path to be added [default: ] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("where PACKAGES... can be one or more packages. Examples: roxy.r # update help pages for package, use cached version roxy.r -n # use non-cached version roxy.r -r NULL # use full roclets i.e. collate,namespace,rd roxy.r -r 'namespace,rd' # use specified roclets i.e. namespace,rd roxy.r -f # use non-cached version and 'NULL' roclets roxy.r -m # shorthand for use 'of namespace,rd' roclets roxy.r is part of littler which brings 'r' to the command-line. See the help for roxygenize for the different 'roclets' arguments; default value 'rd' means to only update Rd files. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (opt$full) { opt$nocache <- TRUE opt$roclets <- "NULL" } if (opt$minimal) { opt$nocache <- FALSE opt$roclets <- "namespace,rd" } ## Works around the marvel that is version 6.1.0 or later if (!opt$nocache && dir.exists("~/.R/cache/roxygen2")) { cat("** Using cached version 6.0.1 of roxygen2.\n") .libPaths("~/.R/cache") } ## load roxygen library(roxygen2) if (!is.null(opt$libpath)) .libPaths(opt$libpath) ## check all command-line arguments (if any are given) for directory status argv <- Filter(function(x) file.info(x)$is.dir, argv) ## loop over all argument, with fallback of the current directory, and ## call roxygenize() on the given directory with roclets="rd" set sapply(ifelse(length(argv) > 0, argv, "."), FUN = roxygenize, roclets = if (tolower(opt$roclets) == "null") NULL else strsplit(opt$roclets,",")[[1]]) littler/inst/examples/installBioc.r0000755000176200001440000001247314321353447017172 0ustar liggesusers#!/usr/bin/env r # # Install a package from BioConductor # # Copyright (C) 2020 - 2022 Dirk Eddelbuettel # Copyright (C) 2022 - 2022 Dirk Eddelbuettel and Pieter Moris # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) ## default to first library location in .libPaths() libloc <- .libPaths()[1] ## configuration for docopt doc <- paste0("Usage: installBioc.r [-l LIBLOC] [-d DEPS] [-n NCPUS] [-r REPO ...] [--error] [--skipinstalled] [-m METHOD] [--force] [--update] [-h] [-x] [PACKAGES ...] -l --libloc LIBLOC location in which to install [default: ", libloc, "] -d --deps DEPS install suggested dependencies as well [default: NA] -n --ncpus NCPUS number of processes to use for parallel install [default: getOption] -r --repo REPO additional repository to use [default: getOption] -e --error throw error and halt instead of a warning [default: FALSE] -s --skipinstalled skip installing already installed packages (takes priority over --force) [default: FALSE] -m --method METHOD method to be used for downloading files [default: auto] -f --force force re-download of packages that are currently up-to-date [default: FALSE] -u --update update old already installed packages [default: FALSE] -h --help show this help text -x --usage show help and short example usage") opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("where PACKAGES... can be one or more BioConductor names. Functionality depends on package 'BiocManger' which has be installed. Examples: installBioc.r -l /tmp/lib S4Vectors # install into given library installBioc.r --update Biobase # install package and update older packages installBioc.r --deps NA --error --skipinstalled # install package without suggested dependencies, # throw an error on installation failure and skip # packages that are already present installBioC.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (!requireNamespace("BiocManager", quietly=TRUE)) { stop("Please install 'BiocManager' first, for example via 'install.r BiocManager'.", call.=FALSE) } ## set repository to empty character vector if not supplied, since ## this is the input expected by BiocManager::install(site_repository=) ## (does not accept NA) ## the custom repository must be a sub-repository of a main BioC_mirror ## e.g. software: https://bioconductor.statistik.tu-dortmund.de/packages/3.15/bioc/ ## annotation: https://ftp.gwdg.de/pub/misc/bioconductor/packages/3.14/data/annotation if (opt$repo == "getOption") { opt$repo = character() } ## check if dependencies need to be installed, see ## https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packages ## the default, NA, means c("Depends", "Imports", "LinkingTo"), but not "Suggests" if (opt$deps == "TRUE" || opt$deps == "FALSE") { opt$deps <- as.logical(opt$deps) } else if (opt$deps == "NA") { opt$deps <- NA } ## set the number of parallel processes to use for a parallel install of ## more than one source package, see ## https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packages if (opt$ncpus == "getOption") { opt$ncpus <- getOption("Ncpus", 1L) } else if (opt$ncpus == "-1") { ## parallel comes with R 2.14+ opt$ncpus <- max(1L, parallel::detectCores()) } ## helper function to catch errors that could arise when package installation has failed ## and to skip installation of packages that are already present (for BiocManager::install() ## these would otherwise result in additional warnings) install_bioc <- function(pkgs, ..., error = FALSE, skipinstalled = FALSE) { e <- NULL capture <- function(e) { if (error) { catch <- grepl("installation of .* packages failed", e$message) || grepl("is not available", e$message) || grepl("had non-zero exit status", e$message) || grepl("compilation failed for package.*", e$message) || grepl("fatal error", e$message) || grepl("No such file or directory", e$message) if (catch) { e <<- e } } } if (skipinstalled) { pkgs <- setdiff(pkgs, installed.packages()[,1]) } if (length(pkgs) > 0) { withCallingHandlers(BiocManager::install(pkgs, ...), warning = capture) if (!is.null(e)) { stop(e$message, call. = FALSE) } } } ## ensure installation is stripped Sys.setenv("_R_SHLIB_STRIP_"="true") ## install requested packages using helper function ## ask must be set to FALSE because user prompts do not appear when calling ## R from the CLI, e.g. ## `R -e 'BiocManager::install("Biobase", ask=TRUE, update=TRUE)'` ## might warn that MASS is out of date, but would not show a user prompt install_bioc(pkgs = opt$PACKAGES, lib = opt$libloc, site_repository = opt$repo, update = opt$update, ask = FALSE, force = opt$force, dependencies = opt$deps, Ncpus = opt$ncpus, method = opt$method, error = opt$error, skipinstalled = opt$skipinstalled) littler/inst/examples/compactpdf.r0000755000176200001440000000156213554554150017045 0ustar liggesusers#!/usr/bin/env r # # A simple wrapper for tools::compactPDF # # Copyright (C) 2019 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) ## configuration for docopt doc <- "Usage: compactpdf.r [-h] [-x] [PATH...] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("Examples: compactpdf.r # compact in current directory compactpdf.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (length(opt$PATH) == 0) { opt$PATH <- list.files(".", pattern=".pdf$") } compactFunction <- function(f) { tools::compactPDF(f, gs_quality="ebook") } sapply(opt$PATH, compactFunction) littler/inst/examples/dratInsert.r0000755000176200001440000000257114353570076017050 0ustar liggesusers#!/usr/bin/env r # # Another example to install one or more (source) packages into a drat # # Copyright (C) 2015 - 2017 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN library(drat) }) ## configuration for docopt doc <- "Usage: drat.r [-h] [-x] [--repo REPO] [--commit MSG] [TARGZ...] -r --repo REPO repository path to use [default: ~/git/drat] -c --commit MSG in github use, commit with MSG (default: no commit) -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("Examples: dratInsert.r myPkg_1.2-3.tar.gz # installs into default (git) repo dratInsert.r -r /srv/R/ myPkg_1.2-3.tar.gz # installs into local directory repo dratInsert.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (is.null(opt$commit)) opt$commit <- FALSE ## helper function installArg <- function(p, repo, commit) { if (!file.exists(p)) stop("No file '", p, "' found. Aborting.", call.=FALSE) insertPackage(p, repo, commit) } ## insert packages using helper function sapply(opt$TARGZ, installArg, opt$repo, opt$commit) littler/inst/examples/silenceTwitterAccount.r0000755000176200001440000000126514005614104021233 0ustar liggesusers#!/usr/bin/r if (is.null(argv) | length(argv) < 1) { cat("Usage: silenceTwitterAccount.r user1 [user2 user3 ...]\n\n") cat("Calls rtweet::post_silence() for the given users.\n") cat("NB: Needs a modified version of rtweet and a twitter token.\n\n") q() } if (!requireNamespace("rtweet", quietly=TRUE)) stop("Please install `rtweet`.", call. = FALSE) if (Sys.getenv("TWITTER_PAT") == "") stop("Please setup a 'TWITTER_PAT' using `rtweet`.", call. = FALSE) library(rtweet) if (is.na(match("post_silence", ls("package:rtweet")))) stop("This needs a version of 'rtweet' with the post_silence() function", call. = FALSE) for (arg in argv) rtweet::post_silence(arg) littler/inst/examples/rhome.r0000755000176200001440000000153013045713217016026 0ustar liggesusers#!/usr/bin/env r ## ## Retrieve R_HOME information ## ## See help(R.home) for details, use arguments "bin", "lib", "etc", ... ## ## ## Note that in shell scripts you may want something like ## ## ## Set R_HOME, respecting an environment variable if set ## : ${R_HOME=$(R RHOME)} ## ## after which expansions use as in ${R_HOME}/bin/Rscript works ## ## In Makefiles you want a similar use via a shell call: ## ## ${R_HOME}/bin/Rscript ## ## as R_HOME is already set with an 'R CMD ...' call (!!). On Windows ## do something like ## ## PKG_LIBS = $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "RcppGSL:::LdFlags()") ## ## to pick up the architecture flag ## ## ## Copyright (C) 2015 Dirk Eddelbuettel ## ## Released under GPL (>= 2) if (is.null(argv) | length(argv) < 1) argv <- "home" cat(sapply(argv, R.home)) littler/inst/examples/installP3M.r0000755000176200001440000000533014536123346016710 0ustar liggesusers#!/usr/bin/env r # # A simple example to install from RSPM/PPM/P3M # # Copyright (C) 2020 - present Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN }) if (Sys.info()[["sysname"]] != "Linux") stop(paste("Currently only supported on Linux.", "Please get in touch if you want to / can help on macOS"), call.=FALSE) code <- "" if (file.exists("/etc/os-release")) { # next block borrowed from my chshli package on GitHub osrel <- read.table("/etc/os-release", sep="=", row.names=1, col.names=c("key","value")) if ("REDHAT_SUPPORT_PRODUCT" %in% rownames(osrel)) { # 'centos7' for CentOS/RHEL 7, 'centos8' for CentOS/RHEL 8 and Fedora ver <- osrel["REDHAT_SUPPORT_PRODUCT_VERSION", "value"] code <- paste0("centos", min(as.numeric(ver), 8)) } else if ("VERSION_CODENAME" %in% rownames(osrel)) { code <- osrel["VERSION_CODENAME", "value"] } } if ((code == "") && (Sys.which("lsb_release") != "")) { code <- system("lsb_release -c | awk '{print $2}'", intern=TRUE) } ## configuration for docopt doc <- paste0("Usage: install(RSPM|PPM|P3M).r [-c code] [-l libloc] [-h] [-x] ARGS... -c --code ARG set code name for distribution [default: ", code, "] -l --libloc ARG location in which to install [default: ", .libPaths()[1], "] -h --help show this help text -x --usage show help and short example usage Note that RSPM/PPM/P3M support may be somewhat experimental. There may not be binaries for every possibly OS, distibution, and R version. Please file issue tickets at the Github repo for littler if you can contribute additional checks and values. As RSPM has been renamed to PPM and then P3M, we now install the script thrice via hardlinks. ") opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n") cat("Basic usage: installRSPM.r digest # install digest for default release '", code, "' installPPM.r -c jammy digest # install digest for Ubuntu 'jammy' installP3M.r -c bookworn digest # install digest for Debian 'bookworm' install(RSPM|PPM|P3M).r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n", sep="") q("no") } if (!is.null(opt$libloc)) .libPaths(opt$libloc) r <- getOption("repos") r["CRAN"] <- paste0("https://p3m.dev/all/__linux__/", opt$code, "/latest") options(repos = r) options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os))) invisible(sapply(opt$ARGS, function(r) install.packages(r))) littler/inst/examples/update.r0000755000176200001440000000450713601412147016201 0ustar liggesusers#!/usr/bin/env r # # A simple example to update packages in /usr/local/lib/R/site-library # Parameters are easily adjustable # # Copyright (C) 2006 - 2019 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) ## configuration for docopt doc <- "Usage: update.r [-r REPO...] [-l LIBLOC] [-n NCPUS] [-h] [-x] -r --repos REPO repository to use, or NULL for file [default: getOption] -l --libloc LIBLOC path to examine for packages to update [default: NULL] -n --ncpus NCPUS number of processes to use for parallel install [default: getOption] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("updates packages, optionally from a given repository, fo a library location. Examples: update.r # update installed packages update.r -l /srv/R-lib # update for this location update,r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } ## docopt results are characters, so if we meant NULL we have to set NULL if (opt$repos == "NULL") { opt$repos <- NULL } else if (opt$repos == "getOption") { ## adjust as necessary, see help('download.packages') opt$repos <- getOption("repos") } if (opt$ncpus == "getOption") { opt$ncpus <- getOption("Ncpus", 1L) } else if (opt$ncpus == "-1") { ## parallel comes with R 2.14+ opt$ncpus <- max(1L, parallel::detectCores()) } if (opt$libloc == "NULL") { ## NULL corresponds to .libPaths() but some directories may be non-writeable ## so we filter out the ones where we can write and use only those canWrite <- function(d) file.access(d, mode=2) == 0 opt$libloc <- Filter(canWrite, .libPaths()) } ## ensure installation is stripped Sys.setenv("_R_SHLIB_STRIP_"="true") ## simply unrolling of all unlink over all files 'repos*' in $TMP clearCache <- function() { sapply(list.files(path=tempdir(), pattern="*rds$", full.names=TRUE), unlink) } ## Always clear caches of remote and local packages clearCache() update.packages(lib.loc=opt$libloc, repos=opt$repos, Ncpus=opt$ncpus, ask=FALSE) ## Always clear caches of remote and local packages clearCache() littler/inst/examples/installDeps2.r0000644000176200001440000000354614574573755017311 0ustar liggesusers#!/usr/bin/env r # # An even simpler example to install dependencies # # Copyright (C) 2024 - present Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt and remotes (or devtools) from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN }) ## configuration for docopt doc <- "Usage: installDeps2.r [-h] [-x] [-s] [DESC] -s --suggests Add 'Suggests' to dependencies -h --help show this help text -x --usage show help and short example usage " opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat(" installDeps2.r The script expects a DESCRIPTION file in the local directory (or given as the argument) which it then parses. The basic mechanics of doing this dependency-free came from a Dockerfile at the `data.table` repository, and are a appreciated. An alternative version, relying on the `remotes` package, has been available for several years with littler as `installDeps.r`. installDeps2.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (length(opt$DESC)==0 && file.exists("DESCRIPTION") && file.exists("NAMESPACE")) { #message("* installing deps for found in current working directory ...") descfile <- "DESCRIPTION" } else { descfile <- opt$DESC } flds <- c("Imports", "Depends", "LinkingTo") if (opt$suggests) flds <- c(flds, "Suggests") res <- read.dcf(descfile)[1,] # we read only one file so first row only res <- res[intersect(names(res), flds)] # intersect available and desired fields pkgs <- tools:::.split_dependencies(res) # parse and split, then diff off base packages instpkgs <- setdiff(names(pkgs), tools:::.get_standard_package_names()$base) install.packages(instpkgs) # and install remainder littler/inst/examples/pkg2bibtex.r0000755000176200001440000000146513521375747016777 0ustar liggesusers#!/usr/bin/env r # # A simple wrapper for toBibtex # # Copyright (C) 2019 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) ## configuration for docopt doc <- "Usage: pkg2bibtex.r [-h] [-x] [PKG...] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("Examples: pkg2bibtex.r anytime nanotime # create two bibtex records pkg2bibtex.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (length(opt$PATH) == 0) { opt$PATH <- "." } res <- sapply(opt$PKG, function(p) toBibtex(citation(p, auto=TRUE)), simplify=FALSE) print(res) littler/inst/examples/compAttr.r0000755000176200001440000000074113245105321016501 0ustar liggesusers#!/usr/bin/env r # # Simple helper script for compileAttributes() # # Dirk Eddelbuettel, July 2014 # # GPL-2 or later ## load Rcpp suppressMessages(library(Rcpp)) ## check all command-line arguments (if any are given) for directory status argv <- Filter(function(x) file.info(x)$is.dir, argv) ## loop over all argument, with fallback of the current directory, and ## call compileAttributes() on the given directory sapply(ifelse(length(argv) > 0, argv, "."), compileAttributes) littler/inst/examples/installRub.r0000755000176200001440000000627714544563575017067 0ustar liggesusers#!/usr/bin/env r # # A installer for r-universe binaries (on Ubuntu 'jammy' only) # # Copyright (C) 2023 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) library(utils) # for osVersion rver <- gsub("^([\\d].[\\d]).*$", "\\1", as.character(getRversion()), perl=TRUE) uburel <- "jammy" ## configuration for docopt doc <- paste0("Usage: installRub.r [-h] [-x] [-k] [-r REL] [-v VER] [-u UNIV] PACKAGES -u --universe UNIV required argument specifying universe [default: ] -v --version VER R 'major.minor' version release pair to install for [default: ", rver, "] -r --release REL Ubuntu LTS release to install to install for [default: ", uburel, "] -k --keepoption so not set option 'bspm.version.check' to 'TRUE' as is default -h --help show this help text -x --usage show help and short example usage. PACKAGES can also be a shorthand 'package@universe'. See '-x | --usage' for more.") opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("In general, PACKAGES... can be one or more R package names available in then selected r-universe repository; its CRAN (as well as some core BioConductor) dependencies will be provided automatically by r2u. It can also be a shorthand 'package@universe'. Note that while CRAN works extremely hard to always provide an installable set of working packages, r-universe works under a different model and its packages cannot offer any such guarantees. Also note that while we use 'r2u' for the CRAN (and, to some extend, BioConductor) parts full-filling *all* dependencies completely, the binaries from r-universe do not carry any (system-)dependency info so you may end up with missing libries you may need to add. Where an r-universe package exists on CRAN you can cover your ground by first installing the CRAN version and then the r-universe version. Examples: installRub.r -u rcppcore Rcpp RcppArmadillo # installs (never than CRAN / r2u) Rcpp(Armadillo) installRub.r -u eddelbuettel RcppKalman # installs non-CRAN package RcppKalman installRub.r rcpp@rcppcore # alternate to install Rcpp from RcppCore universe installRub.r polars@rpolars # alternate to install polars from rpolars universe installRub.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (getRversion() < "4.2.0") stop("R version 4.2.0 or later is required.", call. = FALSE) if (!exists("osVersion")) stop("Cannot find 'osVersion'. Weird.", call. = FALSE) if (!startsWith(utils::osVersion, "Ubuntu")) stop("Ubuntu is required as host system.", call. = FALSE) if (!requireNamespace("bspm", quietly=TRUE)) stop("The 'bspm' package is required.", call. = FALSE) if (is.null(opt$universe) && length(opt$PACKAGES) == 1) { tokens <- strsplit(opt$PACKAGES, "@")[[1]] opt$PACKAGES <- tokens[1] opt$universe <- tokens[2] } univ <- paste0("https://", opt$universe, ".r-universe.dev/bin/linux/", opt$release, "/", opt$version) if (!opt$keepoption) options(bspm.version.check=TRUE) install.packages(pkgs = opt$PACKAGES, repos = c(univ, "https://cloud.r-project.org")) littler/inst/examples/highlightsweave.r0000755000176200001440000000117113245105321020070 0ustar liggesusers#!/usr/bin/env r # # A simple example to invoke Sweave # # Copyright (C) 2014 Dirk Eddelbuettel # # Released under GPL (>= 2) ## use given argument(s) as target files, or else default to .Rnw files in directory files <- if (length(argv) == 0) dir(pattern="*.Rnw") else argv <- Filter(function(x) file.info(x)$is.dir, argv) ## convert all files from Rnw to pdf using the highlight driver invisible(sapply(files, function(srcfile) { Sweave(srcfile, driver=highlight::HighlightWeaveLatex(boxes=TRUE)) tools::texi2pdf(gsub(".Rnw", ".tex", srcfile)) tools::texi2pdf(gsub(".Rnw", ".tex", srcfile), texi2dvi="pdflatex") })) littler/inst/examples/rchk.r0000755000176200001440000000033113477035332015645 0ustar liggesusers#!/usr/bin/env r # # Minimal rhub::check() wrapper using rchk() # # Copyright (C) 2016 - 2019 Dirk Eddelbuettel # # Released under GPL (>= 2) rhub::check(".", "ubuntu-rchk", check_args="--no-manual --no-vignettes") littler/inst/examples/com.r0000755000176200001440000000065313710107314015471 0ustar liggesusers#!/usr/bin/env r # # Minimal rhub::check_on_macos() wrapper # # Copyright (C) 2016 - 2020 Dirk Eddelbuettel # # Released under GPL (>= 2) ##rhub::check_on_macos(check_args="--no-manual --no-vignettes") ## cf https://github.com/r-hub/rhub/issues/368 macos <- "macos-highsierra-release-cran" checkfile <- function(f) if (file.exists(f)) rhub::check(f, platform=macos) if (length(argv) == 0) argv <- "." sapply(argv, checkfile) littler/inst/examples/runit.r0000755000176200001440000000117413144070211016047 0ustar liggesusers#!/usr/bin/env r # # A simple example to invoke unit tests # # Copyright (C) 2014 - 2017 Dirk Eddelbuettel # # Released under GPL (>= 2) suppressMessages({ library(docopt) # we need the docopt package library(RUnit) # we need the RUnit package }) doc <- "Usage: runit.r [-p PACKAGES] [--help] [FILES ...] -p --packages PACKAGES comma-separated list of packages to install [default: ] -h --help show this help text" opt <- docopt(doc) for (p in strsplit(opt$packages, ",")[[1]]) suppressMessages(require(p, character.only=TRUE)) for (f in opt$FILES) runTestFile(f) q(status=0) littler/inst/examples/r2u.r0000755000176200001440000000771614531412752015441 0ustar liggesusers#!/usr/bin/env r # # Simple r2u helper frontend # # Copyright (C) 2022 - 2023 Dirk Eddelbuettel # # Released under GPL (>= 2) library(docopt) doc <- "Usage: r2u.r [--release DIST] [--debug] [--verbose] [--force] [--xvfb] [--bioc] [--suffix SUF] [--debver DBV] [--plusdfsg] [--uncache] [--dryrun] [--compile] [--help] CMD ... Options: -r --release DIST release distribution to use, one of 'focal' or 'jammy' [default: jammy] -d --debug boolean flag for extra debugging -v --verbose boolean flag for verbose operation -f --force boolean flag to force a build -x --xvfb boolean flag to build under 'xvfb' (x11 virtual framebuffer) -b --bioc boolean flag to update BioConductor (subset) not CRAN -s --suffix SUF build version suffix appended [default: .1] -t --debver DBV debian version leading digit [default: 1.] -p --plusdfsg boolean flag if upstream version gets '+dfsg' -u --uncache remove the cached meta data archives of available packages (when using 'package' command) -n --dryrun boolean flag for dry-run of skip build (when using 'package' command) -c --compile boolean flag for ensuring a compilation from source -h --help show this help text Cmd: build updates all packages last reports most recent binary package sync count counts packages downloaded (locally) today table tabulates packages downloaded today package updates the package(s) named in ... and builds " opt <- docopt(doc) if (!is.finite(match(opt$release, c("focal", "jammy")))) stop("Unknown distro '", opt$release, "'.", call. = FALSE) if (length(opt$CMD) > 1) { opt$args <- opt$CMD[-1] opt$CMD <- opt$CMD[1] } if (!is.finite(match(opt$CMD, c("build", "last", "count", "table", "package")))) stop("Unknown command '", opt$CMD, "'.", call. = FALSE) if (is.finite(match(opt$CMD, "build"))) { library(r2u) if (opt$uncache) { for (db in c(r2u:::.defaultCRANDBFile(), r2u:::.defaultAPFile())) if (file.exists(db)) unlink(db) r2u:::.loadDB() r2u:::.loadAP() } buildUpdatedPackages(opt$release, opt$debug, opt$verbose, opt$force, opt$xvfb, opt$bioc) } else if (is.finite(match(opt$CMD, "last"))) { D <- RcppSimdJson::fload("https://packagemanager.posit.co/__api__/sources/1/transactions") ts <- anytime::utctime(D[1,"completed"]) dh <- as.numeric(difftime(Sys.time(), ts, units="hours")) un <- "days" if (dh <= 3) un <- "mins" else if (dh < 25) un <- "hours" cat("P3M/PPM/RSPM last updated", format(round(difftime(Sys.time(), ts, units=un),1)), "ago\n") } else if (is.finite(match(opt$CMD, "count"))) { ll <- readLines(pipe("bash -c ~/bin/web_who_what | grep '.*cranapt\\/pool\\/dists\\/.*\\/r-.*\\.deb$'")) cat(length(ll), ".deb files downloaded\n") } else if (is.finite(match(opt$CMD, "table"))) { con <- pipe("bash -c ~/bin/web_who_what | grep '.*cranapt\\/pool\\/dists\\/.*\\/r-.*\\.deb$'") ll <- readLines(con) close(con) tt <- table(gsub(".*r-(cran|bioc)-(.*)_\\d+.*", "\\2", ll, perl=TRUE)) print(head(tt[order(-tt)], 10)) } else if (is.finite(match(opt$CMD, "package"))) { library(r2u) if (opt$uncache) { for (db in c(r2u:::.defaultCRANDBFile(), r2u:::.defaultAPFile())) if (file.exists(db)) unlink(db) r2u:::.loadDB() r2u:::.loadAP() } for (p in opt$args) { buildPackage(pkg = p, tgt = opt$release, debug = opt$debug, verbose = opt$verbose, force = opt$force, xvfb = opt$xvfb, suffix = opt$suffix, debver = opt$debver, plusdfsg= opt$plusdfsg, dryrun = opt$dryrun, compile = opt$compile) } } littler/inst/examples/cow.r0000755000176200001440000000052013706034372015504 0ustar liggesusers#!/usr/bin/env r # # Minimal rhub::check_on_windows() wrapper # # Copyright (C) 2016 - 2020 Dirk Eddelbuettel # # Released under GPL (>= 2) checkargs <- "--no-manual --no-vignettes" checkfile <- function(f) if (file.exists(f)) rhub::check_on_windows(f, check_args=checkargs) if (length(argv) == 0) argv <- "." sapply(argv, checkfile) littler/inst/examples/c4c.r0000755000176200001440000000051413706034332015364 0ustar liggesusers#!/usr/bin/env r # # Minimal rhub::check_for_cran() wrapper # # Copyright (C) 2016 - 2020 Dirk Eddelbuettel # # Released under GPL (>= 2) checkargs <- "--no-manual --no-vignettes" checkfile <- function(f) if (file.exists(f)) rhub::check_for_cran(f, check_args=checkargs) if (length(argv) == 0) argv <- "." sapply(argv, checkfile) littler/inst/examples/getRStudioDesktop.r0000755000176200001440000000120614372435416020345 0ustar liggesusers#!/usr/bin/env r # # A simple example to install RStudio Desktop # # Copyright (C) 2014 - 2023 Carl Boettiger and Dirk Eddelbuettel # # Released under GPL (>= 2) # # based on earlier https://raw.githubusercontent.com/rocker-org/rstudio-daily/master/latest.R # # todo: cmdline options for different download options / distro flavours setwd("/tmp") # go to /tmp url <- "https://dailies.rstudio.com/rstudio/latest/index.json" js <- jsonlite::fromJSON(url) fileurl <- js$products$electron$platforms$`jammy-amd64`$link file <- basename(fileurl) cat("'", fileurl, "' -> '", file, "'\n", sep="") download.file(fileurl, file) littler/inst/examples/testInstalled.r0000755000176200001440000000165213331043167017536 0ustar liggesusers#!/usr/bin/env r # # a simple example to test one or more installed packages ## load docopt package from CRAN library(docopt) library(tools) ## configuration for docopt doc <- "Usage: test.r [-l LIBLOC] [-o OUTDIR] [-t TYPES] [-s SRCDIR] [-h] [PACKAGES ...] -l --libloc LIBLOC location where package(s) are installed [default: NULL] -o --outdir OUTDIR the directory into which to write output files, should exist. [default: .] -t --types TYPES type(s) of tests to be done. [default: c('examples', 'tests', 'vignettes')] -s --srcdir SRCDIR Optional directory to look for .save files [default: NULL] -h --help show this help text" ## docopt parsing opt <- docopt(doc) ## installation given selected options and arguments testInstalledPackage(pkg = opt$PACKAGES, lib = opt$libloc, outDir = opt$outdir, types = opt$types, srcdir = opt$srcdir) littler/inst/examples/urlUpdate.r0000755000176200001440000000141413736146514016671 0ustar liggesusers#!/usr/bin/env r ## ## A simple tool to update URLs using R's checker ## ## Copyright (C) 2020 - present Dirk Eddelbuettel ## ## Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) if (!requireNamespace("urlchecker", quietly=TRUE)) stop("The 'urlchecker' package is required. Please install it from GitHub.", call.=FALSE) doc <- "Usage: urlUpdate.r [-c] [-h] [PACKAGES ...] -c --check-only check-only, i.e. do not auto-update URLs -h --help show this help text Simple wrapper to 'urlchecker::update_url(...)'. " opt <- docopt(doc) if (length(opt$PACKAGES) == 0) opt$PACKAGES <- "." # default argument current directory for (p in opt$PACKAGES) if (opt$check_only) print(urlchecker::url_check(p)) else urlchecker::url_update(p) littler/inst/examples/kitten.r0000755000176200001440000000231614075403647016224 0ustar liggesusers#!/usr/bin/env r library(docopt) ## configuration for docopt doc <- "Usage: kitten.r [-t TYPE] [-b] [-p] [-h] [-x] PACKAGE -t --type TYPE type of kitten: plain, rcpp, arma, eigen. [default: plain] -b --bunny install roxygen2 documentation example and roxygenize (only for plain) -p --puppy invoke tinytest::puppy to set up testing (only for plain) -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("Examples: kitten.r kitten.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } ## maybe support path, author, maintainer, email, license, ... ign <- switch(opt$type, plain = pkgKitten::kitten(opt$PACKAGE, puppy=opt$puppy, bunny=opt$bunny), rcpp = Rcpp::Rcpp.package.skeleton(opt$PACKAGE), arma = RcppArmadillo::RcppArmadillo.package.skeleton(opt$PACKAGE), eigen = RcppEigen::RcppEigen.package.skeleton(opt$PACKAGE)) if (opt$puppy) { stopifnot(requireNamespace("tinytest", quietly=TRUE)) tinytest::puppy(opt$PACKAGE) } littler/inst/examples/rd2md.r0000755000176200001440000000321014433760535015730 0ustar liggesusers#!/usr/bin/env r # # Convert NEWS.Rd to markdown # # Copyright (C) 2016 - 2017 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) library(tools) ## configuration for docopt doc <- "Usage: rd2md.r [-h] [-x] [--src REPODIR] [--out OUTDIR] [FILES...] -s --src REPODIR source root directory [default: ~/git] -o --out OUTDIR output directory [default: /tmp] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("Examples: rd2md.r foo # implies conversion of ~/git/foo/inst/NEWS.Rd rd2md.r ~/git/foo/inst/NEWS.Rd # converts given file to markdown rd2md.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } ## helper function convertArg <- function(p, src, out) { filename <- mdfile <- NULL if (file.exists(p)) { filename <- p mdfile <- paste0(filename, ".md") } else { filename <- file.path(src, p, "inst", "NEWS.Rd") if (!file.exists(filename)) { stop("No matching file found for ", p, call.=FALSE) } mdfile <- file.path(out, paste0(p, ".news.md")) } htmlfile <- paste0(filename, ".html") Rd2HTML(filename, htmlfile) cmd <- paste("pandoc", htmlfile, "-o", mdfile) system(cmd) unlink(htmlfile) cat("Converted", filename, "into", mdfile, "\n") } ## insert packages using helper function sapply(opt$FILES, convertArg, opt$src, opt$out) littler/inst/examples/getRStudioServer.r0000755000176200001440000000117014372435531020200 0ustar liggesusers#!/usr/bin/env r # # A simple example to install RStudio Desktop # # Copyright (C) 2014 - 2023 Carl Boettiger and Dirk Eddelbuettel # # Released under GPL (>= 2) # # based on earlier https://raw.githubusercontent.com/rocker-org/rstudio-daily/master/latest.R # # todo: cmdline options for different download options / distro flavours setwd("/tmp") # go to /tmp url <- "https://dailies.rstudio.com/rstudio/latest/index.json" js <- jsonlite::fromJSON(url) fileurl <- js$products$server$platforms$`jammy-amd64`$link cat("'", url, "' -> '", file, "'\n", sep="") download.file(fileurl, file) #, method="wget") littler/inst/examples/cos.r0000755000176200001440000000060413713572701015504 0ustar liggesusers#!/usr/bin/env r # # Minimal rhub(".", platform="solaris-x86-patched") # # Copyright (C) 2016 - 2020 Dirk Eddelbuettel # # Released under GPL (>= 2) #checkargs <- "--no-manual --no-vignettes" solaris <- "solaris-x86-patched" checkfile <- function(f) if (file.exists(f)) rhub::check(f, platform=solaris)#, check_args=checkargs) if (length(argv) == 0) argv <- "." sapply(argv, checkfile) littler/inst/examples/cowu.r0000755000176200001440000000055214156430711015673 0ustar liggesusers#!/usr/bin/env r # # Minimal rhub windown UCRT check wrapper # # Copyright (C) 2016 - 2021 Dirk Eddelbuettel # # Released under GPL (>= 2) checkargs <- "--no-manual --no-vignettes" checkfile <- function(f) if (file.exists(f)) rhub::check(f, platform="windows-x86_64-devel-ucrt", check_args=checkargs) if (length(argv) == 0) argv <- "." sapply(argv, checkfile) littler/inst/examples/shiny.r0000755000176200001440000000126613331042746016054 0ustar liggesusers#!/usr/bin/env r # # Another example to run a shiny app # # Copyright (C) 2015 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) ## same as runApp() host <- getOption("shiny.host", "127.0.0.1") ## configuration for docopt doc <- paste0("Usage: shiny.r [-h] [--port PORT] [--host HOST] [--dir DIR] -p --port PORT port to use [default: NULL] -o --host HOST host string to use [default: ", host, "] -d --dir DIR directoru run application from [default: .] -h --help show this help text") ## docopt parsing opt <- docopt(doc) suppressMessages(library(shiny)) runApp(opt$dir, port=as.integer(opt$port), host=opt$host) littler/inst/examples/knit.r0000755000176200001440000000047513245105321015661 0ustar liggesusers#!/usr/bin/env r # # Simple helper script for knitr # # Dirk Eddelbuettel, May 2013 # # GPL-2 or later if (is.null(argv)) { cat("Need an argument FILE.Rnw\n") q(status=-1) } file <- argv[1] if (!file.exists(file)) { cat("File not found: ", file, "\n") q(status=-1) } require(knitr) knit2pdf(file) littler/inst/examples/render.r0000755000176200001440000000211513554556213016201 0ustar liggesusers#!/usr/bin/env r # # Another example to convert markdown # # Copyright (C) 2016 - 2019 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) ## configuration for docopt doc <- "Usage: render.r [-c] [-h] [-x] [FILES...] -c --compact compact pdf file [default: FALSE] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("Examples: render.r foo.Rmd bar.Rmd # convert two given files render.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } library(rmarkdown) ## helper function renderArg <- function(p) { if (!file.exists(p)) stop("No file '", p, "' found. Aborting.", call.=FALSE) render(p) if (opt$compact) { s <- gsub(".Rmd$", ".pdf", p) if (file.exists(s)) tools::compactPDF(s, gs_quality="ebook") } } ## render files using helper function sapply(opt$FILES, renderArg) littler/inst/examples/check.r0000755000176200001440000000664014454520425016002 0ustar liggesusers#!/usr/bin/env r # # Another example to check one or more packages, with option parsing # # Copyright (C) 2015 - 2023 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) ## configuration for docopt doc <- "Usage: check.r [-h] [-x] [--as-cran] [--repo REPO] [--no-manvig] [--install-deps] [--install-kitchen] [--deb-pkgs PKGS...] [--use-sudo] [--library LIB] [--setwd DIR] [TARGZ ...] -a --as-cran customization similar to CRAN's incoming [default: FALSE] -r --repo REPO repository to use, or NULL for file [default: https://cloud.r-project.org] -n --no-manvig set the '--no-manual --no-vignettes' options [default: FALSE] -i --install-deps also install packages along with their dependencies [default: FALSE] -k --install-kitchen even install packages 'kitchen sink'-style up to suggests [default: FALSE] -l --library LIB when installing use this library [default: /usr/local/lib/R/site-library] -s --setwd DIR change to this directory before undertaking the test [default: ] -d --deb-pkgs PKGS also install binary .deb packages with their dependencies [default: FALSE] -u --use-sudo use sudo when installing .deb packages [default: FALSE] -h --help show this help text -x --usage show help and short example usage" ## docopt parsing opt <- docopt(doc) if (opt$usage) { cat(doc, "\n\n") cat("Examples: check.r -a -i -s /tmp myPkg_1.2-3.tar.gz # run a check --as-cran with depends in /tmp # for package myPkg_1.2-3.tar.gz check.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } args <- character() if (opt$as_cran) args <- c(args, "--as-cran") if (opt$no_manvig) args <- c(args, "--no-manual", "--no-vignettes") if (!is.null(opt$libdir)) .libPaths(opt$libdir) r <- getOption("repos") r["CRAN"] <- opt$repo options(repos = r) hasRcmdcheck <- requireNamespace("rcmdcheck", quietly=TRUE) if (hasRcmdcheck) suppressMessages(library("rcmdcheck")) ## helper functions checkArg <- function(p, args) { if (hasRcmdcheck) { #if (length(args) == 0) args <- "" res <- rcmdcheck(p, args=args) } else { tools:::.check_packages(c(p, args)) res <- NULL } res } ## helper function which switches to local (ie NULL) repo if matching file is presented installArg <- function(p, lib, rep) { p <- gsub("_.*tar\\.gz$", "", p) install.packages(pkgs=p, lib=lib, repos=rep, dependencies=if(opt$install_kitchen) c("Depends", "Imports", "LinkingTo", "Suggests") else TRUE ) } ## if binary .deb files are to be installed first: if (length(opt$deb_pkgs) > 1 || opt$deb_pkgs != FALSE) { cmd <- paste0(if (opt$use_sudo) "sudo " else "", "apt-get install -y ", paste(opt$deb_pkgs, collapse=" ")) system(cmd) } ## if dependencies (or even suggests) are to be installed first: if (opt$install_deps || opt$install_kitchen) sapply(opt$TARGZ, installArg, opt$lib, opt$repo) ## change directory if a target directory was given if (!is.null(opt$setwd)) setwd(opt$setwd) ## installation given selected options and arguments sapply(opt$TARGZ, checkArg, args) littler/inst/examples/installBSPM.r0000755000176200001440000000342313735736364017065 0ustar liggesusers#!/usr/bin/env r # # A simple example to install from RSPM # # Copyright (C) 2020 - present Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN }) if (Sys.info()[["sysname"]] != "Linux") stop(paste("Currently only supported on Linux.", "Please get in touch if you want to / can help on macOS"), call.=FALSE) if (!requireNamespace("bspm", quietly=TRUE)) stop("The 'bspm' package is required. Please install it.", call.=FALSE) ## configuration for docopt doc <- paste0("Usage: installBSPM.r [-h] [-x] ARGS... -h --help show this help text -x --usage show help and short example usage Note that BSPM support is still somewhat experimental. It also requires support (via the 'bspm' package) of the underlying system package manager, which is known to work for apt/dpkg (Debian, Ubuntu, ...) and dnf/yum (Fedora/RH/CentOS). Please file issue tickets at the Github repo for littler (or bspm) if you can help with additional settings. Note that to take fullest advantage of BSPM, you also need the system package manager to know about the largest number of pre-compiled packages. For Ubuntu, this means the exanded 'ppa:c2d4u.team/c2d4u4.0+' repo, and for Fedora the say 'iucar/cran' Copr archive. This user-level script does not attempt to later your system-level repository information. ") opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat(" Basic usage: installBSPM.r digest installBSPM.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } library(bspm) bspm::enable() options(bspm.sudo=TRUE) install.packages(opt$ARGS) littler/inst/examples/install.r0000755000176200001440000000516513600257644016376 0ustar liggesusers#!/usr/bin/env r # # A simple example to install one or more packages # # Note that a more featureful version exists in install2.r # with an added dependency on the 'docopt' argument parser # # Copyright (C) 2006 - 2019 Dirk Eddelbuettel # # Released under GPL (>= 2) if (is.null(argv) | length(argv) < 1) { if (file.exists("DESCRIPTION") && file.exists("NAMESPACE")) { ## we are in a source directory, so build it message("* installing *source* package found in current working directory ...") argv <- "." } else { cat("Usage: installr.r pkg1 [pkg2 pkg3 ...]\n\n") cat("Installs pkg1, ... from existing files with matching extension.\n") cat("Use \".\" to install the package in current working directory.\n\n") cat("Use (remote) packages pkgname1 pkgname2 pkgname3 ... for parallel\n") cat("installation if 'Ncpus' option is set (or multiple cores present).\n\n") cat("Set environment variables REPOS and LIBLOC to overrride defaults.\n\n") q() } } ## ensure installation is stripped Sys.setenv("_R_SHLIB_STRIP_"="true") ## adjust as necessary, see help('download.packages') ## littler can now read ~/.littler.r and /etc/littler.r to set this repos <- getOption("repos") ## NULL means install file, and we supported env var previously if (Sys.getenv("REPOS") == "NULL") repos = NULL ## this makes sense on Debian where no packages touch /usr/local lib.loc <- Sys.getenv("LIBLOC", unset="/usr/local/lib/R/site-library") ## helper function to for existing files with matching extension isMatchingFile <- function(f) (file.exists(f) && grepl("(\\.tar\\.gz|\\.tgz|\\.zip)$", f)) || (f == ".") ## helper function which switches to local (ie NULL) repo if matching file is presented installArg <- function(f, lib, rep) install.packages(pkgs=f, lib=lib, repos=if (isMatchingFile(f)) NULL else repos) ## check arguments for local files -- if none, then we can pass vector on isLocal <- sapply(argv, isMatchingFile) if (any(isLocal)) { ## use argv [filtered by installArg()], lib.loc and repos to install the packages sapply(argv, installArg, lib.loc, repos) } else { ## all remote, so pass argv so Ncpus can enter install.packages(pkgs=argv, lib=lib.loc, repos=repos, Ncpus=getOption("Ncpus", max(1L, parallel::detectCores()))) } ## clean up any temp file containing CRAN directory information sapply(list.files(path=tempdir(), pattern="^(repos|libloc).*\\.rds$", full.names=TRUE), unlink) littler/inst/examples/install2.r0000755000176200001440000001502214407063510016442 0ustar liggesusers#!/usr/bin/env r # # A second example to install one or more packages, now with option parsing # # Copyright (C) 2011 - 2014 Dirk Eddelbuettel # Copyright (C) 2014 - 2017 Carl Boettiger and Dirk Eddelbuettel # Copyright (C) 2018 - 2023 Carl Boettiger, Dirk Eddelbuettel, Brandon Bertelsen, and SHIMA Tatsuya # # Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) ## default to first library location in .libPaths() libloc <- .libPaths()[1] ## configuration for docopt doc <- paste0("Usage: install2.r [-l LIBLOC] [-h] [-x] [-s] [-d DEPS] [-n NCPUS] [-r REPOS...] [-m METHOD] [-t TYPE] [--error] [--] [PACKAGES ...] -l --libloc LIBLOC location in which to install [default: ", libloc, "] -d --deps DEPS install suggested dependencies as well [default: NA] -n --ncpus NCPUS number of processes to use for parallel install, -1 selects all cores [default: getOption] -r --repos REPOS repositor(y|ies) to use, or NULL for file [default: getOption] -e --error throw error and halt instead of a warning [default: FALSE] -s --skipinstalled skip installing already installed packages [default: FALSE] -m --method METHOD method to be used for downloading files [default: auto] -t --type TYPE installation type as used by `install.packages` [default: getOption] -h --help show this help text -x --usage show help and short example usage") opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("where PACKAGES... can be one or more CRAN package names, or local (binary or source) package files (where extensions .tar.gz, .tgz and .zip are recognised). Optional arguments understood by R CMD INSTALL can be passed interspersed in the PACKAGES, though this requires use of '--'. Examples: install2.r -l /tmp/lib Rcpp BH # install into given library install2.r -- --with-keep.source drat # keep the source install2.r -- --data-compress=bzip2 stringdist # prefer bz2 compression install2.r \".\" # install package in current directory install2.r -n 6 ggplot2 # parallel install: (6 processes) install2.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (opt$deps == "TRUE" || opt$deps == "FALSE") { opt$deps <- as.logical(opt$deps) } else if (opt$deps == "NA") { opt$deps <- NA } ## docopt results are characters, so if we meant NULL we have to set NULL if (length(opt$repos) == 1 && "NULL" %in% opt$repos) { opt$repos <- NULL } if ("getOption" %in% opt$repos) { ## as littler can now read ~/.littler.r and/or /etc/littler.r we can preset elsewhere opt$repos <- c(opt$repos[which(opt$repos != "getOption")], getOption("repos")) } if (opt$ncpus == "getOption") { opt$ncpus <- getOption("Ncpus", 1L) } else if (opt$ncpus == "-1") { ## parallel comes with R 2.14+ opt$ncpus <- max(1L, parallel::detectCores()) } ## type should reflects bspm where available if (opt$type == "getOption") { opt$type <- getOption("pkgType") #if (requireNamespace("bspm", quietly=TRUE) && Sys.info()[["sysname"]] == "Linux") opt$type <- "binary-source" } ## ensure installation is stripped Sys.setenv("_R_SHLIB_STRIP_"="true") install_packages2 <- function(pkgs, ..., error = FALSE, skipinstalled = FALSE) { e <- NULL capture <- function(e) { if (error) { catch <- grepl("(download|installation) of package .* failed", e$message) || grepl("(dependenc|package).*(is|are) not available", e$message) || grepl("installation of package.*had non-zero exit status", e$message) || grepl("installation of .+ package(|s) failed", e$message) if (catch) { e <<- e } } } if (skipinstalled) { pkgs <- setdiff(pkgs, installed.packages()[,1]) } if (length(pkgs) > 0) { withCallingHandlers(install.packages(pkgs, ...), warning = capture) if (!is.null(e)) { stop(e$message, call. = FALSE) } } } ## helper function to for existing files with matching extension isMatchingFile <- function(f) (file.exists(f) && grepl("(\\.tar\\.gz|\\.tgz|\\.zip)$", f)) || (f == ".") ## helper function which switches to local (ie NULL) repo if matching file is presented installArg <- function(f, lib, rep, dep, iopts, error, skipinstalled, ncpus, method, type) { install_packages2(pkgs=f, lib=lib, repos=if (isMatchingFile(f)) NULL else rep, dependencies=dep, INSTALL_opts=iopts, Ncpus = ncpus, method = method, type = type, error = error, skipinstalled = skipinstalled) } ## strip out arguments to be passed to R CMD INSTALL isArg <- grepl('^--',opt$PACKAGES) installOpts <- opt$PACKAGES[isArg] opt$PACKAGES <- opt$PACKAGES[!isArg] if (length(opt$PACKAGES)==0 && file.exists("DESCRIPTION") && file.exists("NAMESPACE")) { ## we are in a source directory, so build it message("* installing *source* package found in current working directory ...") opt$PACKAGES <- "." } ## helper function to for existing files with matching extension isMatchingFile <- function(f) (file.exists(f) && grepl("(\\.tar\\.gz|\\.tgz|\\.zip)$", f)) || (f == ".") ## check arguments for local files -- if none, then we can pass vector on isLocal <- sapply(opt$PACKAGES, isMatchingFile) ## for any local sources loop explicitly as before, otherwise for remote ## packages pass vector to install_packages2 which does the rest (and ## possibly in parallel using up to ncpus) if (any(isLocal)) { sapply(opt$PACKAGES, installArg, opt$libloc, opt$repos, opt$deps, installOpts, opt$error, opt$skipinstalled, opt$ncpus, opt$method, opt$type) } else { install_packages2(pkgs = opt$PACKAGES, lib = opt$libloc, repos = opt$repos, dependencies = opt$deps, INSTALL_opts = installOpts, Ncpus = opt$ncpus, method = opt$method, type = opt$type, error = opt$error, skipinstalled = opt$skipinstalled) } ## clean up any temp file containing CRAN directory information sapply(list.files(path=tempdir(), pattern="^(repos|libloc).*\\.rds$", full.names=TRUE), unlink) littler/inst/examples/getPandoc.r0000755000176200001440000000100714160343033016611 0ustar liggesusers#!/usr/bin/env r # # A downloader for Pandoc's amd64 .deb # # Copyright (C) 2021 Dirk Eddelbuettel # # Released under GPL (>= 2) # # TODO: Maybe make the .deb filter an option library(RcppSimdJson) url <- "https://api.github.com/repos/jgm/pandoc/releases/latest" res <- RcppSimdJson::fload(url) files <- res$assets[, "browser_download_url"] deb <- files[grepl("-amd64\\.deb$", files)] tgt <- file.path("/tmp", basename(deb)) download.file(deb, tgt, quiet=TRUE) cat("Downloaded '", deb, "' as '", tgt, "'\n", sep="") littler/inst/examples/getQuartoCli.r0000755000176200001440000000077714121367114017330 0ustar liggesusers#!/usr/bin/env r # # A downloader for Quarto # # Copyright (C) 2021 Dirk Eddelbuettel # # Released under GPL (>= 2) # # TODO: Maybe make the .deb filter an option library(RcppSimdJson) url <- "https://api.github.com/repos/quarto-dev/quarto-cli/releases/latest" res <- RcppSimdJson::fload(url) files <- res$assets[, "browser_download_url"] deb <- files[grepl("\\.deb$", files)] tgt <- file.path("/tmp", basename(deb)) download.file(deb, tgt, quiet=TRUE) cat("Downloaded '", deb, "' as '", tgt, "'\n", sep="") littler/inst/examples/fsizes.r0000755000176200001440000000034313245105321016211 0ustar liggesusers#!/usr/bin/env r # # A simple example to do statistics on files # # Copyright (C) 2006 - 2014 Dirk Eddelbuettel # # Released under GPL (>= 2) fsizes <- as.integer(readLines(file("stdin"))) print(summary(fsizes)) stem(fsizes) littler/inst/examples/tt.r0000755000176200001440000000632714565637303015365 0ustar liggesusers#!/usr/bin/env -S r -t # # tinytest wrapper # # Copyright (C) 2019 - 2024 Dirk Eddelbuettel # # Released under GPL (>= 2) if (!requireNamespace("tinytest", quietly=TRUE)) stop("Please install 'tinytest' from CRAN.", call. = FALSE) ## load docopt and tinytest from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN library(tinytest) # or can use devtools as a fallback }) ## configuration for docopt doc <- "Usage: tt.r [-h] [-x] [-a] [-b] [-c] [-d] [-f] [-n NCPUS] [-p] [-s] [-z] [ARG...] -a --all use test_all mode [default: FALSE] -b --build use build-install-test mode [default: FALSE] -c --ci set environment variable CI to TRUE [default: FALSE] -d --directory use directory mode [default: FALSE] -f --file use file mode [default: FALSE] -n --ncpus NCPUS use 'ncpus' in parallel [default: getOption] -p --package use package mode [default: FALSE] -s --silent use silent and do not print result [default: FALSE] -z --effects show side effects [default: FALSE] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("where ARG... can be one or more file name, or directories or package names. Examples: tt.r -a # test 'all files' from current directory tt.r -f testfile.R # test the file 'testfile.R' tt.r -d testdir # test all files in the directory 'testdir' tt.r -p testpkg # test the (installed) package 'testpkg' tt.r -n 1 -p testpkg # test (installed) package 'testpkg' in serial mode tt.r # run test_all() if DESCRIPTION && inst/tinytest/ tt.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } sideeffects <- if (opt$effects) TRUE else FALSE # by default, do not show side effects if (opt$ncpus == "getOption") { opt$ncpus <- getOption("Ncpus", 1L) } else if (opt$ncpus == "-1") { ## parallel comes with R 2.14+ opt$ncpus <- max(1L, parallel::detectCores()) } else { opt$ncpus <- as.integer(opt$ncpus) } if (opt$ci) { Sys.setenv(CI="TRUE") } res <- NULL if (opt$all) { res <- test_all(if (length(opt$ARG) == 0) "." else opt$ARG, side_effects=sideeffects) } else if (opt$build) { res <- build_install_test(if (length(opt$ARG) == 0) "." else opt$ARG, side_effects=sideeffects, ncpu=opt$ncpus) } else if (opt$file) { res <- run_test_file(opt$ARG, side_effects=sideeffects) } else if (opt$directory) { if (length(opt$ARG) == 0 && dir.exists("inst/tinytest")) opt$ARG <- "inst/tinytest" res <- run_test_dir(opt$ARG, side_effects=sideeffects) } else if (opt$package) { if (opt$ncpus == 1L) { res <- test_package(opt$ARG, side_effects=sideeffects) } else { res <- test_package(opt$ARG, side_effects=sideeffects, ncpu=opt$ncpus) } } else if (file.exists("DESCRIPTION") && dir.exists("inst/tinytest")) { res <- test_all(".", side_effects=sideeffects) } if (!opt$silent && !is.null(res)) print(res) littler/inst/examples/installDeps.r0000755000176200001440000000330714532414243017201 0ustar liggesusers#!/usr/bin/env r # # A simple example to install dependencies # # Copyright (C) 2020 - present Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt and remotes (or devtools) from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN library(remotes) # or can use devtools as a fallback }) ## configuration for docopt doc <- "Usage: installDeps.r [-h] [-x] [-s] [-d DEPS] [ARGS] -d --deps DEPS Logical or char, see '?install.packages', use 'TRUE' for all, [default: NA] -s --suggests Add 'Suggests' to dependencies, shortcut for '--deps TRUE' -h --help show this help text -x --usage show help and short example usage " opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat(" Basic usage: installDeps.r . installDeps.r somePackage_1.2.3.tar.gz The argument to '--deps' can be a combinations of 'Depends', 'Imports', 'LinkingTo', 'Suggests', and 'Enhances'. Default of 'NA' means first three, 'TRUE' means the first four. installDeps.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (length(opt$ARGS)==0 && file.exists("DESCRIPTION") && file.exists("NAMESPACE")) { ## we are in a source directory, so build it message("* installing deps for *source* package found in current working directory ...") opt$ARGS <- "." } if (opt$deps == "TRUE") opt$deps <- TRUE if (opt$deps == "NA") opt$deps <- NA if (opt$suggests) opt$deps <- TRUE ## ensure installation is stripped Sys.setenv("_R_SHLIB_STRIP_"="true") invisible(sapply(opt$ARGS, function(r) install_deps(r, dependencies=opt$deps))) littler/inst/examples/ciw.r0000755000176200001440000000527414575567031015521 0ustar liggesusers#!/usr/bin/env r # # ciw wrapper # # Copyright (C) 2024 Dirk Eddelbuettel # # Released under GPL (>= 2) if (!requireNamespace("ciw", quietly=TRUE)) stop("Please install 'eddelbuettel/ciw' from GitHub.", call. = FALSE) ## load docopt and cranincoming suppressMessages({ library(ciw) # at GitHub under eddelbuettel for now library(docopt) # we need docopt (>= 0.3) as on CRAN }) ## configuration for docopt doc <- "Usage: ciw.r [-h] [-x] [-a] [-m] [-i] [-t] [-p] [-w] [-r] [-s] [-n] [-u] [-l rows] [-z] [ARG...] -m --mega use 'mega' mode of all folders (see --usage) -i --inspect visit 'inspect' folder -t --pretest visit 'pretest' folder -p --pending visit 'pending' folder -w --waiting visit 'waiting' folder -r --recheck visit 'recheck' folder -a --archive visit 'archive' folder -n --newbies visit 'newbies' folder -u --publish visit 'publish' folder -s --skipsort skip sorting of aggregate results by age -l --lines rows print top 'rows' of the result object [default: 50] -z --ping run the connectivity check first -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("where ARG... can be one or more file name, or directories or package names. Examples: ciw.r -ip # run in 'inspect' and 'pending' mode ciw.r -a # run with mode 'auto' resolved in incoming() ciw.r # run with defaults, same as '-itpwr' When no argument is given, 'auto' is selected which corresponds to 'inspect', 'waiting', 'pending', 'pretest', and 'recheck'. Selecting '-m' or '--mega' are select as default. Folder selecting arguments are cumulative; but 'mega' is a single selections of all folders (i.e. 'inspect', 'waiting', 'pending', 'pretest', 'recheck', 'archive', 'newbies', 'publish'). ciw.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } args <- character() # start with no arguments folders <- c("inspect", "waiting", "pending", "pretest", "recheck", "archive", "newbies", "publish") for (dir in folders) # grow folder set as a select if (opt[[dir]]) args <- c(args, dir) if (opt$mega) args <- folders # or respect the nuclear option if (length(args) == 0) args <- "auto" chk <- length(args) <= 1 # ask for argument check only on short argument vectoe res <- incoming(args, chk, isFALSE(opt$skipsort), isTRUE(opt$ping)) nr <- as.integer(opt$lines) print(head(res, nr), nrows=nr) littler/inst/examples/mph.r0000755000176200001440000000205312613230464015477 0ustar liggesusers#!/usr/bin/env r # # Convert miles-per-hour, time-distance measure settable # on treadmiles, to different race times. # # Copyright (C) 2006 - 2014 Dirk Eddelbuettel # # Released under GPL (>= 2) if (is.null(argv) | length(argv)<1) { cat("Usage: mph.r mph\n") q() } dig <- 5 mph <- as.numeric(argv[1]) cat("Mph : ",format(mph,digits=dig),"\n"); hourminsec <- function(totalsecs){ ret <- list(hour=0,min=0,sec=0) ret$hour <- floor(totalsecs / 3600) totalsecs <- totalsecs - (ret$hour * 3600) ret$min <- floor(totalsecs / 60) ret$sec <- totalsecs - (ret$min * 60) ret } minutes <- floor(60/mph) pminute <- 60/mph - minutes secs <- floor(60 * (pminute)) secspermile <- 60*minutes + secs outrace <- function(title,miles){ race <- hourminsec(miles*secspermile) cat(sprintf("%-8s: %2.f hours %2.f min %2.f sec\n",title, race$hour,race$min, race$sec)) } kilodiv <- 1.609344 # kilometer divisor outrace('1 mile',1) outrace('3 miles',3) outrace('5k',5/kilodiv) outrace('10k',10/kilodiv) outrace('Marathon',42.195/kilodiv) outrace('Ultra',100) littler/inst/examples/pnrrs.r0000755000176200001440000000025513245105321016054 0ustar liggesusers#!/usr/bin/env r if (getRversion() < "3.4.0") stop("Not available for R (< 3.4.0). Please upgrade.", call.=FALSE) tools::package_native_routine_registration_skeleton(".") littler/inst/examples/installPPM.r0000755000176200001440000000533014536123346016745 0ustar liggesusers#!/usr/bin/env r # # A simple example to install from RSPM/PPM/P3M # # Copyright (C) 2020 - present Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN }) if (Sys.info()[["sysname"]] != "Linux") stop(paste("Currently only supported on Linux.", "Please get in touch if you want to / can help on macOS"), call.=FALSE) code <- "" if (file.exists("/etc/os-release")) { # next block borrowed from my chshli package on GitHub osrel <- read.table("/etc/os-release", sep="=", row.names=1, col.names=c("key","value")) if ("REDHAT_SUPPORT_PRODUCT" %in% rownames(osrel)) { # 'centos7' for CentOS/RHEL 7, 'centos8' for CentOS/RHEL 8 and Fedora ver <- osrel["REDHAT_SUPPORT_PRODUCT_VERSION", "value"] code <- paste0("centos", min(as.numeric(ver), 8)) } else if ("VERSION_CODENAME" %in% rownames(osrel)) { code <- osrel["VERSION_CODENAME", "value"] } } if ((code == "") && (Sys.which("lsb_release") != "")) { code <- system("lsb_release -c | awk '{print $2}'", intern=TRUE) } ## configuration for docopt doc <- paste0("Usage: install(RSPM|PPM|P3M).r [-c code] [-l libloc] [-h] [-x] ARGS... -c --code ARG set code name for distribution [default: ", code, "] -l --libloc ARG location in which to install [default: ", .libPaths()[1], "] -h --help show this help text -x --usage show help and short example usage Note that RSPM/PPM/P3M support may be somewhat experimental. There may not be binaries for every possibly OS, distibution, and R version. Please file issue tickets at the Github repo for littler if you can contribute additional checks and values. As RSPM has been renamed to PPM and then P3M, we now install the script thrice via hardlinks. ") opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n") cat("Basic usage: installRSPM.r digest # install digest for default release '", code, "' installPPM.r -c jammy digest # install digest for Ubuntu 'jammy' installP3M.r -c bookworn digest # install digest for Debian 'bookworm' install(RSPM|PPM|P3M).r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n", sep="") q("no") } if (!is.null(opt$libloc)) .libPaths(opt$libloc) r <- getOption("repos") r["CRAN"] <- paste0("https://p3m.dev/all/__linux__/", opt$code, "/latest") options(repos = r) options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os))) invisible(sapply(opt$ARGS, function(r) install.packages(r))) littler/inst/examples/mdweave2html.r0000755000176200001440000000057214152154325017317 0ustar liggesusers#!/usr/bin/env r # # Simple helper script for simplermarkdown, reusing the older one for knitr # # Dirk Eddelbuettel, May 2013, Dec 2021 # # GPL-2 or later if (is.null(argv)) { cat("Need an argument FILE.md\n") q(status=-1) } file <- argv[1] if (!file.exists(file)) { cat("File not found: ", file, "\n") q(status=-1) } simplermarkdown::mdweave_to_html(file) littler/inst/examples/installGithub.r0000755000176200001440000000472114521176660017537 0ustar liggesusers#!/usr/bin/env r # # A simple example to install one or more packages from GitHub # # Copyright (C) 2014 - 2023 Carl Boettiger and Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt and remotes (or devtools) from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN library(remotes) # or can use devtools as a fallback }) ## configuration for docopt doc <- "Usage: installGithub.r [-h] [-x] [-d DEPS] [-u UPDATE] [-r REPOS...] [-t TYPE] [GHREPOS...] -d --deps DEPS install suggested dependencies as well? [default: NA] -u --update UPDATE update dependencies? [default: TRUE] -r --repos REPOS repositor(y|ies) to use if deps required [default: getOption] -t --type TYPE installation type as used by `install.packages` [default: source] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("where GHREPOS... is one or more GitHub repositories. Basic usage: installGithub.r RcppCore/RcppEigen Install multiple R packages from GitHub: installGithub.r RcppCore/Rcpp RcppCore/RcppEigen Install multiple R packages from GitHub listing the packages on separate lines with some comments: installGithub.r \\ RcppCore/Rcpp \\ RcppCore/RcppEigen Installing a specific branch, tag or commit: installGithub.r RcppCore/Rcpp@1.0.0 Installing from a repo subdirectory: installGithub.r chanzuckerberg/cellxgene-census/api/r/cellxgene.census Setting multiple R package repositories to install dependencies of the R package: installGithub.r -r https://cloud.r-project.org -r https://eddelbuettel.github.io/drat RcppCore/RcppEigen installGithub.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } ## ensure installation is stripped Sys.setenv("_R_SHLIB_STRIP_"="true") if (opt$deps == "TRUE" || opt$deps == "FALSE") { opt$deps <- as.logical(opt$deps) } else if (opt$deps == "NA") { opt$deps <- NA } if (length(opt$repos) == 1 && opt$repos == "getOption") { ## as littler can now read ~/.littler.r and/or /etc/littler.r we can preset elsewhere opt$repos <- getOption("repos") } opt$update <- as.logical(opt$update) invisible(sapply(opt$GHREPOS, function(r) install_github(r, dependencies = opt$deps, upgrade = opt$update, repos = opt$repos, type = opt$type))) littler/inst/examples/tttf.r0000755000176200001440000000310114571654243015701 0ustar liggesusers#!/usr/bin/env -S r -t # # testthat::test_file wrapper # # Copyright (C) 2019 - 2024 Dirk Eddelbuettel # # Released under GPL (>= 2) if (!requireNamespace("testthat", quietly=TRUE)) stop("Please install 'testthat' from CRAN.", call. = FALSE) ## load docopt and tinytest from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN }) ## configuration for docopt doc <- "Usage: tttf.r [-l LIB] [-s FILE] [-c] [-d] [-h] [-x] ARG -l --library LIB load named library, LIB can be comma-separated -s --source FILE source a named file -d --loadall run `devtools::load_all()` -c --ci set environment variable CI to TRUE [default: FALSE] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("where ARG can be a package directory. Examples: tttf.r test-testfile.r # run test_file() on the given file tttf.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (!is.null(opt$library)) { for (s in strsplit(opt$library, ",")[[1]]) { library(s, character.only=TRUE, verbose=TRUE) } } if (!file.exists(opt$ARG)) { stop("No such file.", call. = FALSE) } if (!is.null(opt$source) && file.exists(opt$source)) { source(opt$source) } if (opt$ci) { Sys.setenv(CI="TRUE") } if (opt$loadall) { suppressMessages(devtools::load_all()) } testthat::test_file(path=opt$ARG) littler/inst/examples/installRepo.r0000755000176200001440000000443713600257721017221 0ustar liggesusers#!/usr/bin/env r # # A simple example to install one or more packages from GitHub # # Copyright (C) 2014 - 2017 Carl Boettiger, Dirk Eddelbuettel and Alexios Galanos # # Released under GPL (>= 2) ## load docopt and remotes (or devtools) from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN library(remotes) # can use devtools as a fallback }) ## configuration for docopt doc <- "Usage: installRepo.r [-l LIBLOC] [-h] [-x] [-d DEPS] [-r REPOS] [-s subdir] [SRC] -l --libloc LIBLOC location in which to install [default: /usr/local/lib/R/site-library] -d --deps DEPS Install suggested dependencies as well? [default: NA] -r --repos REPOS The repository, eg github, bitbucket, svn, or url [default: github] -s --subdir SUBDIR For svn or url, an optional sub-directory within the repo -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("where SRC is either a git-style repo (author/repo) or a URL for svn. Examples: installRepo.r RcppCore/RcppEigen # standard GitHub installRepo..r -r bitbucket alexiosg/rugarch # using BitBucket instead installRepo.r -r svn https://github.com/hadley/stringr # from Subversion or a URL installRepo.r -r url https://cran.rstudio.com/src/contrib/Archive/digest/digest_0.5.0.tar.gz installRepo.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (opt$deps == "TRUE" || opt$deps == "FALSE") { opt$deps <- as.logical(opt$deps) } else if (opt$deps == "NA") { opt$deps <- NA } if (is.null(opt$SRC)) q("no") # need optional args to support -x ## ensure installation is stripped Sys.setenv("_R_SHLIB_STRIP_"="true") ## installation given selected options and arguments switch(tolower(opt$repos), github = install_github(opt$SRC, lib=opt$libloc, dependencies=opt$deps), bitbucket = install_bitbucket(opt$SRC, lib=opt$libloc, dependencies=opt$deps), svn = install_svn(opt$SRC, subdir=opt$subdir, lib=opt$libloc, dependencies=opt$deps), url = install_url(opt$SRC, subdir=opt$subdir, lib=opt$libloc, dependencies=opt$deps)) littler/inst/examples/pace.r0000755000176200001440000000201612613230464015622 0ustar liggesusers#!/usr/bin/env r # # a simple example to convert miles and times into a pace # where the convention is that we write e.g. 37 min 15 secs # as 37.15 -- so a call 'pace.r 4.5 37.15' yields a pace of # 8.1667, ie 8 mins 16.67 secs per mile # # Copyright (C) 2006 - 2014 Dirk Eddelbuettel # # Released under GPL (>= 2) if (is.null(argv) | length(argv)!=2) { cat("Usage: pace.r miles time\n") q() } dig <- 5 rundist <- as.numeric(argv[1]) runtime <- as.numeric(argv[2]) cat("Miles : ", format(rundist, digits=dig), "\n") cat("Time : ", format(runtime, digits=dig), "\n") totalseconds <- floor(runtime)*60 + (runtime-floor(runtime))*100 totalsecondspermile <- totalseconds / rundist minutespermile <- floor(totalsecondspermile/60) secondspermile <- totalsecondspermile - minutespermile*60 pace <- minutespermile + secondspermile/100 cat("Pace : ", format(minutespermile, digits=1), "min", format(secondspermile, digits=dig), "sec\n") cat("Mph : ", format( (rundist * 3600)/totalseconds, digits=dig),"\n") littler/inst/examples/fileOps.r0000755000176200001440000000141112613230464016311 0ustar liggesusers#!/usr/bin/env r # # A simple example to do operations on files # # Copyright (C) 2014 Dirk Eddelbuettel # # Released under GPL (>= 2) ## read files files <- dir("..", full.names=TRUE) ## creation time as Date ctimes <- as.Date(file.info(files)$ctime) ## select based on time window -- something arbitrary now <- Sys.Date() ## these are appromiximative, could be refined using DateTimeClasses sixmon <- now - 365.25/2 twelvemon <- now - 365.2 ind <- ctimes >= twelvemon & ctimes <= sixmon if (sum(ind) > 0) { cat("The following files are between six and twelve months old\n") print(files[ind]) } ## do something ## print(files[ind]) ## or rename / move to subdir ## mkdir("newDir") ## file.rename(files[ind], "newDir") ## can also use gsub() etc to rename littler/inst/examples/compiledDeps.r0000755000176200001440000000231114001103143017302 0ustar liggesusers#!/usr/bin/r ## ## Show all dependencies of a package containing native ("compiled") code ## ## Copyright (C) 2021 - present Dirk Eddelbuettel ## ## Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) if (!requireNamespace("data.table", quietly=TRUE)) stop("The 'data.table' package is required. Please install it.", call.=FALSE) doc <- "Usage: urlUpdate.r [-c] [-n] [-h] PACKAGE -c --compact compact, print only package vector -n --nonrecursive non-recursive dependencies [default: FALSE] -h --help show this help text Simple wrapper around 'tools::CRAN_package_db()' and 'tools::package_depdencies()'. " opt <- docopt(doc) suppressMessages(library(data.table)) pkg <- opt$PACKAGE rec <- !opt$nonrecursive db <- setDT(tools::CRAN_package_db(), key="Package") revs <- data.table(Package=tools::package_dependencies(pkg, recursive=rec, db=db)[[1]], key="Package") res <- db[revs, .(Package,Version,Priority,NeedsCompilation)][ is.na(Priority)==TRUE & is.na(Version)==FALSE & NeedsCompilation=="yes"][ ,.(Package,Version)] if (opt$compact) { cat(paste(res[[1]], collapse=" "), "\n") } else { options("datatable.print.nrows"=nrow(res)) print(res) } littler/inst/examples/doi2bib.r0000755000176200001440000000203414574570636016244 0ustar liggesusers#!/usr/bin/env r ## ## Convert a DOI to it bibtext field ## ## Copyright (C) 2024 Dirk Eddelbuettel ## ## Released under GPL (>= 2) ## ## With thanks to https://bsky.app/profile/rmcelreath.bsky.social/post/3knkqvogwbc25 ## load docopt package from CRAN library(docopt) if (!requireNamespace("httr", quietly=TRUE)) stop("Please install 'httr' from CRAN.", call. = FALSE) library(httr) ## configuration for docopt doc <- "Usage: doi2bib.r [-h] [-x] DOI... -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("Examples: doi2bib.r 10.1002/evan.10110 10.1007/978-1-4614-6868-4 doi2bib.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } for (arg in opt$DOI) { res <- GET(paste0("https://doi.org/", arg), add_headers(Accept="application/x-bibtex")) cat(rawToChar(res$content)) } littler/inst/examples/tttl.r0000755000176200001440000000274514565140630015715 0ustar liggesusers#!/usr/bin/env -S r -t # # testthat::test_local wrapper # # Copyright (C) 2019 - 2024 Dirk Eddelbuettel # # Released under GPL (>= 2) if (!requireNamespace("testthat", quietly=TRUE)) stop("Please install 'testthat' from CRAN.", call. = FALSE) ## load docopt and tinytest from CRAN suppressMessages({ library(docopt) # we need docopt (>= 0.3) as on CRAN }) ## configuration for docopt doc <- "Usage: tttl.r [-h] [-x] [-c] [ARG] -c --ci set environment variable CI to TRUE [default: FALSE] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("where ARG can be a package directory. Examples: tttl.r # run test_local() if DESCRIPTION && tests/testthat/ tttl.r # run test_local() if in tests/testthat directory tttl.r is part of littler which brings 'r' to the command-line. See https://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } if (!is.null(opt$ARG) && dir.exists(opt$arg)) { setwd(opt$ARG) } if (opt$ci) { Sys.setenv(CI="TRUE") } if (file.exists(file.path(getwd(), "..", "..", "DESCRIPTION"))) { setwd(file.path(getwd(), "..", "..")) } if (file.exists(file.path(getwd(), "..", "DESCRIPTION"))) { setwd("..") } if (file.exists("DESCRIPTION") && dir.exists("tests/testthat")) { testthat::test_local("tests/testthat") } littler/inst/examples/build.r0000755000176200001440000000142614135774702016026 0ustar liggesusers#!/usr/bin/env r ## ## A simple example to builds a source tar.gz file ## ## Copyright (C) 2017 - 2021 Dirk Eddelbuettel ## ## Released under GPL (>= 2) ## load docopt package from CRAN library(docopt) doc <- "Usage: build.r [-f] [-h] [PACKAGES ...] -f --fast skip building vignettes and manual -h --help show this help text Simple wrapper to 'R CMD build ...' which calls 'tools:::.build_packages()' just like the 'R CMD build' invocation. " opt <- docopt(doc) if (length(opt$PACKAGES) == 0) opt$PACKAGES <- "." # default argument current directory argv <- if (opt$fast) c("--no-build-vignettes", "--no-manual", opt$PACKAGES) else opt$PACKAGES extraargs <- c("--compact-vignettes=both", "--resave-data", argv) tools:::.build_packages(extraargs, no.q=interactive()) littler/inst/doc/0000755000176200001440000000000014577617425013475 5ustar liggesuserslittler/inst/doc/littler-examples.md0000644000176200001440000003054014136370627017303 0ustar liggesusers --- title: "Littler Examples" author: "Dirk Eddelbuettel" date: "Originally written 2015-10-28; Updated 2017-12-10, 2018-05-24, 2019-01-06, 2019-06-09 and 2020-06-16" css: "water.css" --- ## Overview We show and discuss a few of the files included in the `inst/examples/` source directory of [littler](http://dirk.eddelbuettel.com/code/littler.html) (which becomes the `examples/` directory once installed). In a few cases we remove comment lines to keep things more concise on this page. We use `$` to denote a shell (_i.e._ terminal) prompt. Note that some systems (such as macOS) cannot install littler as `r` (as lower-case and upper-case are by default the same; not a great idea). And for example the `zsh` has `r` as a builtin so you would have to use `/usr/bin/r`. See the [littler FAQ](littler-faq.html) for more. ## Simple Direct Command-line Use [littler](http://dirk.eddelbuettel.com/code/littler.html) can be used directly on the command-line just like, say, `bc`, easily consuming standard input from a pipe: ```bash $ echo 'cat(pi^2,"\n")' | r 9.869604 ``` Equivalently, commands that are to be evaluated can be given on the command-line ```bash $ r -e 'cat(pi^2, "\n")' 9.869604 ``` But unlike bc(1), GNU R has a vast number of statistical functions. For example, we can quickly compute a `summary()` and show a stem-and-leaf plot for file sizes in a given directory via ```bash $ ls -l /boot | awk 'BEGIN {print "size"} !/^total/ {print $5}' | \ r -de "print(summary(X[,1])); stem(X[,1])" ``` which produces something like ``` Min. 1st Qu. Median Mean 3rd Qu. Max. 13 512 110100 486900 768400 4735000 The decimal point is 6 digit(s) to the right of the | 0 | 0000001122222279222 2 | 79444 4 | 71888 6 | 8 | 10 | 12 | 14 | 8 16 | 4 18 | 20 | 333 ``` (Note that some systems may not have `/boot` in which case you can try `/sbin` or another directory.) As we saw in the preceding example, the program can also be shortened like using the new `-d` option which reads from stdin and assigns to a `data.frame` named `X`. And, last but not least, this (somewhat unwieldy) expression can be stored in a helper script (where we now switch to using an explicit `readLines()` on `stdin`): ```r #!/usr/bin/env r fsizes <- as.integer(readLines(file("stdin"))) print(summary(fsizes)) stem(fsizes) ``` (where calling `#!/usr/bin/env` is a trick from Python which allows one to forget whether r is installed in `/usr/bin/r`, `/usr/local/bin/r`, `~/bin/r`, ...). ## install.r: Direct CRAN Installation This is one of my favourite [littler](http://dirk.eddelbuettel.com/code/littler.html) scripts which I use frequently to install packages off [CRAN](https://cran.r-project.org). ```r #!/usr/bin/env r if (is.null(argv) | length(argv)<1) { cat("Usage: installr.r pkg1 [pkg2 pkg3 ...]\n") q() } ## adjust as necessary, see help('download.packages') repos <- "https://cran.rstudio.com" ## this makes sense on Debian where no packages touch /usr/local lib.loc <- "/usr/local/lib/R/site-library" install.packages(argv, lib.loc, repos) ``` I invoke it all the time with one, two or more packages to install (or reinstall). ```bash $ install.r digest RcppCNPy ``` It conveniently installs all dependencies, and uses the chosen target directory, all while keeping my R prompt (or prompts with multiple sessions) free to do other things. Also, if used with `options("Ncpu")` set, then (remote CRAN) packages will be installed in parallel. ## install2.r: With Cmdline Parsing Thanks to the fabulous [docopt](https://github.com/edwindj/docopt.R) package, we also have a variant `install2.r` with optional settings of repo and location. It was first installed with [littler 0.2.1](http://dirk.eddelbuettel.com/blog/2014/10/19/). The current (_i.e._, 0.3.3 as of this writing) version is more featureful and longer and included to keep this brief. Some usage examples are ```sh $ install2.r -l /tmp/lib Rcpp BH # install into given library $ install2.r -- --with-keep.source drat # keep the source $ install2.r -- --data-compress=bzip2 stringdist # prefer bz2 compression ``` Another _very_ useful option is `-n N` or `--ncpus N` which will parallelize the installation across `N` processes. This can be set automagically by setting `options("Ncpus")`. ### Installing From Sources Starting with version 0.2.2, `install.r` and `install2.r` now recognise installable source files. So one can also do this: ```bash $ install.r digest_0.6.8.tar.gz ``` and the local source file will the installed via a call to `R CMD INSTALL`. ## check.r: Simple Checker A related use case is to check packages via `check.r`. This script runs `R CMD check`, but also installs package dependencies first as tests may have dependencies not yet satisfied on the test machine. It offers a number of options: ```bash $ check.r -h Usage: check.r [-h] [-x] [--as-cran] [--repo REPO] [--install-deps] [--install-kitchen] [--deb-pkgs PKGS...] [--use-sudo] [--library LIB] [--setwd DIR] [TARGZ ...] -a --as-cran customization similar to CRAN's incoming [default: FALSE] -r --repo REPO repository to use, or NULL for file [default: https://cran.rstudio.com] -i --install-deps also install packages along with their dependencies [default: FALSE] -k --install-kitchen even install packages 'kitchen sink'-style up to suggests [default: FALSE] -l --library LIB when installing use this library [default: /usr/local/lib/R/site-library] -s --setwd DIR change to this directoru before undertaking the test [default: ] -d --deb-pkgs PKGS also install binary .deb packages with their dependencies [default: FALSE] -u --use-sudo use sudo when installing .deb packages [default: TRUE] -h --help show this help text -x --usage show help and short example usage $ ``` ## rcc.r: R CMD check wrapper The script `rcc.r` will also check a source tarball, and offers another set of options: ```bash $ rcc.r -h Usage: rcc.r [-h] [-x] [-c] [-f] [-q] [--args ARGS] [--libpath LIBP] [--repos REPO] [PATH...] -c --as-cran should '--as-cran' be added to ARGS [default: FALSE] -a --args ARGS additional arguments to be passed to 'R CMD CHECK' [default: ] -l --libpath LIBP additional library path to be used by 'R CMD CHECK' [default: ] -r --repos REPO additional repositories to be used by 'R CMD CHECK' [default: ] -f --fast should vignettes and manuals be skipped [default: FALSE] -q --quiet should 'rcmdcheck' be called qietly [default: FALSE] -h --help show this help text -x --usage show help and short example usage $ ``` ## build.r: Building Packages A related script is `build.r` which I often use inside a source repository to quickly build a source tarball. Like `rcc.r`, it has a switch `-f` or `--fast` to omit building of vignettes. ```bash $ build.r # without argument works on current directory $ build.r digest/ # with directory argument builds tar.gz from repo in directory ``` ## installGithub.r: GitHub install Installation directly from [GitHub](https://github.com) is also popular. Here is an example: ```bash $ installGithub.r RcppCore/RcppEigen ``` Installing from github is supported via the following helper script: ```r #!/usr/bin/env r # # A simple example to install one or more packages from GitHub # # Copyright (C) 2014 - 2015 Carl Boettiger and Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt and remotes (or devtools) from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN suppressMessages(library(remotes)) # can use devtools as a fallback ## configuration for docopt doc <- "Usage: installGithub.r [-h] [-d DEPS] REPOS... -d --deps DEPS Install suggested dependencies as well? [default: NA] -h --help show this help text where REPOS... is one or more GitHub repositories. Examples: installGithub.r RcppCore/RcppEigen installGithub.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information. " ## docopt parsing opt <- docopt(doc) if (opt$deps == "TRUE" || opt$deps == "FALSE") { opt$deps <- as.logical(opt$deps) } else if (opt$deps == "NA") { opt$deps <- NA } invisible(sapply(opt$REPOS, function(r) install_github(r, dependencies = opt$deps))) ``` ## update.r: CRAN package update One of the scripts I use the most (interactively) is `update.r` which updates installed packages. An earlier version looked like the following example, the current version is a little longer and has more features: ```r #!/usr/bin/env r # # a simple example to update packages in /usr/local/lib/R/site-library # parameters are easily adjustable ## adjust as necessary, see help('download.packages') repos <- "https://cloud.r-project.org" ## this makes sense on Debian where no package touch /usr/local lib.loc <- "/usr/local/lib/R/site-library" ## r use requires non-interactive use update.packages(repos=repos, ask=FALSE, lib.loc=lib.loc) ``` As above, it has my preferred mirror and library location hard-wired. Another _very_ useful option is `-n N` or `--ncpus N` which will parallelize the upgrade across `N` processes. This can be set automagically by setting `options(Ncpus)`. ## knit.r: Calling knitr Here is another convenience script, `knit.r`, which _knits_ a given file after testing the file actually exists. ```r #!/usr/bin/r # # Simple helper script for knitr # # Dirk Eddelbuettel, May 2013 # # GPL-2 or later if (is.null(argv)) { cat("Need an argument FILE.Rnw\n") q(status=-1) } file <- argv[1] if (!file.exists(file)) { cat("File not found: ", file, "\n") q(status=-1) } require(knitr) knit2pdf(file) ``` ## roxy.r: Running roxygen Similar to the previous example, the script `roxy.r` one uses roxygen to extract documentation from R files -- either in the current directory, or in the given directory or directories. ```r #!/usr/bin/r # # Simple helper script for roxygen2::roxygenize() # # Dirk Eddelbuettel, August 2013 # # GPL-2 or later ## load roxygen library(roxygen2) ## check all command-line arguments (if any are given) for directory status argv <- Filter(function(x) file.info(x)$is.dir, argv) ## loop over all argument, with fallback of the current directory, and ## call compileAttributes() on the given directory sapply(ifelse(length(argv) > 0, argv, "."), FUN=roxygenize, roclets="rd") ``` ## compAttr.r: Compiling Attributes The next script, `compAttr.`, can be used with [Rcpp](http://dirk.eddelbuettel.com/code/rcpp.html), and particularly is powerful _Attributes_ feature, in order to auto-generate helper code. It is similar to the preceding script, but invokes `compileAttributes()` instead. ```r #!/usr/bin/r # # Simple helper script for compileAttributes() # # Dirk Eddelbuettel, July 2014 # # GPL-2 or later ## load Rcpp suppressMessages(library(Rcpp)) ## check all command-line arguments (if any are given) for directory status argv <- Filter(function(x) file.info(x)$is.dir, argv) ## loop over all argument, with fallback of the current directory, and ## call compileAttributes() on the given directory sapply(ifelse(length(argv) > 0, argv, "."), compileAttributes) ``` ## render.r: Render Markdown The `render.r` script generalizes the earlier `knit.r` to convert Markdown into its designated output. ```r #!/usr/bin/env r # # Another example to run a shiny app # # Copyright (C) 2016 Dirk Eddelbuettel # # Released under GPL (>= 2) suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN ## configuration for docopt doc <- "Usage: render.r [-h] [-x] [FILES...] -h --help show this help text -x --usage show help and short example usage" opt <- docopt(doc) # docopt parsing if (opt$usage) { cat(doc, "\n\n") cat("Examples: render.r foo.Rmd bar.Rmd # convert two given files render.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information.\n") q("no") } library(rmarkdown) ## helper function renderArg <- function(p) { if (!file.exists(p)) stop("No file '", p, "' found. Aborting.", call.=FALSE) render(p) } ## render files using helper function sapply(opt$FILES, renderArg) ``` littler/inst/doc/littler-faq.md0000644000176200001440000000714014136370627016234 0ustar liggesusers --- title: "Littler FAQ" author: "Dirk Eddelbuettel" date: "2019-03-23, updated 2020-06-16" css: "water.css" --- ### Well, why? Glad you asked. When the initial work started, `Rscript` did not exist so there was no scripting tool. We take a small amount of pride into beating `Rscript` narrowly to a first release. Of course, by now, `Rscript` is more widely used as it ships with every R installation but we still have some aspects we like about `r`: it is simpler and shorter, deals (in our biased) view more sanely with command-line arguments via the `argv` vector, always loaded package `methods` (which `Rscript` finally came around to a good decade later) and [still starts faster](http://dirk.eddelbuettel.com/blog/2014/09/02/#littler-faster-at-doing-nothing). And `r` is just to cool a command (in relation to the trusted `R`) so someone had to! ### No Printing In the very beginning of `littler`, we made an executive decision to _not_ echo each command output when we evaluate commands in the read-evaluate-print loop. So `2+2` will be evaluated silently: four will be computed, but not shown. That made sense for scripts we wanted to be silent. The idea is that user will add a `print()` or `cat()` as needed. If you desire each step to printed, add a `-p` or `--verbose` argument. ### No `.Renviron` Another early decision was to make `r` start _faster_ than the alternatives. Our `r` is "just" a small little binary. Whereas `R` and `Rscript` are front-end shell scripts sourcing a number of things and setting them dynamically, we determine values _at compilation time_ and freeze them into the binary. That may seem _risqué_ but worked out just fine. However, while we later added the ability to source `Rprofile` files (which contain R code we can evaluate) there is no way for us to source the `Renviron` files _and to modify the already running process_. So if you want to source `Renviron` you could add an explicit `readEnviron()` to `~/.littler.r` or `/etc/littler/r`. ### Lower-case / upper-case This is mostly an issue on macOS where the brain surgeons behind the OS decided that `r` is the same as `R`. What can we say? On that OS you may need to rename the build to `lr` instead. Please send your complaints to Cupertino, California. ### Adding the binary to your path When the package is installed from source, it displays ``` * * new binary $(TGT) installed in bin/ subdirectory" * consider adding a symbolic link from, e.g., /usr/local/bin" * on OS X, you may have to name this 'lr' instead" * see the littler-faq vignette for more details" * ``` where the variable `$(TGT)` normally expands to `r`. As the text suggests you may want to create a [symbolic link](https://en.wikipedia.org/wiki/Symbolic_link) from a directory in the to make the newly built binary available to users. On Linux you may do ``` cd /usr/local/bin sudo ln -s /usr/local/lib/R/site-library/littler/bin/r . ``` to create a link for `r` in `/usr/local/bin`. On macOS, as suggested, you may want ``` cd /usr/local/bin sudo ln -s /usr/local/lib/R/site-library/littler/bin/r lr ``` to create a command `lr` instead; see the previous question as to why. In either case adjust the source part of the `ln` command to where your binary is -- which R can tell you via `system.file("bin", "r", package="littler")`. Also note that _e.g._ the [zsh](https://zsh.sourceforge.io/) has a builtin command `r` which may conflict, so using the explicit path of, say, `/usr/bin/r` or `/usr/local/bin/r` or ... may provide an alternative. littler/inst/doc/littler-examples.html0000644000176200001440000013007214577617425017661 0ustar liggesusers Littler Examples

Littler Examples

Dirk Eddelbuettel

Originally written 2015-10-28; Updated 2017-12-10, 2018-05-24, 2019-01-06, 2019-06-09 and 2020-06-16

Overview

We show and discuss a few of the files included in the inst/examples/ source directory of littler (which becomes the examples/ directory once installed). In a few cases we remove comment lines to keep things more concise on this page. We use $ to denote a shell (i.e. terminal) prompt.

Note that some systems (such as macOS) cannot install littler as r (as lower-case and upper-case are by default the same; not a great idea). And for example the zsh has r as a builtin so you would have to use /usr/bin/r. See the littler FAQ for more.

Simple Direct Command-line Use

littler can be used directly on the command-line just like, say, bc, easily consuming standard input from a pipe:

$ echo 'cat(pi^2,"\n")' | r
9.869604

Equivalently, commands that are to be evaluated can be given on the command-line

$ r -e 'cat(pi^2, "\n")'
9.869604

But unlike bc(1), GNU R has a vast number of statistical functions. For example, we can quickly compute a summary() and show a stem-and-leaf plot for file sizes in a given directory via

$ ls -l /boot | awk 'BEGIN {print "size"} !/^total/ {print $5}' | \
     r -de "print(summary(X[,1])); stem(X[,1])"

which produces something like

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
     13     512  110100  486900  768400 4735000

  The decimal point is 6 digit(s) to the right of the |

   0 | 0000001122222279222
   2 | 79444
   4 | 71888
   6 | 
   8 | 
  10 | 
  12 | 
  14 | 8
  16 | 4
  18 | 
  20 | 333

(Note that some systems may not have /boot in which case you can try /sbin or another directory.)

As we saw in the preceding example, the program can also be shortened like using the new -d option which reads from stdin and assigns to a data.frame named X.

And, last but not least, this (somewhat unwieldy) expression can be stored in a helper script (where we now switch to using an explicit readLines() on stdin):

#!/usr/bin/env r

fsizes <- as.integer(readLines(file("stdin")))
print(summary(fsizes))
stem(fsizes)

(where calling #!/usr/bin/env is a trick from Python which allows one to forget whether r is installed in /usr/bin/r, /usr/local/bin/r, ~/bin/r, …).

install.r: Direct CRAN Installation

This is one of my favourite littler scripts which I use frequently to install packages off CRAN.

#!/usr/bin/env r

if (is.null(argv) | length(argv)<1) {
  cat("Usage: installr.r pkg1 [pkg2 pkg3 ...]\n")
  q()
}

## adjust as necessary, see help('download.packages')
repos <- "https://cran.rstudio.com" 

## this makes sense on Debian where no packages touch /usr/local
lib.loc <- "/usr/local/lib/R/site-library"

install.packages(argv, lib.loc, repos)

I invoke it all the time with one, two or more packages to install (or reinstall).

$ install.r digest RcppCNPy

It conveniently installs all dependencies, and uses the chosen target directory, all while keeping my R prompt (or prompts with multiple sessions) free to do other things. Also, if used with options("Ncpu") set, then (remote CRAN) packages will be installed in parallel.

install2.r: With Cmdline Parsing

Thanks to the fabulous docopt package, we also have a variant install2.r with optional settings of repo and location. It was first installed with littler 0.2.1. The current (i.e., 0.3.3 as of this writing) version is more featureful and longer and included to keep this brief. Some usage examples are

$ install2.r -l /tmp/lib Rcpp BH                         # install into given library
$ install2.r -- --with-keep.source drat                  # keep the source
$ install2.r -- --data-compress=bzip2 stringdist         # prefer bz2 compression

Another very useful option is -n N or --ncpus N which will parallelize the installation across N processes. This can be set automagically by setting options("Ncpus").

Installing From Sources

Starting with version 0.2.2, install.r and install2.r now recognise installable source files. So one can also do this:

$ install.r digest_0.6.8.tar.gz

and the local source file will the installed via a call to R CMD INSTALL.

check.r: Simple Checker

A related use case is to check packages via check.r. This script runs R CMD check, but also installs package dependencies first as tests may have dependencies not yet satisfied on the test machine. It offers a number of options:

$ check.r  -h
Usage: check.r [-h] [-x] [--as-cran] [--repo REPO] [--install-deps] [--install-kitchen] [--deb-pkgs PKGS...] [--use-sudo] [--library LIB] [--setwd DIR] [TARGZ ...]

-a --as-cran          customization similar to CRAN's incoming [default: FALSE]
-r --repo REPO        repository to use, or NULL for file [default: https://cran.rstudio.com]
-i --install-deps     also install packages along with their dependencies [default: FALSE]
-k --install-kitchen  even install packages 'kitchen sink'-style up to suggests [default: FALSE]
-l --library LIB      when installing use this library [default: /usr/local/lib/R/site-library]
-s --setwd DIR        change to this directoru before undertaking the test [default: ]
-d --deb-pkgs PKGS    also install binary .deb packages with their dependencies [default: FALSE]
-u --use-sudo         use sudo when installing .deb packages [default: TRUE]
-h --help             show this help text
-x --usage            show help and short example usage
$

rcc.r: R CMD check wrapper

The script rcc.r will also check a source tarball, and offers another set of options:

$ rcc.r -h
Usage: rcc.r [-h] [-x] [-c] [-f] [-q] [--args ARGS] [--libpath LIBP] [--repos REPO] [PATH...]

-c --as-cran          should '--as-cran' be added to ARGS [default: FALSE]
-a --args ARGS        additional arguments to be passed to 'R CMD CHECK' [default: ]
-l --libpath LIBP     additional library path to be used by 'R CMD CHECK' [default: ]
-r --repos REPO       additional repositories to be used by 'R CMD CHECK' [default: ]
-f --fast             should vignettes and manuals be skipped [default: FALSE]
-q --quiet            should 'rcmdcheck' be called qietly [default: FALSE]
-h --help             show this help text
-x --usage            show help and short example usage
$

build.r: Building Packages

A related script is build.r which I often use inside a source repository to quickly build a source tarball. Like rcc.r, it has a switch -f or --fast to omit building of vignettes.

$ build.r            # without argument works on current directory
$ build.r digest/    # with directory argument builds tar.gz from repo in directory

installGithub.r: GitHub install

Installation directly from GitHub is also popular. Here is an example:

$ installGithub.r RcppCore/RcppEigen

Installing from github is supported via the following helper script:

#!/usr/bin/env r
#
# A simple example to install one or more packages from GitHub
#
# Copyright (C) 2014 - 2015  Carl Boettiger and Dirk Eddelbuettel
#
# Released under GPL (>= 2)

## load docopt and remotes (or devtools) from CRAN
suppressMessages(library(docopt))       # we need docopt (>= 0.3) as on CRAN
suppressMessages(library(remotes))      # can use devtools as a fallback

## configuration for docopt
doc <- "Usage: installGithub.r [-h] [-d DEPS] REPOS...

-d --deps DEPS      Install suggested dependencies as well? [default: NA]
-h --help           show this help text

where REPOS... is one or more GitHub repositories.

Examples:
  installGithub.r RcppCore/RcppEigen                     

installGithub.r is part of littler which brings 'r' to the command-line.
See http://dirk.eddelbuettel.com/code/littler.html for more information.
"

## docopt parsing
opt <- docopt(doc)
if (opt$deps == "TRUE" || opt$deps == "FALSE") {
    opt$deps <- as.logical(opt$deps)
} else if (opt$deps == "NA") {
    opt$deps <- NA
}

invisible(sapply(opt$REPOS, function(r) install_github(r, dependencies = opt$deps)))

update.r: CRAN package update

One of the scripts I use the most (interactively) is update.r which updates installed packages. An earlier version looked like the following example, the current version is a little longer and has more features:

#!/usr/bin/env r 
#
# a simple example to update packages in /usr/local/lib/R/site-library
# parameters are easily adjustable

## adjust as necessary, see help('download.packages')
repos <- "https://cloud.r-project.org" 

## this makes sense on Debian where no package touch /usr/local
lib.loc <- "/usr/local/lib/R/site-library"

## r use requires non-interactive use
update.packages(repos=repos, ask=FALSE, lib.loc=lib.loc)

As above, it has my preferred mirror and library location hard-wired.

Another very useful option is -n N or --ncpus N which will parallelize the upgrade across N processes. This can be set automagically by setting options(Ncpus).

knit.r: Calling knitr

Here is another convenience script, knit.r, which knits a given file after testing the file actually exists.

#!/usr/bin/r
#
# Simple helper script for knitr
#
# Dirk Eddelbuettel, May 2013
#
# GPL-2 or later

if (is.null(argv)) {
    cat("Need an argument FILE.Rnw\n")
    q(status=-1)
}


file <- argv[1]
if (!file.exists(file)) {
    cat("File not found: ", file, "\n")
    q(status=-1)
}

require(knitr)
knit2pdf(file)

roxy.r: Running roxygen

Similar to the previous example, the script roxy.r one uses roxygen to extract documentation from R files – either in the current directory, or in the given directory or directories.

#!/usr/bin/r
#
# Simple helper script for roxygen2::roxygenize() 
#
# Dirk Eddelbuettel, August 2013
#
# GPL-2 or later

## load roxygen
library(roxygen2)

## check all command-line arguments (if any are given) for directory status
argv <- Filter(function(x) file.info(x)$is.dir, argv)

## loop over all argument, with fallback of the current directory, and
## call compileAttributes() on the given directory
sapply(ifelse(length(argv) > 0, argv, "."), FUN=roxygenize, roclets="rd")

compAttr.r: Compiling Attributes

The next script, compAttr., can be used with Rcpp, and particularly is powerful Attributes feature, in order to auto-generate helper code. It is similar to the preceding script, but invokes compileAttributes() instead.

#!/usr/bin/r
#
# Simple helper script for compileAttributes() 
#
# Dirk Eddelbuettel, July 2014
#
# GPL-2 or later

## load Rcpp
suppressMessages(library(Rcpp))

## check all command-line arguments (if any are given) for directory status
argv <- Filter(function(x) file.info(x)$is.dir, argv)

## loop over all argument, with fallback of the current directory, and
## call compileAttributes() on the given directory
sapply(ifelse(length(argv) > 0, argv, "."), compileAttributes)

render.r: Render Markdown

The render.r script generalizes the earlier knit.r to convert Markdown into its designated output.

#!/usr/bin/env r
#
# Another example to run a shiny app
#
# Copyright (C) 2016  Dirk Eddelbuettel
#
# Released under GPL (>= 2)

suppressMessages(library(docopt))       # we need docopt (>= 0.3) as on CRAN

## configuration for docopt
doc <- "Usage: render.r [-h] [-x] [FILES...]

-h --help            show this help text
-x --usage           show help and short example usage"

opt <- docopt(doc)          # docopt parsing

if (opt$usage) {
    cat(doc, "\n\n")
    cat("Examples:
  render.r foo.Rmd bar.Rmd        # convert two given files

render.r is part of littler which brings 'r' to the command-line.
See http://dirk.eddelbuettel.com/code/littler.html for more information.\n")
    q("no")
}

library(rmarkdown)

## helper function 
renderArg <- function(p) {
    if (!file.exists(p)) stop("No file '", p, "' found. Aborting.", call.=FALSE)
    render(p)
}

## render files using helper function 
sapply(opt$FILES, renderArg)
littler/inst/doc/littler-faq.html0000644000176200001440000001431114577617425016607 0ustar liggesusers Littler FAQ

Littler FAQ

Dirk Eddelbuettel

2019-03-23, updated 2020-06-16

Well, why?

Glad you asked. When the initial work started, Rscript did not exist so there was no scripting tool. We take a small amount of pride into beating Rscript narrowly to a first release. Of course, by now, Rscript is more widely used as it ships with every R installation but we still have some aspects we like about r: it is simpler and shorter, deals (in our biased) view more sanely with command-line arguments via the argv vector, always loaded package methods (which Rscript finally came around to a good decade later) and still starts faster. And r is just to cool a command (in relation to the trusted R) so someone had to!

No Printing

In the very beginning of littler, we made an executive decision to not echo each command output when we evaluate commands in the read-evaluate-print loop. So 2+2 will be evaluated silently: four will be computed, but not shown.

That made sense for scripts we wanted to be silent. The idea is that user will add a print() or cat() as needed. If you desire each step to printed, add a -p or --verbose argument.

No .Renviron

Another early decision was to make r start faster than the alternatives. Our r is “just” a small little binary. Whereas R and Rscript are front-end shell scripts sourcing a number of things and setting them dynamically, we determine values at compilation time and freeze them into the binary. That may seem risqué but worked out just fine. However, while we later added the ability to source Rprofile files (which contain R code we can evaluate) there is no way for us to source the Renviron files and to modify the already running process. So if you want to source Renviron you could add an explicit readEnviron() to ~/.littler.r or /etc/littler/r.

Lower-case / upper-case

This is mostly an issue on macOS where the brain surgeons behind the OS decided that r is the same as R. What can we say? On that OS you may need to rename the build to lr instead. Please send your complaints to Cupertino, California.

Adding the binary to your path

When the package is installed from source, it displays

*
* new binary $(TGT) installed in bin/ subdirectory"
* consider adding a symbolic link from, e.g., /usr/local/bin"
* on OS X, you may have to name this 'lr' instead"
* see the littler-faq vignette for more details"
*

where the variable $(TGT) normally expands to r. As the text suggests you may want to create a symbolic link from a directory in the to make the newly built binary available to users. On Linux you may do

cd /usr/local/bin 
sudo ln -s /usr/local/lib/R/site-library/littler/bin/r .

to create a link for r in /usr/local/bin. On macOS, as suggested, you may want

cd /usr/local/bin 
sudo ln -s /usr/local/lib/R/site-library/littler/bin/r lr

to create a command lr instead; see the previous question as to why. In either case adjust the source part of the ln command to where your binary is – which R can tell you via system.file("bin", "r", package="littler").

Also note that e.g. the zsh has a builtin command r which may conflict, so using the explicit path of, say, /usr/bin/r or /usr/local/bin/r or … may provide an alternative.

littler/inst/NEWS.Rd0000644000176200001440000004221114577617361013772 0ustar liggesusers\name{NEWS} \title{News for Package \pkg{littler}} \newcommand{\ghpr}{\href{https://github.com/eddelbuettel/littler/pull/#1}{##1}} \newcommand{\ghit}{\href{https://github.com/eddelbuettel/littler/issues/#1}{##1}} \section{Changes in littler version 0.3.20 (2024-03-23)}{ \itemize{ \item Changes in examples scripts \itemize{ \item New (dependency-free) helper \code{installDeps2.r} to install dependencies \item Scripts \code{rcc.r}, \code{tt.r}, \code{tttf.r}, \code{tttlr.r} use \code{env} argument \code{-S} to set \code{-t} to \code{r} \item \code{tt.r} can now fill in \code{inst/tinytest} if it is present \item New script \code{ciw.r} wrapping new package \pkg{ciw} \item \code{tttf.t} can now use \pkg{devtools} and its \code{loadall} \item New script \code{doi2bib.r} to call the DOI converter REST service (following a skeet by Richard McElreath) } \item Changes in package \itemize{ \item The CI setup use checkout@v4 and the r-ci-setup action \item The Suggests: is a little tighter as we do not list all packages optionally used in the the examples (as R does not check for it either) \item The package load messag can account for the rare build of R under different architecture (Berwin Turlach in \ghpr{117} closing \ghit{116}) \item In non-vanilla mode, the temporary directory initialization in re-run allowing for a non-standard temp dir via config settings } } } \section{Changes in littler version 0.3.19 (2023-12-17)}{ \itemize{ \item Changes in examples scripts \itemize{ \item The help or usage text display for \code{r2u.r}, \code{ttt.r}, \code{check.r} has been improved, expanded or corrected, respectively \item \code{installDeps.r} has a new argument for dependency selection \item An initial 'single test file' runner \code{tttf.r} has been added \item \code{r2u.r} has two new options for setting / varying the Debian build version of package that is built, and one for BioConductor builds, one for a 'dry run' build, and a new \code{--compile} option \item \code{installRSPM.r}, \code{installPPM.r}, \code{installP3M.r} have been updates to reflect the name changes \item \code{installRub.r} now understands 'package@universe' too \item \code{tt.r} flips the default of the \code{--effects} switch } } } \section{Changes in littler version 0.3.18 (2023-03-25)}{ \itemize{ \item Changes in examples scripts \itemize{ \item \code{roxy.r} can now set an additional \code{--libpath} \item \code{getRStudioDesktop.r} and \code{getRStudioServer.r} have updated default download file \item \code{install2.r} and \code{installGithub.r} can set \code{--type} \item \code{r2u.r} now has a \code{--suffix} option \item \code{tt.r} removes a redundant \code{library} call \item \code{tttl.r} has been added for \code{testthat::test_local()} \item \code{installRub.r} has been added to install r-universe binaries on Ubuntu \item \code{install2.r} has updated error capture messages (Tatsuya Shima and Dirk in \ghpr{104}) } } } \section{Changes in littler version 0.3.17 (2022-10-29)}{ \itemize{ \item Changes in package \itemize{ \item An internal function prototype was updated for \code{clang-15}. } \item Changes in examples \itemize{ \item Scripts \code{install2.r} and \code{installBioc.r} were updated for an update in R-devel (Tatsuya Shima and Dirk in \ghpr{104}). } } } \section{Changes in littler version 0.3.16 (2022-08-28)}{ \itemize{ \item Changes in package \itemize{ \item The \code{configure} code checks for two more headers \item The RNG seeding matches the current version in R (Dirk) } \item Changes in examples \itemize{ \item A \code{cowu.r} 'check Window UCRT' helper was added (Dirk) \item A \code{getPandoc.r} downloader has been added (Dirk) \item The \code{-r} option tp \code{install2.r} has been generalzed (Tatsuya Shima in \ghpr{95}) \item The \code{rcc.r} code / package checker now has \code{valgrind} option (Dirk) \item \code{install2.r} now installs to first element in \code{.libPaths()} by default (Dirk) \item A very simple \code{r2u.r} help has been added (Dirk) \item The \code{installBioc.r} has been generalized and extended similar to \code{install2.r} (Pieter Moris in \ghpr{103}) } } } \section{Changes in littler version 0.3.15 (2021-12-03)}{ \itemize{ \item Changes in examples \itemize{ \item The \code{install2} script can select download methods, and cope with errors from parallel download (thanks to Gergely Daroczi) \item The \code{build.r} now uses \code{both} as argument to \code{--compact-vignettes} \item The RStudio download helper were once again updated for changed URLs \item New caller for simplermarkdown::mdweave_to_html } \item Changes in package \itemize{ \item Several typos were correct (thanks to John Kerl) \item Travis artifacts and badges have been pruned \item Vignettes now use \pkg{simplermarkdown} } } } \section{Changes in littler version 0.3.14 (2021-10-05)}{ \itemize{ \item Changes in examples \itemize{ \item Updated RStudio download helper to changed file names \item Added a new option to \code{roxy.r} wrapper \item Added a downloader for Quarto command-line tool } \item Changes in package \itemize{ \item The \code{configure} files were updated to the standard of version 2.69 following a CRAN request } } } \section{Changes in littler version 0.3.13 (2021-07-24)}{ \itemize{ \item Changes in examples \itemize{ \item New script \code{compiledDeps.r} to show which dependencies are compiled \item New script \code{silenceTwitterAccount.r} wrapping \pkg{rtweet} \item The \code{-c} or \code{--code} option for \code{installRSPM.r} was corrected \item The \code{kitten.r} script now passes options \sQuote{bunny} and \sQuote{puppy} on to the \code{pkgKitten::kitten()} call; new options to call the Arma and Eigen variants were added \item The \code{getRStudioDesktop.r} and \code{getRStudioServer.r} scripts were updated for a change in \pkg{rvest} \item Two typos in the \code{tt.r} help message were correct (Aaron Wolen in \ghpr{86}) \item The message in \code{cranIncoming.r} was corrected. } \item Changes in package \itemize{ \item Added Continuous Integration runner via \code{run.sh} from \href{https://eddelbuettel.github.io/r-ci/}{r-ci}. \item Two vignettes got two extra vignette attributes. \item The mkdocs-material documentation input was moved. \item The basic unit tests were slightly refactored and updated. } } } \section{Changes in littler version 0.3.12 (2020-10-04)}{ \itemize{ \item Changes in examples \itemize{ \item Updates to scripts \code{tt.r}, \code{cos.r}, \code{cow.r}, \code{c4r.r}, \code{com.r} \item New script \code{installDeps.r} to install dependencies \item Several updates tp script \code{check.r} \item New script \code{installBSPM.r} and \code{installRSPM.r} for binary package installation (Dirk and Iñaki in \ghpr{81}) \item New script \code{cranIncoming.r} to check in Incoming \item New script \code{urlUpdate.r} validate URLs as R does } \item Changes in package \itemize{ \item Travis CI now uses BSPM \item A package documentation website was added \item Vignettes now use \pkg{minidown} resulting in \emph{much} reduced filesizes: from over 800kb to under 50kb (Dirk in \ghpr{83}) } } } \section{Changes in littler version 0.3.11 (2020-06-26)}{ \itemize{ \item Changes in examples \itemize{ \item Scripts \code{check.r} and \code{rcc.r} updated to reflect updated \pkg{docopt} 0.7.0 behaviour of quoted arguments \item The \code{roxy.r} script has a new ease-of-use option \code{-f | --full} regrouping two other options. } } } \section{Changes in littler version 0.3.10 (2020-06-02)}{ \itemize{ \item Changes in examples \itemize{ \item The \code{update.r} script only considers writeable directories. \item The \code{rcc.r} script tries to report full logs by setting \code{_R_CHECK_TESTS_NLINES_=0}. \item The \code{tt.r} script has an improved \code{ncpu} fallback. \item Several installation and updating scripts set \code{_R_SHLIB_STRIP_} to \code{TRUE}. \item A new script \code{installBioc.r} was added. \item The \code{--error} option to \code{install2.r} was generalized (Sergio Oller in \ghpr{78}). \item The \code{roxy.r} script was extended a little. } \item Changes in package \itemize{ \item Travis CI now uses R 4.0.0 and the bionic distro } } } \section{Changes in littler version 0.3.9 (2019-10-27)}{ \itemize{ \item Changes in examples \itemize{ \item The use of \code{call.} in \code{stop()} was corrected (Stefan Widgren in \ghpr{72}). \item New script \code{cos.r} to check (at rhub) on Solaris. \item New script \code{compactpdf.r} to compact pdf files. \item The \code{build.r} script now compacts vignettes and resaves data. \item The \code{tt.r} script now supports parallel tests and side effects. \item The \code{rcc.r} script can now report error codes. \item The `--libloc` option to \code{update.r} was updated. \item The \code{render.r} script can optionally compact pdfs. \item New script \code{sweave.r} to render (and compact) pdfs. \item New script \code{pkg2bibtex.r} to show bibtex entries. \item The \code{kitten.r} script has a new option \code{--puppy} to add \pkg{tinytest} support in purring packages. } } } \section{Changes in littler version 0.3.8 (2019-06-09)}{ \itemize{ \item Changes in examples \itemize{ \item The \code{install.r} and \code{install2.r} scripts now use parallel installation using \code{options{Ncpu}} on remote packages. \item The \code{install.r} script has an expanded help text mentioning the environment variables it considers. \item A new script \code{tt.r} was added to support \code{tinytest}. \item The rhub checking scripts now all suppress builds of manual and vignettes as asking for working latex appears to be too much. } \item Changes in package \itemize{ \item On startup checks if \code{r} is in \code{PATH} and if not references new FAQ entry; text from \code{Makevars} mentions it too. } \item Changes in documentation \itemize{ \item The FAQ vignette now details setting \code{r} to \code{PATH}. } } } \section{Changes in littler version 0.3.7 (2019-03-15)}{ \itemize{ \item Changes in examples \itemize{ \item The scripts \code{installGithub.r} and \code{install2.r} get a new option \code{-r | --repos} (Gergely Daroczi in \ghpr{67}) } \item Changes in build system \itemize{ \item The \code{AC_DEFINE} macro use rewritten to please R CMD check. } } } \section{Changes in littler version 0.3.6 (2019-01-26)}{ \itemize{ \item Changes in examples \itemize{ \item The scripts \code{install.r} and \code{install2.r} now support argument \code{"."}, and add it if called in a source directory. \item The script \code{install2.r} can set \code{Ncpus} for \code{install.packages()} (Colin Gillespie in \ghpr{63} fixing \ghpr{62}) \item The script \code{update.r} can also set \code{Ncpus} for \code{install.packages()}. \item A new vignette "litter-faq" was added. } } } \section{Changes in littler version 0.3.5 (2018-10-04)}{ \itemize{ \item Changes in examples \itemize{ \item The script \code{roxy.r} now uses a cached copy of \pkg{roxygen2} version 6.0.1 (if available) as the current version 6.1.0 changed behaviour. \item The script \code{rcc.r} was updated as the underlying \pkg{rcmdcheck} changed parameter order. \item A new simpler wrapper \code{rchk.r} was added to use RHub with the \code{rchk} image. } \item Changes in package \itemize{ \item Travis CI now uses the R 3.5 PPA } } } \section{Changes in littler version 0.3.4 (2018-08-24)}{ \itemize{ \item Changes in examples \itemize{ \item The shebang line is now \code{#!/usr/bin/env r} to work with either \code{/usr/local/bin/r} or \code{/usr/bin/r}. \item New example script to only install packages not yet installed (Brandon Bertelsen in \ghpr{59}); later added into \code{install2.r}. \item Functions \code{getRStudioDesktop.r} and \code{getRStudioServer.r} updated their internal URLs. \item Several minor enhancements were made to example scripts. } } } \section{Changes in littler version 0.3.3 (2017-12-17)}{ \itemize{ \item Changes in examples \itemize{ \item The script \code{installGithub.r} now correctly uses the \code{upgrade} argument (Carl Boettiger in \ghpr{49}). \item New script \code{pnrrs.r} to call the package-native registration helper function added in R 3.4.0 \item The script \code{install2.r} now has more robust error handling (Carl Boettiger in \ghpr{50}). \item New script \code{cow.r} to use R Hub's \code{check_on_windows} \item Scripts \code{cow.r} and \code{c4c.r} use \code{#!/usr/bin/env r} \item New option \code{--fast} (or \code{-f}) for scripts \code{build.r} and \code{rcc.r} for faster package build and check \item The \code{build.r} script now defaults to using the current directory if no argument is provided. \item The RStudio getters now use the \code{rvest} package to parse the webpage with available versions. } \item Changes in package \itemize{ \item Travis CI now uses https to fetch script, and sets the group } } } \section{Changes in littler version 0.3.2 (2017-02-14)}{ \itemize{ \item Changes in examples \itemize{ \item New scripts \code{getRStudioServer.r} and \code{getRStudioDesktop.r} to download daily packages, currently defaults to Ubuntu amd64 \item New script \code{c4c.r} calling \code{rhub::check_for_cran()} \item New script \code{rd2md.r} to convert Rd to markdown. \item New script \code{build.r} to create a source tarball. \item The \code{installGitHub.r} script now use package \CRANpkg{remotes} (PR \ghpr{44}, \ghpr{46}) } } } \section{Changes in littler version 0.3.1 (2016-08-06)}{ \itemize{ \item Changes in examples \itemize{ \item \code{install2.r} now passes on extra options past \code{--} to \code{R CMD INSTALL} (PR \ghpr{37} by Steven Pav) \item Added \code{rcc.r} to run \code{rcmdcheck::rcmdcheck()} \item Added (still simple) \code{render.r} to render (R)markdown \item Several examples now support the \code{-x} or \code{--usage} flag to show extended help. } \item Changes in build system \itemize{ \item The \code{AM_LDFLAGS} variable is now set and used too (PR \ghpr{38} by Mattias Ellert) \item Three more directories, used when an explicit installation directory is set, are excluded (also \ghpr{38} by Mattias) \item Travis CI is now driven via \code{run.sh} from our fork, and deploys all packages as .deb binaries using our PPA where needed } \item Changes in package \itemize{ \item SystemRequirements now mentions the need for \code{libR}, i.e. an R built with a shared library so that we can embed R. \item The \CRANpkg{docopt} and \CRANpkg{rcmdcheck} packages are now suggested, and added to the Travis installation. \item A new helper function \code{r()} is now provided and exported so that the package can be imported (closes \ghit{40}). \item URL and BugReports links were added to DESCRIPTION. } \item Changes in documentation \itemize{ \item The help output for \code{installGithub.r} was corrected (PR \ghpr{39} by Brandon Bertelsen) } } } \section{Changes in littler version 0.3.0 (2015-10-29)}{ \itemize{ \item Changes in build system \itemize{ \item First CRAN Release as R package following nine years of source releases \item Script \code{configure}, \code{src/Makevars.in} and remainder of build system rewritten to take advantage of the R package build infrastructure \item Reproducible builds are better supported as the (changing) compilation timestamps etc are only inserted for 'verbose builds' directly off the git repo, but not for Debian (or CRAN) builds off the release tarballs } \item Changes in littler functionality \itemize{ \item Also source \code{$R_HOME/etc/Rprofile.site} and \code{~/.Rprofile} if present } \item Changes in littler documentation \itemize{ \item Added new vignette with examples } } } littler/inst/man-page/0000755000176200001440000000000012613230464014374 5ustar liggesuserslittler/inst/man-page/r.10000644000176200001440000001057112613230464014723 0ustar liggesusers.\" hey, Emacs: -*- nroff -*- .\" littler is free software; you can redistribute it and/or modify .\" it under the terms of the GNU General Public License as published by .\" the Free Software Foundation; either version 2 of the License, or .\" (at your option) any later version. .\" .\" This program is distributed in the hope that it will be useful, .\" but WITHOUT ANY WARRANTY; without even the implied warranty of .\" MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the .\" GNU General Public License for more details. .\" .\" You should have received a copy of the GNU General Public License .\" along with this program; see the file COPYING. If not, write to .\" the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA. .\" .\" Use .\" help2man ./r --no-info \ .\" --name="Provides hash-bang (#!) capability for R (www.r-project.org)"\ .\" --output /tmp/r.1 .\" to create a new stub directly from the executable .\" .TH R "1" "September 2006" "r " "User Commands" .\" .\" Please update the above date whenever this man page is modified. .\" .\" Some roff macros, for reference: .\" .nh disable hyphenation .\" .hy enable hyphenation .\" .ad l left justify .\" .ad b justify to both left and right margins (default) .\" .nf disable filling .\" .fi enable filling .\" .br insert line break .\" .sp insert n+1 empty lines .\" for manpage-specific macros, see man(7) .\" .SH NAME r \- Provides hash-bang (#!) capability for R (www.r-project.org) .SH SYNOPSIS .B r [\fIoptions\fR] [\fI-|file\fR] [\fIR arguments\fR] .SH DESCRIPTION Launches GNU R to execute the specified file containing R commands, or takes commands from stdin if '-' is used to denote stdin, using the specified options. This makes it suitable to create R scripts via the so\-called shebang '#!/' line. The optional \fBR arguments\fR are stored in the \fBR\fR vector \fBargv\fR. .SH OPTIONS .TP \fB\-h\fR, \fB\-\-help\fR Display a short help list. .TP \fB\-\-usage\fR Give a short usage message. .TP \fB\-V\fR, \fB\-\-version\fR Show the version number. .TP \fB\-v\fR, \fB\-\-vanilla\fR Pass the '\-\-vanilla' option to R. .TP \fB\-t\fR, \fB\-\-rtemp\fR Use a per-session temporary directory as R does. .TP \fB\-i\fR, \fB\-\-interactive\fR Force 'interactive()' to evaluate to TRUE, whereas the default is FALSE. .TP \fB\-q\fR, \fB\-\-quick\fR Skip autoload (i.e. delayed assign) of default libraries. .TP \fB\-p\fR, \fB\-\-verbose\fR Print the value of expressions to the console. .TP \fB\-l\fR, \fB\-\-packages\fR list Load the R packages from the comma\-separated 'list'. .TP \fB\-d\fR, \fB\-\-datastdin\fR Evaluates 'X <- read.csv(file="stdin", stringsAsFactors=FALSE)' to read a data set from stdin. .TP \fB\-L\fR, \fB\-\-libpath\fR dir Add directory to library path via '.libPaths(dir)'. .TP \fB\-e\fR, \fB\-\-eval expr\fR Evaluate 'expr' in R. .PP .SH USAGE \fBr\fR can be used in command-line 'pipes' as well as in 'shebang'-style scripts. .SH EXAMPLES Piping \fBR\fP commands: echo 'cat(pi^2,"\\n")' | r Equivalently, \fBR\fP commands can be given on the command-line: r -e 'cat(pi^2, "\\n")' Alternatively, commands can be stored in a file, which in turn might use \fBR\fP command 'readLines' to process stdin input: $ cat examples/fsizes.r fsizes <- as.integer(readLines()) print(summary(fsizes)) stem(fsizes) which can be evaluated by \fBr\fP with the following command: ls -l /boot | awk '!/^total/ {print $5}' | r examples/fsizes.r The script file may contain a "shebang" line: $ cat examples/install.r #!/usr/bin/env r # a simple example to install one or more packages if (is.null(argv) | length(argv)<1) { cat("Usage: installr.r pkg1 [pkg2 pkg3 ...]\n") q() } repos <- "http://cran.us.r-project.org" lib.loc <- "/usr/local/lib/R/site-library" install.packages(argv, lib.loc, repos, dependencies=TRUE) and if it is executable, it can be called as: examples/install.r "TeachingDemos" See the examples directory in the sources for more. .SH NOTE The executable program is called \fBr\fR, but the project is called \fBlittler\fR to avoid confusion with the real \fBGNU R\fR. .SH SEE ALSO The \fBGNU R\fR language is documented extensively at the R website (http://www.r-project.org) and in several manuals available in html, info and pdf. .SH AUTHORS Jeffrey Horner . Dirk Eddelbuettel . littler/inst/script-tests/0000755000176200001440000000000012614402214015346 5ustar liggesuserslittler/inst/script-tests/dotLast.r0000755000176200001440000000031312613230464017150 0ustar liggesusers#!/usr/bin/env r # function to be called at exit .Last <- function() { cat("Really done, so bye-bye from .Last\n") } # imagine we're doing something now... # end, and .Last is now called q(status=42) littler/inst/script-tests/exitstatus.sh0000755000176200001440000000124112613230464020125 0ustar liggesusers#!/bin/bash echo "Testing value of 'q(status=...)' exits for r:" echo "q(status=123)" | ../r echo " Got: $? via stdin" echo "q(status=124)" | ../r - echo " Got: $? via file '-'" ../r -e "q(status=125)" echo " Got: $? from 'r -e'" tempfile=`tempfile` echo "q(status=126)" > $tempfile ../r $tempfile echo -n " Got: $? from temp. file and " rm -v $tempfile echo "Testing value of 'q(status=...)' exits for Rscript:" echo "q(status=123)" | Rscript - echo " Got: $? via stdin" Rscript -e "q(status=124)" echo " Got: $? from 'r -e'" tempfile=`tempfile` echo "q(status=125)" > $tempfile Rscript $tempfile echo -n " Got: $? from temp. file and " rm -v $tempfile littler/inst/script-tests/dat.txt0000644000176200001440000000015512613230464016665 0ustar liggesusers31538 79 628 4096 1250 112 1811 3860 182259 2155 17992 1793 105252 15785 24 838 20594 2431 997 271 4096 4096 littler/inst/script-tests/argParse.sh0000755000176200001440000000152112613230464017455 0ustar liggesusers#!/bin/bash ## run this test from the build directory, ie above tests/ littler=./r echo "Shebang 1" $littler tests/shebang foo echo "Shebang 2" $littler tests/shebang foo bar echo "Shebang 2, verbose" $littler --verbose tests/shebang foo bar echo "Piping a file to r" cat tests/test1.R | $littler echo "Piping a file to r -" cat tests/test1.R | $littler - echo "Looking at what argv contains" $littler -e 'print(argv)' -- -a -b echo "Looking at what argv contains, piped" echo 'print(argv)' | $littler - -- -a -b echo "" echo "Eval expr: cat('Hello, world\n')" $littler -e "cat('Hello, world\n')" echo "Eval expr: a=2;print(\"a^2\")" $littler --verbose -e 'a<-2; cat(a^2,"\n")' echo "" echo "Jeffrey's Grand Test of Tukey summary() of /bin/ls output" ls -l | awk '!/^total/ {print $5}' | $littler -e 'print(summary(as.integer(readLines())))' littler/inst/script-tests/longline.R0000755000176200001440000000056712613230464017320 0ustar liggesusers#!/usr/bin/env r longline <- function(len){ n <- floor(len/10) m = len %% 10 if (m>0){ x <- paste(rep(seq(0,9),n),collapse='') y <- paste(seq(0,m-1),collapse='') z <- paste(x,y,sep='') } else { z <- paste(rep(seq(0,9),n),collapse='') } z } cat("x<-\"", longline(1020), "\";",sep=""); cat("cat(x,\"\\n\"",")\n",sep=""); cat("cat(nchar(x),\"\\n\"",")\n",sep=""); littler/inst/script-tests/timing.sh0000755000176200001440000000153512613230464017205 0ustar liggesusers#!/bin/bash N=10 function loopBC { echo echo -n " --- GNU bc doing the addition $N times" i=0 while [ $i -lt $N ] do echo "1+2" | bc -l > /dev/null i=$((i + 1)) done } function loopLittleR { echo echo -n " --- our r doing the addition $N times" i=0 while [ $i -lt $N ] do echo "cat(1+2,'\n')" | ../r --vanilla > /dev/null i=$((i + 1)) done } function loopRscript { echo echo -n " --- GNU R's Rscript doing the addition $N times" i=0 while [ $i -lt $N ] do echo "cat(1+2,'\n')" | Rscript - > /dev/null i=$((i + 1)) done } function loopR { echo echo -n " --- GNU R doing the addition $N times" i=0 while [ $i -lt $N ] do echo "cat(1+2,'\n')" | R --slave --vanilla > /dev/null i=$((i + 1)) done } time loopBC time loopLittleR time loopRscript time loopR littler/inst/script-tests/error.R0000755000176200001440000000010512613230464016626 0ustar liggesusers#!/usr/bin/env r cat(search(),"\n") stop("FOO") cat(ls("Autoloads")) littler/inst/script-tests/summary2.R0000755000176200001440000000010412613230464017253 0ustar liggesusers#!/usr/bin/env r print(summary(as.integer(readLines("dat.txt")))); littler/inst/script-tests/ts.R0000755000176200001440000000066112613230464016132 0ustar liggesusers#!/usr/bin/env r # This should dynamically load stats cat("Is stats loaded?\n"); cat("search: ",search(),"\n"); if(!("package:stats" %in% search())){ cat("Nope!\n"); } cat("Calling ts(1:10)\n"); cat(ts(1:10),"\n"); cat("Now stats is loaded!\n"); cat("search: ",search(),"\n"); if(!("package:utils" %in% search())){ cat("No utils!\n"); cat("Calling timestamp()\n"); cat(timestamp(),"\n"); cat("search: ",search(),"\n"); } littler/inst/script-tests/shebang0000755000176200001440000000015012613230464016704 0ustar liggesusers#!/usr/bin/env r if (!is.null(argv)){ for ( i in 1:length(argv)){ cat("<",argv[i],">\n",sep='') } } littler/inst/script-tests/summary.R0000755000176200001440000000007312613230464017176 0ustar liggesusers#!/usr/bin/env r print(summary(as.integer(readLines()))); littler/inst/script-tests/test1.R0000755000176200001440000000030212613230464016534 0ustar liggesusers#!/usr/bin/env r cat("hello world!\n"); for (i in 1:10){ cat("i is",i,"\n"); } foo <- function(x=1){ if (x == 1){ cat("x is 1\n"); } else { cat("x is",x,":NOT 1\n"); } } foo(2) foo() littler/inst/script-tests/test_longline.R0000755000176200001440000000206212613230464020347 0ustar liggesusers#!/usr/bin/env r x<-"012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789";cat(x,"\n") cat(nchar(x),"\n") littler/inst/script-tests/timing2.sh0000755000176200001440000000115512613230464017265 0ustar liggesusers#!/bin/bash N=20 function loopLittleR { echo echo -n " --- our r calling summary() $N times" i=0 while [ $i -lt $N ] do ./summary2.R >/dev/null i=$((i + 1)) done } function loopRscript { echo echo -n " --- GNU R's Rscript calling summary() $N times" i=0 while [ $i -lt $N ] do Rscript ./summary2.R >/dev/null i=$((i + 1)) done } function loopR { echo echo -n " --- GNU R calling summary() $N times" i=0 while [ $i -lt $N ] do R --silent --vanilla < ./summary2.R >/dev/null i=$((i + 1)) done } time loopLittleR time loopRscript time loopR littler/cleanup0000755000176200001440000000040114577617426013324 0ustar liggesusers#!/bin/sh rm -f aclocal.m4 \ src/config.h \ config.status config.log \ src/Makevars \ src/autoloads.h src/ldflags.txt src/littler.h \ src/r src/gitversion.h *~ *.o \ stamp-h1 rm -rf autom4te.cache .deps inst/bin/ littler/configure0000755000176200001440000041562214577617426013675 0ustar liggesusers#! /bin/sh # Guess values for system-dependent variables and create Makefiles. # Generated by GNU Autoconf 2.71 for littler 0.3.20. # # Report bugs to . # # # Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation, # Inc. # # # This configure script is free software; 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It is necessary to write \x00 == 0 to get something that is true only with -std. */ int osf4_cc_array ['\''\x00'\'' == 0 ? 1 : -1]; /* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters inside strings and character constants. */ #define FOO(x) '\''x'\'' int xlc6_cc_array[FOO(a) == '\''x'\'' ? 1 : -1]; int test (int i, double x); struct s1 {int (*f) (int a);}; struct s2 {int (*f) (double a);}; int pairnames (int, char **, int *(*)(struct buf *, struct stat *, int), int, int);' # Test code for whether the C compiler supports C89 (body of main). ac_c_conftest_c89_main=' ok |= (argc == 0 || f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]); ' # Test code for whether the C compiler supports C99 (global declarations) ac_c_conftest_c99_globals=' // Does the compiler advertise C99 conformance? #if !defined __STDC_VERSION__ || __STDC_VERSION__ < 199901L # error "Compiler does not advertise C99 conformance" #endif #include extern int puts (const char *); extern int printf (const char *, ...); extern int dprintf (int, const char *, ...); extern void *malloc (size_t); // Check varargs macros. These examples are taken from C99 6.10.3.5. // dprintf is used instead of fprintf to avoid needing to declare // FILE and stderr. #define debug(...) dprintf (2, __VA_ARGS__) #define showlist(...) puts (#__VA_ARGS__) #define report(test,...) ((test) ? puts (#test) : printf (__VA_ARGS__)) static void test_varargs_macros (void) { int x = 1234; int y = 5678; debug ("Flag"); debug ("X = %d\n", x); showlist (The first, second, and third items.); report (x>y, "x is %d but y is %d", x, y); } // Check long long types. #define BIG64 18446744073709551615ull #define BIG32 4294967295ul #define BIG_OK (BIG64 / BIG32 == 4294967297ull && BIG64 % BIG32 == 0) #if !BIG_OK #error "your preprocessor is broken" #endif #if BIG_OK #else #error "your preprocessor is broken" #endif static long long int bignum = -9223372036854775807LL; static unsigned long long int ubignum = BIG64; struct incomplete_array { int datasize; double data[]; }; struct named_init { int number; const wchar_t *name; double average; }; typedef const char *ccp; static inline int test_restrict (ccp restrict text) { // See if C++-style comments work. // Iterate through items via the restricted pointer. // Also check for declarations in for loops. for (unsigned int i = 0; *(text+i) != '\''\0'\''; ++i) continue; return 0; } // Check varargs and va_copy. static bool test_varargs (const char *format, ...) { va_list args; va_start (args, format); va_list args_copy; va_copy (args_copy, args); const char *str = ""; int number = 0; float fnumber = 0; while (*format) { switch (*format++) { case '\''s'\'': // string str = va_arg (args_copy, const char *); break; case '\''d'\'': // int number = va_arg (args_copy, int); break; case '\''f'\'': // float fnumber = va_arg (args_copy, double); break; default: break; } } va_end (args_copy); va_end (args); return *str && number && fnumber; } ' # Test code for whether the C compiler supports C99 (body of main). ac_c_conftest_c99_main=' // Check bool. _Bool success = false; success |= (argc != 0); // Check restrict. if (test_restrict ("String literal") == 0) success = true; char *restrict newvar = "Another string"; // Check varargs. success &= test_varargs ("s, d'\'' f .", "string", 65, 34.234); test_varargs_macros (); // Check flexible array members. struct incomplete_array *ia = malloc (sizeof (struct incomplete_array) + (sizeof (double) * 10)); ia->datasize = 10; for (int i = 0; i < ia->datasize; ++i) ia->data[i] = i * 1.234; // Check named initializers. struct named_init ni = { .number = 34, .name = L"Test wide string", .average = 543.34343, }; ni.number = 58; int dynamic_array[ni.number]; dynamic_array[0] = argv[0][0]; dynamic_array[ni.number - 1] = 543; // work around unused variable warnings ok |= (!success || bignum == 0LL || ubignum == 0uLL || newvar[0] == '\''x'\'' || dynamic_array[ni.number - 1] != 543); ' # Test code for whether the C compiler supports C11 (global declarations) ac_c_conftest_c11_globals=' // Does the compiler advertise C11 conformance? #if !defined __STDC_VERSION__ || __STDC_VERSION__ < 201112L # error "Compiler does not advertise C11 conformance" #endif // Check _Alignas. char _Alignas (double) aligned_as_double; char _Alignas (0) no_special_alignment; extern char aligned_as_int; char _Alignas (0) _Alignas (int) aligned_as_int; // Check _Alignof. enum { int_alignment = _Alignof (int), int_array_alignment = _Alignof (int[100]), char_alignment = _Alignof (char) }; _Static_assert (0 < -_Alignof (int), "_Alignof is signed"); // Check _Noreturn. int _Noreturn does_not_return (void) { for (;;) continue; } // Check _Static_assert. struct test_static_assert { int x; _Static_assert (sizeof (int) <= sizeof (long int), "_Static_assert does not work in struct"); long int y; }; // Check UTF-8 literals. #define u8 syntax error! char const utf8_literal[] = u8"happens to be ASCII" "another string"; // Check duplicate typedefs. typedef long *long_ptr; typedef long int *long_ptr; typedef long_ptr long_ptr; // Anonymous structures and unions -- taken from C11 6.7.2.1 Example 1. struct anonymous { union { struct { int i; int j; }; struct { int k; long int l; } w; }; int m; } v1; ' # Test code for whether the C compiler supports C11 (body of main). ac_c_conftest_c11_main=' _Static_assert ((offsetof (struct anonymous, i) == offsetof (struct anonymous, w.k)), "Anonymous union alignment botch"); v1.i = 2; v1.w.k = 5; ok |= v1.i != 5; ' # Test code for whether the C compiler supports C11 (complete). ac_c_conftest_c11_program="${ac_c_conftest_c89_globals} ${ac_c_conftest_c99_globals} ${ac_c_conftest_c11_globals} int main (int argc, char **argv) { int ok = 0; ${ac_c_conftest_c89_main} ${ac_c_conftest_c99_main} ${ac_c_conftest_c11_main} return ok; } " # Test code for whether the C compiler supports C99 (complete). ac_c_conftest_c99_program="${ac_c_conftest_c89_globals} ${ac_c_conftest_c99_globals} int main (int argc, char **argv) { int ok = 0; ${ac_c_conftest_c89_main} ${ac_c_conftest_c99_main} return ok; } " # Test code for whether the C compiler supports C89 (complete). ac_c_conftest_c89_program="${ac_c_conftest_c89_globals} int main (int argc, char **argv) { int ok = 0; ${ac_c_conftest_c89_main} return ok; } " as_fn_append ac_header_c_list " stdio.h stdio_h HAVE_STDIO_H" as_fn_append ac_header_c_list " stdlib.h stdlib_h HAVE_STDLIB_H" as_fn_append ac_header_c_list " string.h string_h HAVE_STRING_H" as_fn_append ac_header_c_list " inttypes.h inttypes_h HAVE_INTTYPES_H" as_fn_append ac_header_c_list " stdint.h stdint_h HAVE_STDINT_H" as_fn_append ac_header_c_list " strings.h strings_h HAVE_STRINGS_H" as_fn_append ac_header_c_list " sys/stat.h sys_stat_h HAVE_SYS_STAT_H" as_fn_append ac_header_c_list " sys/types.h sys_types_h HAVE_SYS_TYPES_H" as_fn_append ac_header_c_list " unistd.h unistd_h HAVE_UNISTD_H" # Check that the precious variables saved in the cache have kept the same # value. ac_cache_corrupted=false for ac_var in $ac_precious_vars; do eval ac_old_set=\$ac_cv_env_${ac_var}_set eval ac_new_set=\$ac_env_${ac_var}_set eval ac_old_val=\$ac_cv_env_${ac_var}_value eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 printf "%s\n" "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} ac_cache_corrupted=: ;; ,set) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 printf "%s\n" "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_cache_corrupted=: ;; ,);; *) if test "x$ac_old_val" != "x$ac_new_val"; then # differences in whitespace do not lead to failure. ac_old_val_w=`echo x $ac_old_val` ac_new_val_w=`echo x $ac_new_val` if test "$ac_old_val_w" != "$ac_new_val_w"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 printf "%s\n" "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} ac_cache_corrupted=: else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 printf "%s\n" "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} eval $ac_var=\$ac_old_val fi { printf "%s\n" "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 printf "%s\n" "$as_me: former value: \`$ac_old_val'" >&2;} { printf "%s\n" "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 printf "%s\n" "$as_me: current value: \`$ac_new_val'" >&2;} fi;; esac # Pass precious variables to config.status. if test "$ac_new_set" = set; then case $ac_new_val in *\'*) ac_arg=$ac_var=`printf "%s\n" "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;; *) ac_arg=$ac_var=$ac_new_val ;; esac case " $ac_configure_args " in *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy. *) as_fn_append ac_configure_args " '$ac_arg'" ;; esac fi done if $ac_cache_corrupted; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 printf "%s\n" "$as_me: error: in \`$ac_pwd':" >&2;} { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 printf "%s\n" "$as_me: error: changes in the environment can compromise the build" >&2;} as_fn_error $? "run \`${MAKE-make} distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 fi ## -------------------- ## ## Main body of script. ## ## -------------------- ## ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu # Look for ancillary configure tools in tools # Ensure R_HOME is set yet respect a previously set value : ${R_HOME=`R RHOME`} if test -z "${R_HOME}"; then as_fn_error $? "Could not determine R_HOME." "$LINENO" 5 fi RPROG=${R_HOME}/bin/R CC=`${RPROG} CMD config CC` AM_CFLAGS=`${RPROG} CMD config CFLAGS` AM_LDFLAGS=`${RPROG} CMD config LDFLAGS` # create a config.h file ac_config_headers="$ac_config_headers src/config.h" # commenting this out relieves us from requiring tools/ with all the scripts # Checks for programs. ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. set dummy ${ac_tool_prefix}gcc; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_CC+y} then : printf %s "(cached) " >&6 else $as_nop if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_prog_CC="${ac_tool_prefix}gcc" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 printf "%s\n" "$CC" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi fi if test -z "$ac_cv_prog_CC"; then ac_ct_CC=$CC # Extract the first word of "gcc", so it can be a program name with args. set dummy gcc; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_ac_ct_CC+y} then : printf %s "(cached) " >&6 else $as_nop if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CC="gcc" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 printf "%s\n" "$ac_ct_CC" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi if test "x$ac_ct_CC" = x; then CC="" else case $cross_compiling:$ac_tool_warned in yes:) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 printf "%s\n" "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac CC=$ac_ct_CC fi else CC="$ac_cv_prog_CC" fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. set dummy ${ac_tool_prefix}cc; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_CC+y} then : printf %s "(cached) " >&6 else $as_nop if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_prog_CC="${ac_tool_prefix}cc" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 printf "%s\n" "$CC" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi fi fi if test -z "$CC"; then # Extract the first word of "cc", so it can be a program name with args. set dummy cc; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_CC+y} then : printf %s "(cached) " >&6 else $as_nop if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else ac_prog_rejected=no as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then if test "$as_dir$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then ac_prog_rejected=yes continue fi ac_cv_prog_CC="cc" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS if test $ac_prog_rejected = yes; then # We found a bogon in the path, so make sure we never use it. set dummy $ac_cv_prog_CC shift if test $# != 0; then # We chose a different compiler from the bogus one. # However, it has the same basename, so the bogon will be chosen # first if we set CC to just the basename; use the full file name. shift ac_cv_prog_CC="$as_dir$ac_word${1+' '}$@" fi fi fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 printf "%s\n" "$CC" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then for ac_prog in cl.exe do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_CC+y} then : printf %s "(cached) " >&6 else $as_nop if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_prog_CC="$ac_tool_prefix$ac_prog" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 printf "%s\n" "$CC" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi test -n "$CC" && break done fi if test -z "$CC"; then ac_ct_CC=$CC for ac_prog in cl.exe do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_prog_ac_ct_CC+y} then : printf %s "(cached) " >&6 else $as_nop if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS case $as_dir in #((( '') as_dir=./ ;; */) ;; *) as_dir=$as_dir/ ;; esac for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CC="$ac_prog" printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 printf "%s\n" "$ac_ct_CC" >&6; } else { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 printf "%s\n" "no" >&6; } fi test -n "$ac_ct_CC" && break done if test "x$ac_ct_CC" = x; then CC="" else case $cross_compiling:$ac_tool_warned in yes:) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 printf "%s\n" "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac CC=$ac_ct_CC fi fi fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}clang", so it can be a program name with args. set dummy ${ac_tool_prefix}clang; ac_word=$2 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 printf %s "checking for $ac_word... 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