littler/ChangeLog0000644000175000017500000004715112614402411012424 0ustar00eddedd2015-10-29 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/DESCRIPTION0000644000175000017500000000147412614410525012363 0ustar00eddeddPackage: littler Type: Package Title: R at the Command-Line via 'r' Version: 0.3.0 Date: 2015-10-29 Author: Dirk Eddelbuettel 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. License: GPL (>= 2) OS_type: unix Suggests: knitr VignetteBuilder: knitr NeedsCompilation: yes Packaged: 2015-10-29 12:30:13.34583 UTC; edd littler/NAMESPACE0000644000175000017500000000000012613717532012063 0ustar00eddeddlittler/R/0000755000175000017500000000000012614022075011047 5ustar00eddeddlittler/R/init.R0000644000175000017500000000170512614022075012140 0ustar00eddedd .onAttach <- function(libname, pkgname) { packageStartupMessage("The littler package provides 'r' as a binary.") if (Sys.info()[["sysname"]] == "Linux") { if (unname(Sys.which("r")) == "") { packageStartupMessage("You could link to the 'r' binary installed in\n'", system.file("bin", "r", package="littler"), "' from '/usr/local/bin' in order to use 'r' for scripting.") } } if (Sys.info()[["sysname"]] == "Darwin") { packageStartupMessage("On OS X, 'r' and 'R' are the same so 'lr' is an alternate name for littler.") if (unname(Sys.which("lr")) == "") { packageStartupMessage("You could link to the 'r' binary installed in\n'", system.file("bin", "r", package="littler"), "' as '/usr/local/bin/lr' in order to use 'lr' for scripting.") } } } littler/R/test.R0000644000175000017500000000037112613717574012170 0ustar00eddeddtest <- function(src = "cat(2 + 2)") { r <- file.path(system.file(package="littler"), "bin", paste0("r", ifelse(.Platform$OS.type=="windows", ".exe", ""))) system2(r, c("-e", shQuote(src)), stdout = TRUE, stderr = TRUE) } littler/README.md0000644000175000017500000000367312613230541012134 0ustar00eddedd## littler [![Build Status](https://travis-ci.org/eddelbuettel/littler.png)](https://travis-ci.org/eddelbuettel/littler) [![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html) A scripting and command-line front-end for GNU R permitting use of R in command-line contexts. ### Installation #### Version 0.3.0 or later _Once the package hits a [drat](http://dirk.eddelbuettel.com/code/drat.html) repository_, just run ``` install.packages("littler") ``` #### 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 risk 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 main littler page](http://dirk.eddelbuettel.com/code/littler.html) * [Dirk's page with littler examples](http://dirk.eddelbuettel.com/code/littler.examples.html) ### Authors Jeff Horner and Dirk Eddelbuettel ### License GPL (>= 2) littler/build/0000755000175000017500000000000012614410525011746 5ustar00eddeddlittler/build/vignette.rds0000644000175000017500000000031512614410525014304 0ustar00eddeddb```b`fbb`b2 1# ',)I-MH-I- MAS#Q U&/aFFIn"[|80!ɳ%bZ]?4-ީE0=(jؠjX2sRad9.nP&c0Gq?gQ~ 6@btr$$ |littler/cleanup0000755000175000017500000000041112614246414012224 0ustar00eddedd#!/bin/sh rm -f aclocal.m4 \ config.h config.h.in \ 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/configure0000755000175000017500000042160312614410420012556 0ustar00eddedd#! /bin/sh # Guess values for system-dependent variables and create Makefiles. # Generated by GNU Autoconf 2.69 for littler 0.3.0. # # # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc. # # # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. ## -------------------- ## ## M4sh Initialization. ## ## -------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. 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AC_PATH_PROG(NAMETOOL, install_name_tool) AC_DEFUN([NAMETOOL_FUN],[ if test "${NAMETOOL}" != ""; then RUN_NAMETOOL="${NAMETOOL} -change libR.dylib `${RPROG} RHOME`/lib/libR.dylib r" fi ]) NAMETOOL_FUN AC_SUBST(RPROG) AC_SUBST(CC) AC_SUBST(AM_CFLAGS) AC_SUBST(AM_LDFLAGS) AC_SUBST(EXTRA_LDFLAGS) AC_SUBST(RUN_NAMETOOL) AC_SUBST(GITREVISION) AC_SUBST(GITDATE) AC_OUTPUT([src/Makevars src/gitversion.h]) littler/inst/0000755000175000017500000000000012614410525011624 5ustar00eddeddlittler/inst/NEWS.Rd0000644000175000017500000000221512614402164012667 0ustar00eddedd\name{NEWS} \title{News for Package 'littler'} \newcommand{\ghrepo}{\href{https://github.com/#1}{\pkg{#1}}} \newcommand{\ghpr}{\href{https://github.com/eddelbuettel/littler/pull/#1}{##1}} \newcommand{\ghit}{\href{https://github.com/eddelbuettel/littler/issues/#1}{##1}} \section{Changes in littler version 0.3.0 (2015-10-29)}{ \itemize{ \item Changes in build system \itemize{ \item First CRAN Release as R package following nine years of source releases \item Script \code{configure}, \code{src/Makevars.in} and remainder of build system rewritten to take advantage of the R package build infrastructure \item Reproducible builds are better supported as the (changing) compilation timestamps etc are only inserted for 'verbose builds' directly off the git repo, but not for Debian (or CRAN) builds off the release tarballs } \item Changes in littler functionality \itemize{ \item Also source \code{$R_HOME/etc/Rprofile.site} and \code{~/.Rprofile} if present } \item Changes in littler documentation \itemize{ \item Added new vignette with examples } } } littler/inst/doc/0000755000175000017500000000000012614410525012371 5ustar00eddeddlittler/inst/doc/littler-examples.Rmd0000644000175000017500000002165512614410525016341 0ustar00eddedd--- title: "Littler Examples" author: "Dirk Eddelbuettel" date: "2015-10-28" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Littler Examples} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc} --- ## Examples 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. ### Simple Command-line Use [littler](http://dirk.eddelbuettel.com/code/littler.html) can be used directly on the command-line just like, say, `bc`: ```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 ``` 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`, ...). ### CRAN package installation #### Direct 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](http://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 <- "http://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. #### With Command-Line Parsing Thanks to the fabulous [docopt](https://github.com/edwindj/docopt.R) package, we also have a variant with optional settings of repo and location. Below is the updated version from [littler 0.2.1](http://dirk.eddelbuettel.com/blog/2014/10/19#littler-0.2.1): ```r #!/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 - 2015 Carl Boettiger and Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN ## configuration for docopt doc <- "Usage: install.r [-r REPO] [-l LIBLOC] [-h] [-d DEPS] [--error] [PACKAGES ...] -r --repos REPO repository to install from [default: http://cran.rstudio.com] -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] -e --error Throw error and halt instead of a warning [default: FALSE] -h --help show this help text" ## 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 } ## installation given selected options and arguments if (opt$error) { withCallingHandlers( install.packages(pkgs = opt$PACKAGES, lib = opt$libloc, repos = opt$repos, dependencies=opt$deps), warning = stop) } else { install.packages(pkgs = opt$PACKAGES, lib = opt$libloc, repos = opt$repos, dependencies=opt$deps) } ``` #### 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`. ### Checking Packages A related use case is to check packages via `check.r`. This script run `R CMD check`, but also installs package dependencies first as tests may have dependencies not yet satisfied on the test machine. ### GitHub package installation Installation directly from [GitHub](https://github.com) is also popular, and now supported via a new 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 devtools from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN suppressMessages(library(devtools)) ## configuration for docopt doc <- "Usage: installGithub.r [-r REPO] [-l LIBLOC] [-h] [-d DEPS] [PACKAGES ...] -r --repos REPO repository to install from [default: http://cran.rstudio.com] -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] -h --help show this help text" ## docopt parsing opt <- docopt(doc) if(opt$deps == "TRUE" || opt$deps == "FALSE") opt$deps <- as.logical(opt$deps) if(opt$deps == "NA") opt$deps <- NA ## installation given selected options and arguments options(repos = opt$repos) install_github(repo = opt$PACKAGES, paste("-l =", opt$libloc), dependencies = opt$deps) ``` ### CRAN package update One of the scripts I use the most (interactively) updates installed packages: ```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 <- "http://cran.rstudio.com" ## 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. ### Calling knitr Here is another convenience script 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) ``` ### Running roxygen Similar to the previous example, this 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)$is.dir, argv) ## loop over all argument, with fallback of the current directory, and ## call compileAttributes() on the given directory sapply(ifelse(length(argv) > 0, argv, "."), FUN=roxygenize, roclets="rd") ``` ### Compiling Attributes The next script can be used with [Rcpp](http://dirk.eddelbuettel.com/code/rcpp.html), and particularly is powerful _Attributes_ feature, in order to auto-generate helper code. It is similar to the preceding script, but invokes `compileAttributes()` instead. ```r #!/usr/bin/r # # Simple helper script for compileAttributes() # # Dirk Eddelbuettel, July 2014 # # GPL-2 or later ## load Rcpp suppressMessages(library(Rcpp)) ## check all command-line arguments (if any are given) for directory status argv <- Filter(function(x) file.info(x)$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) ``` littler/inst/doc/littler-examples.html0000644000175000017500000005744312614410525016567 0ustar00eddedd Littler Examples

Examples

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.

Simple Command-line Use

littler can be used directly on the command-line just like, say, bc:

$ 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

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, …).

CRAN package installation

Direct 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 <- "http://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.

With Command-Line Parsing

Thanks to the fabulous docopt package, we also have a variant with optional settings of repo and location. Below is the updated version from littler 0.2.1:

#!/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 - 2015  Carl Boettiger and Dirk Eddelbuettel
#
# Released under GPL (>= 2)

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

## configuration for docopt
doc <- "Usage: install.r [-r REPO] [-l LIBLOC] [-h] [-d DEPS] [--error] [PACKAGES ...]

-r --repos REPO     repository to install from [default: http://cran.rstudio.com]
-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]
-e --error          Throw error and halt instead of a warning [default: FALSE]
-h --help           show this help text"

## 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
}

## installation given selected options and arguments

if (opt$error) {
    withCallingHandlers(
        install.packages(pkgs  = opt$PACKAGES,
                         lib   = opt$libloc,
                         repos = opt$repos,
                         dependencies=opt$deps),
        warning = stop)

} else { 
    install.packages(pkgs  = opt$PACKAGES,
                     lib   = opt$libloc,
                     repos = opt$repos,
                     dependencies=opt$deps)
}

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.

Checking Packages

A related use case is to check packages via check.r. This script run R CMD check, but also installs package dependencies first as tests may have dependencies not yet satisfied on the test machine.

GitHub package installation

Installation directly from GitHub is also popular, and now supported via a new 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 devtools from CRAN
suppressMessages(library(docopt))       # we need docopt (>= 0.3) as on CRAN
suppressMessages(library(devtools)) 

## configuration for docopt
doc <- "Usage: installGithub.r [-r REPO] [-l LIBLOC] [-h] [-d DEPS] [PACKAGES ...]

-r --repos REPO     repository to install from [default: http://cran.rstudio.com]
-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]
-h --help           show this help text"

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

## installation given selected options and arguments
options(repos = opt$repos)
install_github(repo  = opt$PACKAGES,
               paste("-l =", opt$libloc),
               dependencies = opt$deps)

CRAN package update

One of the scripts I use the most (interactively) updates installed packages:

#!/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 <- "http://cran.rstudio.com" 

## 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.

Calling knitr

Here is another convenience script 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)

Running roxygen

Similar to the previous example, this 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")

Compiling Attributes

The next script 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)
littler/inst/examples/0000755000175000017500000000000012613230464013443 5ustar00eddeddlittler/inst/examples/check.r0000755000175000017500000000571412613230464014715 0ustar00eddedd#!/usr/bin/env r # # Another example to check one or more packages, with option parsing # # Copyright (C) 2015 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN ## configuration for docopt doc <- "Usage: check.r [-h] [--as-cran] [--repo REPO] [--install-deps] [--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: http://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 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 http://dirk.eddelbuettel.com/code/littler.html for more information. " ## docopt parsing opt <- docopt(doc) args <- character() if (opt$`as-cran`) args <- c(args, "--as-cran") ## doctopt results are characters, so if we meant NULL we have to set NULL if (opt$repo == "NULL") opt$repo = NULL r <- getOption("repos") r["CRAN"] <- opt$repo options(repos = r) ## helper functions checkArg <- function(p, args) { tools:::.check_packages(c(p, args)) } ## 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$repo) ## change directory if a target directory was given if (opt$setwd != "") setwd(opt$setwd) ## installation given selected options and arguments sapply(opt$TARGZ, checkArg, args) littler/inst/examples/compAttr.r0000755000175000017500000000073612613230464015430 0ustar00eddedd#!/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)$is.dir, argv) ## loop over all argument, with fallback of the current directory, and ## call compileAttributes() on the given directory sapply(ifelse(length(argv) > 0, argv, "."), compileAttributes) littler/inst/examples/dratInsert.r0000755000175000017500000000236212613230464015753 0ustar00eddedd#!/usr/bin/env r # # Another example to install one or more (source) packages into a drat # # Copyright (C) 2015 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN suppressMessages(library(drat)) ## configuration for docopt doc <- "Usage: drat.r [-h] [--repo REPO] [--commit MSG] TARGZ... -r --repo REPO repository path to use [default: ~/git/drat] -c --commit MSG in github use, commit with MSG (default: no commit) -h --help show this help text Examples: dratInsert.r myPkg_1.2-3.tar.gz # installs into default (git) repo dratInsert.r -r /srv/R/ myPkg_1.2-3.tar.gz # installs into local directory repo dratInstert.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information. " ## docopt parsing opt <- docopt(doc) if (is.null(opt$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/fileOps.r0000755000175000017500000000141112613230464015227 0ustar00eddedd#!/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)$ctime) ## select based on time window -- something arbitrary now <- Sys.Date() ## these are appromiximative, could be refined using DateTimeClasses sixmon <- now - 365.25/2 twelvemon <- now - 365.2 ind <- ctimes >= twelvemon & ctimes <= sixmon if (sum(ind) > 0) { cat("The following files are between six and twelve months old\n") print(files[ind]) } ## do something ## print(files[ind]) ## or rename / move to subdir ## mkdir("newDir") ## file.rename(files[ind], "newDir") ## can also use gsub() etc to rename littler/inst/examples/fsizes.r0000755000175000017500000000034212613230464015133 0ustar00eddedd#!/usr/bin/r -i # # A simple example to do statistics on files # # Copyright (C) 2006 - 2014 Dirk Eddelbuettel # # Released under GPL (>= 2) fsizes <- as.integer(readLines(file("stdin"))) print(summary(fsizes)) stem(fsizes) littler/inst/examples/highlightsweave.r0000755000175000017500000000116512613230464017016 0ustar00eddedd#!/usr/bin/r # # A simple example to invoke Sweave # # Copyright (C) 2014 Dirk Eddelbuettel # # Released under GPL (>= 2) ## use given argument(s) as target files, or else default to .Rnw files in directory files <- if (length(argv) == 0) dir(pattern="*.Rnw") else argv <- Filter(function(x) file.info(x)$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/install.r0000755000175000017500000000303012613230464015273 0ustar00eddedd#!/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 - 2015 Dirk Eddelbuettel # # Released under GPL (>= 2) if (is.null(argv) | length(argv) < 1) { cat("Usage: installr.r pkg1 [pkg2 pkg3 ...]\n\n") cat("Set environment variables REPOS and LIBLOC to overrride defaults.\n") cat("Installs pkg1, ... from existing files with matching extension.\n") q() } ## 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)$", f) ## helper function which switches to local (ie NULL) repo if matching file is presented installArg <- function(f, lib, rep) install.packages(f, lib, if (isMatchingFile(f)) NULL else repos) ## use argv [filtered by installArg()], lib.loc and repos to install the packages sapply(argv, installArg, lib.loc, repos) ## clean up any temp file containing CRAN directory information sapply(list.files(path=tempdir(), pattern="^(repos|libloc).*\\.rds$", full.names=TRUE), unlink) littler/inst/examples/install2.r0000755000175000017500000000501112613230464015356 0ustar00eddedd#!/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 Carl Boettiger and Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN ## configuration for docopt doc <- "Usage: install2.r [-r REPO...] [-l LIBLOC] [-h] [-d DEPS] [--error] [PACKAGES ...] -r --repos REPO repository to use, or NULL for file [default: getOption] -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] -e --error throw error and halt instead of a warning [default: FALSE] -h --help show this help text 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). Examples: install2.r -l /tmp/lib Rcpp BH # installs into given library install2.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 } ## doctopt results are characters, so if we meant NULL we have to set NULL if (opt$repos == "NULL") { opt$repos = NULL } else if (opt$repos == "getOption") { ## as littler can now read ~/.littler.r and/or /etc/littler.r we can preset elsewhere opt$repos = getOption("repos") } ## helper function to for existing files with matching extension isMatchingFile <- function(f) file.exists(f) && grepl("(\\.tar\\.gz|\\.tgz|\\.zip)$", f) ## helper function which switches to local (ie NULL) repo if matching file is presented installArg <- function(f, lib, rep, dep) { install.packages(pkgs=f, lib=lib, repos=if (isMatchingFile(f)) NULL else rep, dependencies=dep) } ## installation given selected options and arguments if (opt$error) { withCallingHandlers(sapply(opt$PACKAGES, installArg, opt$libloc, opt$repos, opt$deps), warning = stop) } else { sapply(opt$PACKAGES, installArg, opt$libloc, opt$repos, opt$deps) } ## clean up any temp file containing CRAN directory information sapply(list.files(path=tempdir(), pattern="^(repos|libloc).*\\.rds$", full.names=TRUE), unlink) littler/inst/examples/installGithub.r0000755000175000017500000000205012613230464016437 0ustar00eddedd#!/usr/bin/env r # # A simple example to install one or more packages from GitHub # # Copyright (C) 2014 - 2015 Carl Boettiger and Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt and devtools from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN suppressMessages(library(devtools)) ## configuration for docopt doc <- "Usage: installGithub.r [-h] [-d DEPS] REPOS... -d --deps DEPS Install suggested dependencies as well? [default: NA] -h --help show this help text where REPOS... is one or more GitHub repositories. Examples: installGithub.r RcppCore/RcppEigen installGithub.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information. " ## docopt parsing opt <- docopt(doc) if (opt$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$deps))) littler/inst/examples/installRepo.r0000755000175000017500000000373012613230464016130 0ustar00eddedd#!/usr/bin/env r # # A simple example to install one or more packages from GitHub # # Copyright (C) 2014 - 2015 Carl Boettiger, Dirk Eddelbuettel and Alexios Galanos # # Released under GPL (>= 2) ## load docopt and devtools from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN suppressMessages(library(devtools)) ## configuration for docopt doc <- "Usage: installRepo.r [-l LIBLOC] [-h] [-d DEPS] [-r REPOS] [-s subdir] SRC -l --libloc LIBLOC location in which to install [default: /usr/local/lib/R/site-library] -d --deps DEPS Install suggested dependencies as well? [default: NA] -r --repos REPOS The repository, eg github, bitbucket, svn, or url [default: github] -s --subdir SUBDIR For svn or url, an optional sub-directory within the repo -h --help show this help text where SRC is either a git-style repo (author/repo) or a URL for svn. Examples: installRepo.r RcppCore/RcppEigen # standard GitHub installRepo..r -r bitbucket alexiosg/rugarch # using BitBucket instead installRepo.r -r svn https://github.com/hadley/stringr # from Subversion or a URL installRepo.r -r url https://cran.rstudio.com/src/contrib/Archive/digest/digest_0.5.0.tar.gz installRepo.r is part of littler which brings 'r' to the command-line. See http://dirk.eddelbuettel.com/code/littler.html for more information. " ## docopt parsing opt <- docopt(doc) if (opt$deps == "TRUE" || opt$deps == "FALSE") { opt$deps <- as.logical(opt$deps) } else if (opt$deps == "NA") { opt$deps <- NA } ## installation given selected options and arguments switch(tolower(opt$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/knit.r0000755000175000017500000000047112613230464014600 0ustar00eddedd#!/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) littler/inst/examples/mph.r0000755000175000017500000000205312613230464014415 0ustar00eddedd#!/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/pace.r0000755000175000017500000000201612613230464014540 0ustar00eddedd#!/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/roxy.r0000755000175000017500000000074312613230464014636 0ustar00eddedd#!/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)$is.dir, argv) ## loop over all argument, with fallback of the current directory, and ## call compileAttributes() on the given directory sapply(ifelse(length(argv) > 0, argv, "."), FUN=roxygenize, roclets="rd") littler/inst/examples/runit.r0000755000175000017500000000122312613230464014770 0ustar00eddedd#!/usr/bin/env r # # A simple example to invoke unit tests # # Copyright (C) 2014 Dirk Eddelbuettel # # Released under GPL (>= 2) suppressMessages(library(docopt)) # we need the docopt package suppressMessages(library(RUnit)) # we need the RUnit package doc <- "Usage: runit.r [-p PACKAGES] [--help] [FILES ...] -p --packages PACKAGES comma-separated list of packages to install [default: ] -h --help show this help text" opt <- docopt(doc, args=argv) for (p in strsplit(opt[["--packages"]], ",")[[1]]) suppressMessages(require(p, character.only=TRUE)) for (f in opt[["FILES"]]) runTestFile(f) q(status=0) littler/inst/examples/shiny.r0000755000175000017500000000136412613230464014767 0ustar00eddedd#!/usr/bin/env r # # Another example to run a shiny app # # Copyright (C) 2015 Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN ## same as runApp() host <- getOption("shiny.host", "127.0.0.1") ## configuration for docopt doc <- paste0("Usage: shiny.r [-h] [--port PORT] [--host HOST] [--dir DIR] -p --port PORT port to use [default: NULL] -o --host HOST host string to use [default: ", host, "] -d --dir DIR directoru run application from [default: .] -h --help show this help text") ## docopt parsing opt <- docopt(doc) suppressMessages(library(shiny)) runApp(opt$dir, port=as.integer(opt$port), host=opt$host) littler/inst/examples/testInstalled.r0000755000175000017500000000203612613230464016451 0ustar00eddedd#!/usr/bin/env r # # a simple example to test one or more installed packages ## load docopt package from CRAN, or stop if not available suppressMessages(library(docopt)) # we need the docopt package 0.3 or later suppressMessages(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/update.r0000755000175000017500000000154312613230464015116 0ustar00eddedd#!/usr/bin/env r # # A simple example to update packages in /usr/local/lib/R/site-library # Parameters are easily adjustable # # Copyright (C) 2006 - 2015 Dirk Eddelbuettel # # Released under GPL (>= 2) ## adjust as necessary, see help('download.packages') ## littler can now read ~/.littler.r and /etc/littler.r to set this repos <- getOption("repos") ## this makes sense on Debian where no package touch /usr/local lib.loc <- "/usr/local/lib/R/site-library" ## 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() ## r use requires non-interactive use update.packages(repos=repos, ask=FALSE, lib.loc=lib.loc) ## Always clear caches of remote and local packages clearCache() littler/inst/man-page/0000755000175000017500000000000012613230464013312 5ustar00eddeddlittler/inst/man-page/r.10000644000175000017500000001057112613230464013641 0ustar00eddedd.\" 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/0000755000175000017500000000000012614402214014264 5ustar00eddeddlittler/inst/script-tests/argParse.sh0000755000175000017500000000152112613230464016373 0ustar00eddedd#!/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/dat.txt0000644000175000017500000000015512613230464015603 0ustar00eddedd31538 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/dotLast.r0000755000175000017500000000031312613230464016066 0ustar00eddedd#!/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/error.R0000755000175000017500000000010512613230464015544 0ustar00eddedd#!/usr/bin/env r cat(search(),"\n") stop("FOO") cat(ls("Autoloads")) littler/inst/script-tests/exitstatus.sh0000755000175000017500000000124112613230464017043 0ustar00eddedd#!/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/longline.R0000755000175000017500000000056712613230464016236 0ustar00eddedd#!/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/shebang0000755000175000017500000000015012613230464015622 0ustar00eddedd#!/usr/bin/env r if (!is.null(argv)){ for ( i in 1:length(argv)){ cat("<",argv[i],">\n",sep='') } } littler/inst/script-tests/summary.R0000755000175000017500000000007312613230464016114 0ustar00eddedd#!/usr/bin/env r print(summary(as.integer(readLines()))); littler/inst/script-tests/summary2.R0000755000175000017500000000010412613230464016171 0ustar00eddedd#!/usr/bin/env r print(summary(as.integer(readLines("dat.txt")))); littler/inst/script-tests/test1.R0000755000175000017500000000030212613230464015452 0ustar00eddedd#!/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.R0000755000175000017500000000206212613230464017265 0ustar00eddedd#!/usr/bin/env r x<-"012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789";cat(x,"\n") cat(nchar(x),"\n") littler/inst/script-tests/timing.sh0000755000175000017500000000153512613230464016123 0ustar00eddedd#!/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/timing2.sh0000755000175000017500000000115512613230464016203 0ustar00eddedd#!/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/inst/script-tests/ts.R0000755000175000017500000000066112613230464015050 0ustar00eddedd#!/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/man/0000755000175000017500000000000012614021142011413 5ustar00eddeddlittler/man/littler.Rd0000644000175000017500000000414512614021653013374 0ustar00eddedd\name{littler} \alias{littler} \alias{r} \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/src/0000755000175000017500000000000012614410525011436 5ustar00eddeddlittler/src/Makevars.in0000644000175000017500000000202612614410525013537 0ustar00eddedd## -*- mode: Makefile; tab-width: 8 -*- ## ## Makevars.in for littler ## Based on older Makefile.am ## ## Copyright (C) 2006 - 2015 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/ 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 "*" littler/src/config-const.h0000644000175000017500000000015412614410525014200 0ustar00eddedd /* Name of package */ #define PACKAGE "littler" /* Version number of package */ #define VERSION "0.2.9.1" littler/src/config.h0000644000175000017500000000447012614410525013061 0ustar00eddedd/* src/config.h. Generated from config.h.in by configure. */ /* config.h.in. Generated from configure.ac by autoheader. */ /* Define to 1 if you have the header file. */ /* #undef HAVE_ERRNO_H */ /* Define to 1 if you have . */ #define HAVE_GETOPT_H 1 /* Define if you have the gettimeofday function. */ #define HAVE_GETTIMEOFDAY 1 /* Define to 1 if you have the header file. */ #define HAVE_INTTYPES_H 1 /* Define to 1 if you have the header file. */ #define HAVE_MEMORY_H 1 /* Define if you have the setenv function. */ #define HAVE_SETENV 1 /* Define to 1 if you have the header file. */ #define HAVE_STDINT_H 1 /* Define to 1 if you have the header file. */ /* #undef HAVE_STDIO_H */ /* Define to 1 if you have the header file. */ #define HAVE_STDLIB_H 1 /* Define to 1 if you have the header file. */ #define HAVE_STRINGS_H 1 /* Define to 1 if you have the header file. */ #define HAVE_STRING_H 1 /* Define to 1 if you have the header file. */ #define HAVE_SYS_STAT_H 1 /* Define to 1 if you have the header file. */ #define HAVE_SYS_TYPES_H 1 /* Define if you have the time function. */ #define HAVE_TIME 1 /* Define to 1 if you have the header file. */ #define HAVE_UNISTD_H 1 /* 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 */ /* Name of package */ /* #undef PACKAGE */ /* Define to the address where bug reports for this package should be sent. */ #define PACKAGE_BUGREPORT "" /* Define to the full name of this package. */ #define PACKAGE_NAME "littler" /* Define to the full name and version of this package. */ #define PACKAGE_STRING "littler 0.3.0" /* Define to the one symbol short name of this package. */ #define PACKAGE_TARNAME "littler" /* Define to the home page for this package. */ #define PACKAGE_URL "" /* Define to the version of this package. */ #define PACKAGE_VERSION "0.3.0" /* Define to 1 if you have the ANSI C header files. */ #define STDC_HEADERS 1 /* Version number of package */ /* #undef VERSION */ /* when git is seen, we want a more verbose build */ #define VERBOSE_BUILD 1 littler/src/config.h.in0000644000175000017500000000416012614246414013466 0ustar00eddedd/* config.h.in. Generated from configure.ac by autoheader. */ /* Define to 1 if you have the header file. */ #undef HAVE_ERRNO_H /* 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_STDIO_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 /* Name of package */ #undef PACKAGE /* 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 /* Version number of package */ #undef VERSION /* when git is seen, we want a more verbose build */ #undef VERBOSE_BUILD littler/src/gitversion.h.in0000644000175000017500000000065312614246414014415 0ustar00eddedd /* * 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/littler.c0000644000175000017500000006151512614410525013271 0ustar00eddedd/* -*- mode: C; c-indent-level: 8; c-basic-offset: 4; indent-tabs-mode: nil; -*- * * littler - Provides hash-bang (#!) capability for R (www.r-project.org) * * Copyright (C) 2006 - 2015 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 "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() { 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() { 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() { 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 - 2015 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() { 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() */ void init_rand() { unsigned int seed; #if HAVE_GETTIMEOFDAY { struct timeval tv; gettimeofday (&tv, NULL); /* changed uint64_t to unsigned int. Need to figure out why PBR used that instead. */ seed = ((unsigned int) tv.tv_usec << 16) ^ tv.tv_sec; } #elif HAVE_TIME seed = (unsigned int) time(NULL); #else /* unlikely, but use random contents */ #endif srand(seed); } 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/scripts/0000755000175000017500000000000012613230464013126 5ustar00eddeddlittler/src/scripts/autoloads.R0000644000175000017500000000135112613230464015244 0ustar00eddedddp <- 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/ldflags.R0000644000175000017500000000031612613230464014665 0ustar00eddedd 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/src/scripts/littler.R0000644000175000017500000000055712613230464014737 0ustar00eddeddExcludeVars <- c("R_SESSION_TMPDIR","R_HISTFILE","R_LIBS_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/tests/0000755000175000017500000000000012613717574012026 5ustar00eddeddlittler/tests/simpleTests.R0000644000175000017500000000024112613717574014462 0ustar00eddeddlibrary(littler) stopifnot(identical(littler:::test(), "4")) # default test is cat(2+2) stopifnot(as.numeric(littler:::test('cat(R.version$year)')) >= 2015) littler/vignettes/0000755000175000017500000000000012614410525012657 5ustar00eddeddlittler/vignettes/littler-examples.Rmd0000644000175000017500000002165512614402546016633 0ustar00eddedd--- title: "Littler Examples" author: "Dirk Eddelbuettel" date: "2015-10-28" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Littler Examples} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc} --- ## Examples 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. ### Simple Command-line Use [littler](http://dirk.eddelbuettel.com/code/littler.html) can be used directly on the command-line just like, say, `bc`: ```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 ``` 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`, ...). ### CRAN package installation #### Direct 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](http://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 <- "http://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. #### With Command-Line Parsing Thanks to the fabulous [docopt](https://github.com/edwindj/docopt.R) package, we also have a variant with optional settings of repo and location. Below is the updated version from [littler 0.2.1](http://dirk.eddelbuettel.com/blog/2014/10/19#littler-0.2.1): ```r #!/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 - 2015 Carl Boettiger and Dirk Eddelbuettel # # Released under GPL (>= 2) ## load docopt package from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN ## configuration for docopt doc <- "Usage: install.r [-r REPO] [-l LIBLOC] [-h] [-d DEPS] [--error] [PACKAGES ...] -r --repos REPO repository to install from [default: http://cran.rstudio.com] -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] -e --error Throw error and halt instead of a warning [default: FALSE] -h --help show this help text" ## 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 } ## installation given selected options and arguments if (opt$error) { withCallingHandlers( install.packages(pkgs = opt$PACKAGES, lib = opt$libloc, repos = opt$repos, dependencies=opt$deps), warning = stop) } else { install.packages(pkgs = opt$PACKAGES, lib = opt$libloc, repos = opt$repos, dependencies=opt$deps) } ``` #### 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`. ### Checking Packages A related use case is to check packages via `check.r`. This script run `R CMD check`, but also installs package dependencies first as tests may have dependencies not yet satisfied on the test machine. ### GitHub package installation Installation directly from [GitHub](https://github.com) is also popular, and now supported via a new 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 devtools from CRAN suppressMessages(library(docopt)) # we need docopt (>= 0.3) as on CRAN suppressMessages(library(devtools)) ## configuration for docopt doc <- "Usage: installGithub.r [-r REPO] [-l LIBLOC] [-h] [-d DEPS] [PACKAGES ...] -r --repos REPO repository to install from [default: http://cran.rstudio.com] -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] -h --help show this help text" ## docopt parsing opt <- docopt(doc) if(opt$deps == "TRUE" || opt$deps == "FALSE") opt$deps <- as.logical(opt$deps) if(opt$deps == "NA") opt$deps <- NA ## installation given selected options and arguments options(repos = opt$repos) install_github(repo = opt$PACKAGES, paste("-l =", opt$libloc), dependencies = opt$deps) ``` ### CRAN package update One of the scripts I use the most (interactively) updates installed packages: ```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 <- "http://cran.rstudio.com" ## 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. ### Calling knitr Here is another convenience script 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) ``` ### Running roxygen Similar to the previous example, this 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)$is.dir, argv) ## loop over all argument, with fallback of the current directory, and ## call compileAttributes() on the given directory sapply(ifelse(length(argv) > 0, argv, "."), FUN=roxygenize, roclets="rd") ``` ### Compiling Attributes The next script can be used with [Rcpp](http://dirk.eddelbuettel.com/code/rcpp.html), and particularly is powerful _Attributes_ feature, in order to auto-generate helper code. It is similar to the preceding script, but invokes `compileAttributes()` instead. ```r #!/usr/bin/r # # Simple helper script for compileAttributes() # # Dirk Eddelbuettel, July 2014 # # GPL-2 or later ## load Rcpp suppressMessages(library(Rcpp)) ## check all command-line arguments (if any are given) for directory status argv <- Filter(function(x) file.info(x)$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) ```