├── .makerrc ├── LICENSE ├── Makefile ├── README.md ├── RECIPES.md ├── hooks ├── pre-commit-READMERmd.sh ├── pre-commit-newsmd.sh └── setup-hooks.sh └── include ├── Rprofile ├── check-reverse-dependencies.R ├── color-output.sh ├── increment-version.R ├── install-dependencies.R └── run-demos.R /.makerrc: -------------------------------------------------------------------------------- 1 | ## configuration Makefile for maker 2 | 3 | ## don't build vignettes 4 | VIG := 0 5 | ## always use --as-cran 6 | CRAN := 1 7 | ## specify output format for time (needs GNU time) 8 | ## see "man time" for details 9 | # TIMEFORMAT := -f "time: %e" 10 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | {one line to give the program's name and a brief idea of what it does.} 635 | Copyright (C) {year} {name of author} 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | {project} Copyright (C) {year} {fullname} 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | ## ideas and most of the code stolen from https://github.com/tudo-r/makeR 2 | ## updated to be run outside of the package directory 3 | 4 | ## Documentation is done directly in the Makefile using roxygen2-like syntax. 5 | ## To document a target use #' directly after the target and it dependencies 6 | ## (in the same line). Use @section to start a new section and @note to create 7 | ## a new note in the help output. 8 | 9 | R_HOME = "$(shell R RHOME)" 10 | R = "$(R_HOME)/bin/R" 11 | RSCRIPT = "$(R_HOME)/bin/Rscript" 12 | RM := rm -rf 13 | PKG := maker## default package (there must be no whitespace behind the PKG name) 14 | PKGDIR = ${PKG}/ 15 | PKGNAME = $(shell sed -n 's/Package: *//p' ${PKGDIR}/DESCRIPTION 2> /dev/null) 16 | VERSION = $(shell sed -n 's/Version: *//p' ${PKGDIR}/DESCRIPTION 2> /dev/null) 17 | TARGZ = ${PKGNAME}_${VERSION}.tar.gz 18 | BUILDARGS := --no-build-vignettes 19 | CHECKARGS := --no-vignettes --no-build-vignettes --no-stop-on-test-error 20 | RELEASERARGS := --no-save --no-restore --no-site-file --no-environ --vanilla --no-init-file 21 | RELEASETARGETS := | clean-all build check-only 22 | INSTALLARGS := --install-tests 23 | IGNORE := ".git/* .svn/* sandbox/*" 24 | IGNOREPATTERN = $(shell echo "${IGNORE}" | sed 's:\([^[:space:]]\+\):-a -not -path "${PKGDIR}/\1":g; s:/\{2,\}:/:g; s:^-a \+::') 25 | MAKERDIR := $(dir $(realpath $(lastword $(MAKEFILE_LIST)))) 26 | INCLUDEDIR := ${MAKERDIR}/include/ 27 | PKGFILES = $(shell find ${PKGDIR} -type f \( ${IGNOREPATTERN} \) 2>/dev/null) 28 | VIGFILES = $(shell find ${PKGDIR} -type f -name *.Rnw 2>/dev/null) 29 | MAKERVERSION := $(shell cd ${MAKERDIR} && git log -1 --format="%h [%ci]") 30 | MAKERMAKEFILE := $(lastword $(MAKEFILE_LIST)) 31 | ## targets that don't need an R package (PKG could be empty) 32 | NONPKGTARGETS := get-default-pkg help maker maker-README.md targets usage version 33 | 34 | PKGBUILDFLAGSFILE := /tmp/${PKGNAME}.buildflags 35 | 36 | ## user variables 37 | MAKERRC := ~/.makerrc 38 | WARNINGS_AS_ERRORS := 1 39 | VIG := 1 40 | CRAN := 0 41 | BIOC = $(shell grep -s "biocViews" ${PKGDIR}/DESCRIPTION >/dev/null && echo 1 || echo 0) 42 | COLOURS := 1 43 | RPROFILE := ${INCLUDEDIR}/Rprofile 44 | TIMEFORMAT := 45 | 46 | .DEFAULT_GOAL := help 47 | 48 | ## overwrite default variables by variables in ~/.makerrc 49 | ifneq ($(wildcard ${MAKERRC}),) 50 | include ${MAKERRC} 51 | endif 52 | 53 | ## test whether PKGDIR is an R package 54 | ## if not throw an error if the user ask for a PKG-specific target 55 | ifeq ($(wildcard ${PKGDIR}/DESCRIPTION),) 56 | ifneq ($(filter-out ${NONPKGTARGETS},${MAKECMDGOALS}),) 57 | $(error ${PKGDIR} seems to be no R package. Did you set PKG/PKGDIR?) 58 | endif 59 | endif 60 | 61 | ifeq (${VIG},1) 62 | BUILDARGS := $(filter-out --no-build-vignettes,$(BUILDARGS)) 63 | CHECKARGS := $(filter-out --no-vignettes,$(CHECKARGS)) 64 | endif 65 | 66 | ifeq (${CRAN},1) 67 | CHECKARGS += --as-cran 68 | RELEASECHECKARGSCHECKARGS += --as-cran 69 | endif 70 | 71 | ifeq (${BIOC},1) 72 | RELEASETARGETS += bioccheck-only 73 | endif 74 | 75 | .PHONY: build vignettes check check-only bioccheck bioccheck-only \ 76 | check-downstream check-reverse-dependencies clean clean-all clean-tar \ 77 | compile-attributes force help install install-only install-dependencies install-upstream \ 78 | maker .maker maker-README.md remove release roxygen document rd run-demos \ 79 | setup-git-hooks targets usage win-builder version \ 80 | pkg-home pkg-news pkg-refs pkg-vigs pkg-all pkgdown README.md NEWS 81 | 82 | #'@section Usage 83 | #'@note make TARGET PKG=package 84 | #'@note e.g. make build PKG=MSnbase 85 | 86 | ## pseudo target to force evaluation of other targets, e.g. ${PKGBUILDFLAGSFILE} 87 | force: 88 | 89 | ${PKGBUILDFLAGSFILE}: force 90 | echo "${VIG}" | cmp --silent - $@ || echo "${VIG}" > $@ 91 | 92 | #'@section Build 93 | build: clean ${TARGZ} #' build source package 94 | 95 | ${TARGZ}: ${PKGFILES} ${PKGBUILDFLAGSFILE} 96 | ${R} CMD build ${BUILDARGS} ${PKGDIR} | \ 97 | COLOURS=$(COLOURS) ${INCLUDEDIR}/color-output.sh 98 | 99 | vignettes: #' build vignettes in ./${PKGDIR}/vignettes/ 100 | cd ${PKGDIR}/vignettes/ && \ 101 | test -f Makefile && \ 102 | make all || \ 103 | ( for v in $$(ls *.Rnw *.Rmd 2>/dev/null); do \ 104 | ${R} CMD Sweave --engine=knitr::knitr --pdf $$v; \ 105 | done ) 106 | 107 | compile-attributes: #' run Rcpp::compileAttributes() 108 | ${R} -e "library(Rcpp); compileAttributes('"$(PKGDIR)"')"; 109 | 110 | release: export R_PROFILE_USER=${RPROFILE} 111 | release: R := ${R} ${RELEASERARGS} 112 | release: CHECKARGS := ${RELEASECHECKARGS} 113 | release: BUILDARGS := ${RELEASEBUILDARGS} 114 | release: ${RELEASETARGETS} #' build package for Bioc/CRAN release (includes vignettes etc.) 115 | 116 | #'@section Check 117 | check: CHECKARGS := $(filter-out --no-vignettes,$(CHECKARGS)) 118 | check: | build check-only #' build and check package; the check will always use "--no-vignettes" because vignettes are checked by the build process before 119 | 120 | check-only: #' check package and time checking 121 | { time ${TIMEFORMAT} ${R} CMD check ${CHECKARGS} ${TARGZ} 2>&1; } | \ 122 | COLOURS=$(COLOURS) ${INCLUDEDIR}/color-output.sh && \ 123 | grep "WARNING" ${PKGNAME}.Rcheck/00check.log > /dev/null ; \ 124 | if [ $$? -eq 0 ] ; then exit ${WARNINGS_AS_ERRORS}; fi 125 | 126 | bioccheck: | check bioccheck-only #' build, check and BiocCheck package 127 | 128 | bioccheck-only: #' BiocCheck package 129 | ${R} -e 'BiocCheck::BiocCheck("${TARGZ}")' 2>&1 | \ 130 | COLOURS=$(COLOURS) ${INCLUDEDIR}/color-output.sh && \ 131 | grep "WARNING" ${PKGNAME}.Rcheck/00check.log > /dev/null ; \ 132 | if [ $$? -eq 0 ] ; then exit ${WARNINGS_AS_ERRORS}; fi 133 | 134 | check-reverse-dependencies: #' check packages which depend on this package 135 | check-downstream: #' check packages which depend on this package 136 | check-reverse-dependencies check-downstream: install 137 | cd ${PKGDIR} && ${RSCRIPT} ${INCLUDEDIR}/check-reverse-dependencies.R 138 | 139 | #'@section Clean 140 | clean: #' remove temporary files and .Rcheck 141 | ${RM} ${PKGDIR}/src/*.o ${PKGNAME}/src/*.so 142 | ${RM} ${PKGDIR}/*~ 143 | find . -name '.Rhistory' -exec rm '{}' \; 144 | ${RM} ${PKGDIR}/vignettes/.\#* 145 | ${RM} ${PKGDIR}/vignettes/\#* 146 | ${RM} ${PKGNAME}.Rcheck 147 | 148 | clean-tar: #' remove .tar.gz archive 149 | ${RM} ${TARGZ} 150 | 151 | clean-vignettes: #' remove vignettes in inst/doc/ 152 | test -f ${PKGDIR}/vignettes/Makefile && \ 153 | (cd ${PKGDIR}/vignettes/ && make clean) || \ 154 | ( ${RM} $(VIGFILES:.Rnw=.pdf) && \ 155 | ${RM} ${PKGDIR}/vignettes/.build.timestamp ) 156 | 157 | clean-all: clean clean-tar clean-vignettes #' combine "clean", "clean-tar" and "clean-vignettes" 158 | 159 | #'@section Increment version 160 | increment-version-major: #' increment major version number (X++.1) and set the "Date" field in the DESCRIPTION file 161 | @cd ${PKGDIR} && ${RSCRIPT} ${INCLUDEDIR}/increment-version.R major 162 | 163 | increment-version-minor: #' increment minor version number (1.X++) and set the "Date" field in the DESCRIPTION file 164 | @cd ${PKGDIR} && ${RSCRIPT} ${INCLUDEDIR}/increment-version.R minor 165 | 166 | increment-version-patch: #' increment patch version number (1.1.X++) and set the "Date" field in the DESCRIPTION file 167 | @cd ${PKGDIR} && ${RSCRIPT} ${INCLUDEDIR}/increment-version.R patch 168 | 169 | #'@section Adminstration 170 | install: | build install-only #' build and install package 171 | 172 | install-only: #' install package 173 | ${R} CMD INSTALL ${INSTALLARGS} ${TARGZ} | \ 174 | COLOURS=$(COLOURS) ${INCLUDEDIR}/color-output.sh 175 | 176 | install-dependencies install-upstream: '# install package dependencies 177 | cd ${PKGDIR} && ${RSCRIPT} ${INCLUDEDIR}/install-dependencies.R 178 | 179 | remove: #' remove package 180 | ${R} CMD REMOVE ${PKGNAME} 181 | 182 | #'@section Documentation 183 | roxygen: clean #' roxygenize package 184 | ${R} -e "library(roxygen2); roxygenize('"$(PKGDIR)"')"; 185 | 186 | document: clean #' document package 187 | ${R} -e "library(devtools); document('"$(PKGDIR)"')"; 188 | 189 | rd: clean #' roxygenize rd rocklet 190 | ${R} -e "library(devtools); document('"$(PKGDIR)"', roclets=\"rd\")"; 191 | 192 | pkg-home: clean #' pkgdown home 193 | ${R} -e "setwd('"$(PKGDIR)"'); library(pkgdown); build_home()"; 194 | 195 | pkg-news: clean #' pkgdown news 196 | ${R} -e "setwd('"$(PKGDIR)"'); library(pkgdown); build_news()"; 197 | 198 | pkg-refs: clean #' pkgdown references (manuals) 199 | ${R} -e "setwd('"$(PKGDIR)"'); library(pkgdown); build_reference()"; 200 | 201 | pkg-vigs: clean #' pkgdown articles (Rmd vignettes) 202 | ${R} -e "setwd('"$(PKGDIR)"'); library(pkgdown); build_articles()"; 203 | 204 | pkg-all: clean #' pkgdonw home, refs, articles and news (in that order) 205 | $(MAKE) -f $(MAKERMAKEFILE) pkg-home 206 | $(MAKE) -f $(MAKERMAKEFILE) pkg-refs 207 | $(MAKE) -f $(MAKERMAKEFILE) pkg-vigs 208 | $(MAKE) -f $(MAKERMAKEFILE) pkg-news 209 | 210 | pkgdown: clean #' full pkgdown site using the pkgdown::build_site 211 | ${R} -e "setwd('"$(PKGDIR)"'); library(pkgdown); build_site()"; 212 | 213 | deploy: clean #' deploy pkgdown to branch 214 | ${R} -e "setwd('"$(PKGDIR)"'); pkgdown::deploy_to_branch(new_process = FALSE)"; 215 | 216 | README.md: #' knit README.Rmd if available 217 | cd ${PKGDIR} && ${R} -e "if (file.exists('README.Rmd')) knitr::knit('README.Rmd')"; 218 | 219 | NEWS: #' defunct: see issue 33 (`news()` supports `NEWS.md` now) 220 | @echo "Defunct: \`news()\` supports \`NEWS.md\` files since R 3.6.0; see also https://github.com/ComputationalProteomicsUnit/maker/issues/33." 221 | 222 | #'@section Maker specific targets 223 | maker: .maker #' update maker toolbox 224 | 225 | .maker: 226 | cd ${MAKERDIR} && git checkout master && git pull 227 | 228 | maker-README.md: #' update help output in README.md 229 | $(MAKE) --silent help | sed -i '/^\$$ make help/,/^```$$/{/^\$$ make help$$/!{/^```$$/!d}}; /^\$$ make help/r /dev/stdin' README.md 230 | 231 | version: #' prints latest git hash and date of maker 232 | @echo ${MAKERVERSION} 233 | 234 | #'@section Available variables 235 | #'@param PKG/PKGDIR path to the target package (default is 'maker') 236 | #'@param MAKERRC path to the maker configuration file (default is '~/.makerrc') 237 | #'@param VIG vignettes be build (default is 1). If 0, build --no-build-vignettes is used 238 | #'@param WARNINGS_AS_ERRORS fail on warnings (default is 1) 239 | #'@param CRAN check using --as-cran (default is 0) 240 | #'@param COLOURS using colours for R CMD check results (default is 1) 241 | #'@param RPROFILE path to .Rprofile (default is ${MAKEDIR}/include/Rprofile) 242 | #'@param TIMEFORMAT time format (default: empty) 243 | 244 | #'@section Misc 245 | #'@note Vignettes are not build when checking: R CMD check --no-build-vignettes\n 246 | 247 | win-builder: check #' build package and send to win-builder.r-project.org 248 | ncftpput win-builder.r-project.org R-devel ${TARGZ} 249 | 250 | run-demos: #' source and run demo/*.R files 251 | cd ${PKGDIR} && ${RSCRIPT} ${INCLUDEDIR}/run-demos.R 252 | 253 | get-default-pkg: #' print current default PKG 254 | @grep "^[[:space:]]*PKG[[:space:]]*=" ${MAKERRC} || echo "No default PKG set." 255 | 256 | set-default-pkg: #' set new default PKG 257 | (test -f ${MAKERRC} && \ 258 | grep -q "^[[:space:]]*PKG[[:space:]]*=" ${MAKERRC} && \ 259 | sed -i --follow-symlinks 's/^[[:space:]]*PKG[[:space:]]*=.*/PKG=${PKG}/' ${MAKERRC}) || \ 260 | (echo PKG=${PKG} >> ${MAKERRC}) 261 | @echo 262 | @echo "Default PKG set to ${PKG}." 263 | 264 | remove-default-pkg: #' remove current default PKG 265 | (test -f ${MAKERRC} && \ 266 | sed -i --follow-symlinks '/^[[:space:]]*PKG[[:space:]]*=.*/d' ${MAKERRC}) 267 | 268 | setup-git-hooks: #' setup git hooks 269 | ${MAKERDIR}/hooks/setup-hooks.sh ${PKGDIR} 270 | 271 | #'@section Getting help 272 | help target usage: #' print this help text 273 | @sed -n "s/\\\\n/|/g; \ 274 | s/^#' *@section \(.*\)$$/\n\1:\n/p; \ 275 | s/^#' *@note \(.*\)$$/ \1/p; \ 276 | s/^#' *@param \([^ ]*\) \+\(.*\)\$$/ \1\t\2/p; \ 277 | s/^\([^:]\+\):.*#' \([^@]\+\)\$$/ \1\t\2/p" $(MAKEFILE_LIST) | expand -t 30 | tr '|' '\n' 278 | #'@note \n Create an issue on https://github.com/ComputationalProteomicsUnit/maker/issues/ or \n write an e-mail to Sebastian Gibb and Laurent Gatto . 279 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Makefile for R packages 2 | 3 | `maker` is based on https://github.com/tudo-r/makeR. This version has 4 | been updated to be run outside of the package directory and reduce 5 | external `Rscript` dependencies. 6 | 7 | ## Contact 8 | 9 | You are welcome to: 10 | 11 | * submit suggestions and bug-reports at: 12 | 13 | 14 | * fork and send a pull request on: 15 | 16 | 17 | * compose an e-mail to: 18 | 19 | ## Integrate `maker` into your project 20 | 21 | Our version of `maker` is meant to be installed and run outside of the 22 | package directory. Start by cloning `maker` (for example in the base 23 | directory that contains your `R` package(s)), create the appropriate 24 | symlinks and use it. 25 | 26 | git clone git@github.com:ComputationalProteomicsUnit/maker.git 27 | ln -s maker/Makefile . 28 | make help 29 | 30 | ## Update `maker` 31 | 32 | make maker 33 | 34 | ## Help 35 | 36 | ```sh 37 | $ make help 38 | 39 | Usage: 40 | 41 | make TARGET PKG=package 42 | e.g. make build PKG=MSnbase 43 | 44 | Build: 45 | 46 | build build source package 47 | vignettes build vignettes in ./${PKGDIR}/vignettes/ 48 | compile-attributes run Rcpp::compileAttributes() 49 | release build package for Bioc/CRAN release (includes vignettes etc.) 50 | 51 | Check: 52 | 53 | check build and check package; the check will always use "--no-vignettes" because vignettes are checked by the build process before 54 | check-only check package and time checking 55 | bioccheck build, check and BiocCheck package 56 | bioccheck-only BiocCheck package 57 | check-reverse-dependencies check packages which depend on this package 58 | check-downstream check packages which depend on this package 59 | 60 | Clean: 61 | 62 | clean remove temporary files and .Rcheck 63 | clean-tar remove .tar.gz archive 64 | clean-vignettes remove vignettes in inst/doc/ 65 | clean-all combine "clean", "clean-tar" and "clean-vignettes" 66 | 67 | Increment version: 68 | 69 | increment-version-major increment major version number (X++.1) and set the "Date" field in the DESCRIPTION file 70 | increment-version-minor increment minor version number (1.X++) and set the "Date" field in the DESCRIPTION file 71 | increment-version-patch increment patch version number (1.1.X++) and set the "Date" field in the DESCRIPTION file 72 | 73 | Adminstration: 74 | 75 | install build and install package 76 | install-only install package 77 | remove remove package 78 | 79 | Documentation: 80 | 81 | roxygen roxygenize package 82 | document document package 83 | rd roxygenize rd rocklet 84 | pkg-home pkgdown home 85 | pkg-news pkgdown news 86 | pkg-refs pkgdown references (manuals) 87 | pkg-vigs pkgdown articles (Rmd vignettes) 88 | pkg-all pkgdonw home, refs, articles and news (in that order) 89 | pkgdown full pkgdown site using the pkgdown::build_site 90 | README.md knit README.Rmd if available 91 | NEWS defunct: see issue 33 (`news()` supports `NEWS.md` now) 92 | 93 | Maker specific targets: 94 | 95 | maker update maker toolbox 96 | maker-README.md update help output in README.md 97 | version prints latest git hash and date of maker 98 | 99 | Available variables: 100 | 101 | PKG/PKGDIR path to the target package (default is 'maker') 102 | MAKERRC path to the maker configuration file (default is '~/.makerrc') 103 | VIG vignettes be build (default is 1). If 0, build --no-build-vignettes is used 104 | WARNINGS_AS_ERRORS fail on warnings (default is 1) 105 | CRAN check using --as-cran (default is 0) 106 | COLOURS using colours for R CMD check results (default is 1) 107 | RPROFILE path to .Rprofile (default is ${MAKEDIR}/include/Rprofile) 108 | TIMEFORMAT time format (default: empty) 109 | 110 | Misc: 111 | 112 | Vignettes are not build when checking: R CMD check --no-build-vignettes 113 | 114 | win-builder build package and send to win-builder.r-project.org 115 | run-demos source and run demo/*.R files 116 | get-default-pkg print current default PKG 117 | set-default-pkg set new default PKG 118 | remove-default-pkg remove current default PKG 119 | setup-git-hooks setup git hooks 120 | 121 | Getting help: 122 | 123 | help target usage print this help text 124 | 125 | Create an issue on https://github.com/ComputationalProteomicsUnit/maker/issues/ or 126 | write an e-mail to Sebastian Gibb and Laurent Gatto . 127 | ``` 128 | 129 | ## Additional targets via external Makefile 130 | 131 | To add new project specific target to `maker`, you could create a 132 | `makefiles` directory in your main `maker` directory (defined as 133 | `${MAKERDIR}`) and add the following to your `~/.makerrc` configuration 134 | file: 135 | 136 | ADDMAKEFILESDIR := ${MAKERDIR}/makefiles/ 137 | include ${ADDMAKEFILESDIR}/Makefile.* 138 | 139 | to automatically include new Makefiles. See 140 | [issue 8](https://github.com/ComputationalProteomicsUnit/maker/issues/8) 141 | for a short discussion and an example. 142 | 143 | ## Configuration 144 | 145 | You could specify your own default variables in `~/.makerrc`. Please see, e.g. 146 | [.makerrc](.makerrc): 147 | 148 | ```basemake 149 | ## configuration Makefile for maker 150 | 151 | ## don't build vignettes 152 | VIG := 0 153 | 154 | ## always use --as-cran 155 | CRAN := 1 156 | ``` 157 | 158 | The `~/.makerrc` file is a Makefile as well. So you can use every 159 | supported Makefile command. 160 | 161 | See the 162 | [`Setting R_HOME`](https://github.com/ComputationalProteomicsUnit/maker/issues/11) 163 | issue to use multiple `R` installations with `maker`. 164 | 165 | ## More recipes 166 | 167 | See the [`RECIPES.md`](RECIPES.md) file for additional/contributed recipes. 168 | -------------------------------------------------------------------------------- /RECIPES.md: -------------------------------------------------------------------------------- 1 | # More `maker` recipes 2 | 3 | To use any of these contributed recipes, copy the relevant chunks 4 | into your `.makerrc` file or add new targets as described in the 5 | `README.md` file. 6 | 7 | 21 | 22 | ### R devel 23 | 24 | To switch easily between R stable and R devel you could use the following in 25 | your `.makerrc`: 26 | 27 | ```Makefile 28 | ifeq (${DEV},1) 29 | R_HOME := /opt/Rdevel 30 | endif 31 | ``` 32 | 33 | `make PKG=foo check` uses R stable and `make PKG=foo check DEV=1` R devel, 34 | respectively. 35 | 36 | ### Spell check 37 | 38 | We can use `tools::aspell_*` functions; in what follows we assume 39 | [aspell](http://aspell.net) to be installed. 40 | 41 | Main targets are `aspell-rd`, `aspell-vignette`, `aspell-r` and `aspell-c`: 42 | they provide access to `aspell_package_Rd_files`, 43 | `aspell_package_vignettes`, `aspell_package_R_files` and 44 | `aspell_package_C_files` respectively. A pager is used to display aspell 45 | output. 46 | 47 | Finally `aspell-all` does all the checks. 48 | 49 | ```Makefile 50 | # - - - - - 51 | # Variables 52 | # - - - - - 53 | 54 | MAKER_PAGER := less 55 | ASPELL_MASTER_DICT := en_US 56 | ASPELL_EXTRA_DICT := en_GB 57 | ASPELL_COMMAND_PRE := ${R} --vanilla --quiet -e "library(tools); 58 | ASPELL_COMMAND_POST := ('"$(PKG)"', control = c('--master="$(ASPELL_MASTER_DICT)"', '--add-extra-dicts="$(ASPELL_EXTRA_DICT)"'), dictionaries = Sys.glob(file.path(R.home('share'), 'dictionaries', '*.rds')))" 59 | ASPELL_RD_FUN := aspell_package_Rd_files 60 | ASPELL_VIGNETTE_FUN := aspell_package_vignettes 61 | ASPELL_C_FUN := aspell_package_C_files 62 | ASPELL_R_FUN := aspell_package_R_files 63 | ASPELL_RD_COMMAND := ${ASPELL_COMMAND_PRE}${ASPELL_RD_FUN}${ASPELL_COMMAND_POST} 64 | ASPELL_VIGNETTE_COMMAND := ${ASPELL_COMMAND_PRE}${ASPELL_VIGNETTE_FUN}${ASPELL_COMMAND_POST} 65 | ASPELL_C_COMMAND := ${ASPELL_COMMAND_PRE}${ASPELL_C_FUN}${ASPELL_COMMAND_POST} 66 | ASPELL_R_COMMAND := ${ASPELL_COMMAND_PRE}${ASPELL_R_FUN}${ASPELL_COMMAND_POST} 67 | 68 | # - - - - - 69 | # Targets 70 | # - - - - - 71 | 72 | .aspell-rd: 73 | ${ASPELL_RD_COMMAND} 74 | .aspell-vignette: 75 | ${ASPELL_VIGNETTE_COMMAND} 76 | .aspell-r: 77 | ${ASPELL_R_COMMAND} 78 | .aspell-c: 79 | ${ASPELL_C_COMMAND} 80 | 81 | aspell-rd: 82 | make .aspell-rd | ${MAKER_PAGER} 83 | aspell-vignette: 84 | make .aspell-vignette | $(MAKER_PAGER) 85 | aspell-r: 86 | make .aspell-r | $(MAKER_PAGER) 87 | aspell-c: 88 | make .aspell-c | $(MAKER_PAGER) 89 | 90 | aspell-all: 91 | (make .aspell-rd ; make .aspell-vignette; make .aspell-r; make .aspell-c) | $(MAKER_PAGER) 92 | 93 | ``` 94 | 95 | 96 | ### `codetools` check 97 | 98 | `check-codetools` target checks the package with `codetools::checkUsage` 99 | too. It's a check with the most rigorous functions code analysis 100 | (a NOTE is risen, false positive are possible, but can be anyhow useful). 101 | 102 | The user can set different options (variable `CODETOOLS_OPTION`) to choose 103 | what to check as a comma separated value pairs (eg `a=TRUE, b=FALSE`, more 104 | info 105 | [here](http://cran.r-project.org/doc/manuals/r-release/R-ints.html#Tools) 106 | and [here](http://stackoverflow.com/questions/10017702/)). 107 | 108 | By default, below all checks are performed. If the user set up 109 | `~/.R/check.Renviron` `CODETOOLS_OPTION` is ignored. 110 | 111 | 112 | ``` Makefile 113 | # - - - - - 114 | # Variables 115 | # - - - - - 116 | 117 | CODETOOLS_OPTIONS := "all=TRUE" 118 | 119 | # - - - - - 120 | # Targets 121 | # - - - - - 122 | 123 | check-codetools: 124 | export _R_CHECK_CODETOOLS_PROFILE_=$(CODETOOLS_OPTIONS) && make check PKG=$(PKG) 125 | 126 | ``` 127 | 128 | ### Lint with `lintr` 129 | lintr checks adherence to a given style, syntax errors and possible semantic issues 130 | 131 | ``` Makefile 132 | # - - - - - 133 | # Variables 134 | # - - - - - 135 | # linters are passed as a list of functions; see ?linters for a 136 | # full list of default and available linters. Below (eg, my settings) i use 137 | # the default linters without object_camel_case_linter 138 | 139 | # > names(default_linters) # (as of 2015-01-22) 140 | # [1] "assignment_linter" "single_quotes_linter" 141 | # [3] "absolute_paths_linter" "no_tab_linter" 142 | # [5] "line_length_linter" "commas_linter" 143 | # [7] "infix_spaces_linter" "spaces_left_parentheses_linter" 144 | # [9] "spaces_inside_linter" "open_curly_linter" 145 | # [11] "closed_curly_linter" "object_camel_case_linter" 146 | # [13] "object_multiple_dots_linter" "object_length_linter" 147 | # [15] "object_usage_linter" "trailing_whitespace_linter" 148 | # [17] "trailing_blank_lines_linter" 149 | 150 | LINTR_LINTERS = default_linters[-12] 151 | 152 | # - - - - - 153 | # Targets 154 | # - - - - - 155 | 156 | lint: 157 | ${R} -e "library(lintr); lint_package('"$(PKGDIR)"', linters = $(LINTR_LINTERS), relative_path = FALSE)" 158 | 159 | ``` 160 | 161 | 162 | ### Coverage report with `covr` 163 | 164 | ``` Makefile 165 | 166 | # - - - - - 167 | # Targets 168 | # - - - - - 169 | covr: 170 | ${R} -e "library(covr); package_coverage('"$(PKGDIR)"')" 171 | 172 | ``` 173 | 174 | 175 | 176 | ### Further documenting targets 177 | 178 | `devtools::document` targets and `clean` option for both 179 | `roxygen::roxygenize` and `devtools::document`. 180 | 181 | ``` Makefile 182 | # - - - - - 183 | # Targets 184 | # - - - - - 185 | 186 | document: clean 187 | ${R} -e "library(devtools); document('"$(PKG)"')"; 188 | document-rd: clean 189 | ${R} -e "library(devtools); document('"$(PKG)"', roclets='rd')"; 190 | 191 | ``` 192 | 193 | 194 | ### Continuous Integration with GitHub 195 | 196 | `ci-add-travis` and `ci-add-appveyor` can be useful for adding continuous 197 | integration with [r-travis](https://github.com/craigcitro/r-travis) and 198 | [r-appveyor](https://github.com/krlmlr/r-appveyor). 199 | 200 | ``` Makefile 201 | # - - - - - 202 | # Variables 203 | # - - - - - 204 | 205 | GITHUB_USER := yourUsernameHere# 206 | 207 | # - - - - - 208 | # Targets 209 | # - - - - - 210 | 211 | .travis: 212 | wget https://raw.githubusercontent.com/craigcitro/r-travis/master/sample.travis.yml -O $(PKG)/.travis.yml 213 | 214 | ci-add-travis: .travis 215 | echo "[![Build Status](https://travis-ci.org/$(GITHUB_USER)/$(PKG).svg)](https://travis-ci.org/$(GITHUB_USER)/$(PKG))" >> $(PKG)/README.md 216 | echo '^\.travis\.yml' >> $(PKG)/.Rbuildignore 217 | 218 | .appveyor: 219 | wget https://raw.githubusercontent.com/krlmlr/r-appveyor/master/sample.appveyor.yml -O $(PKG)/appveyor.yml 220 | wget https://raw.githubusercontent.com/krlmlr/r-appveyor/master/.gitattributes -O $(PKG)/.gitattributes 221 | 222 | ci-add-appveyor: .appveyor 223 | echo '^appveyor\.yml' >> $(PKG)/.Rbuildignore 224 | @ echo ; 225 | @ echo " Now you can add a badge to your README.md " ; 226 | @ echo " Go to https://ci.appveyor.com/project/$(GITHUB_USER)/$(PKG)/settings/badges " ; 227 | @ echo ; 228 | 229 | ``` 230 | -------------------------------------------------------------------------------- /hooks/pre-commit-READMERmd.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | if [[ README.Rmd -nt README.md ]]; then 3 | echo "README.md is out of date; please re-knit README.Rmd" 4 | exit 1 5 | fi 6 | -------------------------------------------------------------------------------- /hooks/pre-commit-newsmd.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | REPOURL=$(git config --get remote.origin.url | sed 's/^.*git@github.com:/https:\/\/github.com\//; s/.git$/\/issues\//g; s/\//\\\//g') 3 | 4 | # Replace #XXX issue numbers by [#XXX](https://github.com/lgatto/MSnbase/issues/XXX 5 | sed -i '/\(^\| \)#[0-9]\+[^]]\?/{s/#\([0-9]\+\)/[#\1]('${REPOURL}'\1)/g;h};${x;/./{x;q1};x;q0}' NEWS.md 6 | ## explanation: 7 | ## sed -i (in place replacement) 8 | ## /#[0-9]\+[^]]/ search for issues #XXX at the beginning of a line or after a space 9 | ## and apply the substition command just to this numbers 10 | ## {s/#\([0-9]\+\)/[#\1](https:\/\/github.com\/lgatto\/MSnbase\/issues\/\1)/g;} 11 | ## build the link 12 | ## "h" copy the result into the "hold space" (initial empty) 13 | ## ${x;/./{x;q1};x;q0} when add the end of file "$", swap "hold" and "pattern" 14 | ## space via "x", if now anything was found in the "pattern" space "/./" swap 15 | ## again and return 1 (q1); if nothing was found also swap and return 0 (q0) 16 | 17 | if [[ $? -ne 0 ]]; then 18 | echo "Issue link in NEWS.md was modified by '$(basename ${0})' hook; please review and recommit" 19 | exit 1 20 | fi 21 | -------------------------------------------------------------------------------- /hooks/setup-hooks.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | if [[ ! -d "${1}" ]] ; then 3 | echo "Directory ${1} doesn't exist!" 4 | exit 1 5 | fi 6 | 7 | GITHOOKDIR="${1}/.git/hooks" 8 | PRECOMMIT="${GITHOOKDIR}/pre-commit" 9 | MAKERHOOKDIR="$(dirname $(readlink -f ${0}))" 10 | 11 | if [[ ! -f "${PRECOMMIT}" ]] ; then 12 | touch ${PRECOMMIT} 13 | chmod +x ${PRECOMMIT} 14 | fi 15 | 16 | for h in ${MAKERHOOKDIR}/pre-commit*; do 17 | grep "${h}" "${PRECOMMIT}" || echo "${h} || exit 1" >> "${PRECOMMIT}" 18 | done 19 | -------------------------------------------------------------------------------- /include/Rprofile: -------------------------------------------------------------------------------- 1 | repos <- structure(c(CRAN="http://cran.at.r-project.org")) 2 | options(repos=repos) 3 | rm(repos) 4 | -------------------------------------------------------------------------------- /include/check-reverse-dependencies.R: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env Rscript --vanilla 2 | 3 | library("devtools") 4 | 5 | res <- revdep_check() 6 | l <- sapply(res, length) 7 | 8 | if (any(l != 0)) { 9 | stop("Check for ", paste0(names(res)[l], collapse=", "), " failed!") 10 | } 11 | 12 | message("everything fine") 13 | -------------------------------------------------------------------------------- /include/color-output.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | RED="\x1b[31;01m" 4 | GREEN="\x1b[30;01m" 5 | BLUE="\x1b[34;01m" 6 | YELLOW="\x1b[33;01m" 7 | CYAN="\x1b[1;36m" 8 | NOCOLOUR="\x1b[0m" 9 | 10 | if [ ${COLOURS} -eq 1 ] ; then 11 | sed 's#^.*NOTE.*$#'${YELLOW}'&'${NOCOLOUR}'#g; 12 | s#^.*CONSIDER.*$#'${CYAN}'&'${NOCOLOUR}'#g; 13 | s#^.*SKIPPED*$#'${BLUE}'&'${NOCOLOUR}'#g; 14 | s#^.*WARNING.*$#'${RED}'&'${NOCOLOUR}'#g; 15 | s#^.*RECOMMENDED.*$#'${RED}'&'${NOCOLOUR}'#g; 16 | s#^.*REQUIRED.*$#'${RED}'&'${NOCOLOUR}'#g; 17 | s#^.*ERROR.*$#'${RED}'&'${NOCOLOUR}'#g; 18 | s#^.*time: *\([3-9][0-9][0-9]\|[0-9]\{4,\}\)\.[0-9]\+.*$#'${RED}'& (check time should be < 5 min)'${NOCOLOUR}'#g;' 19 | else 20 | cat 21 | fi 22 | 23 | -------------------------------------------------------------------------------- /include/increment-version.R: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env Rscript --vanilla 2 | 3 | arg <- match.arg(commandArgs(TRUE), c("major", "minor", "patch")) 4 | 5 | dcf <- read.dcf("DESCRIPTION") 6 | 7 | version <- dcf[, "Version"] 8 | version <- as.numeric(strsplit(version, "\\.")[[1L]][1L:3L]) 9 | if (arg == "major") { 10 | version <- c(version[1L]+1L, 11 | 0L, 12 | NA) 13 | } else if (arg == "minor") { 14 | version <- c(version[1L], 15 | version[2L]+1L, 16 | NA) 17 | } else if (arg == "patch") { 18 | version <- c(version[1L], 19 | version[2L], 20 | ifelse(is.na(version[3]), 1L, version[3]+1L)) 21 | } 22 | 23 | dcf[, "Version"] <- paste(na.omit(version), collapse=".") 24 | 25 | curDate <- format(Sys.time(), "%Y-%m-%d") 26 | 27 | if ("Date" %in% colnames(dcf)) { 28 | dcf[, "Date"] <- curDate 29 | } else { 30 | dcf <- cbind(dcf, Date=curDate) 31 | } 32 | 33 | write.dcf(dcf, "DESCRIPTION") 34 | 35 | message("New version of ", dcf[, "Package"], " is ", dcf[, "Version"], 36 | " (release date updated to ", dcf[, "Date"], ")") 37 | 38 | -------------------------------------------------------------------------------- /include/install-dependencies.R: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env Rscript --vanilla 2 | 3 | library("devtools") 4 | 5 | deps <- as.package(".")[c("imports", "depends", "suggests", "linkingto")] 6 | deps <- deps[!is.na(names(deps))] 7 | deps <- lapply(deps, function(x)parse_deps(x)[, c("name", "version")]) 8 | deps <- do.call(rbind, deps) 9 | 10 | installed <- installed.packages(fields=c("Package", "Version"))[, c("Package", "Version")] 11 | 12 | deps$installed <- installed[, "Version"][match(deps$name, installed[, "Package"], nomatch=NA_character_)] 13 | 14 | install <- is.na(deps$installed) | 15 | (!is.na(deps$version) && 16 | package_version(deps$version) > package_version(deps$installed)) 17 | 18 | if (any(install)) { 19 | source("http://bioconductor.org/biocLite.R") 20 | biocLite(deps$name[install], ask = FALSE) 21 | } 22 | 23 | -------------------------------------------------------------------------------- /include/run-demos.R: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env Rscript --vanilla 2 | 3 | library("devtools") 4 | 5 | rundemos <- function() { 6 | wd <- getwd() 7 | on.exit(setwd(wd)) 8 | setwd(tempdir()) 9 | files <- list.files(file.path(wd, "demo/"), 10 | pattern="^.*\\.R$", 11 | full.names=TRUE) 12 | invisible(lapply(files, function(x) { 13 | message(basename(x)) 14 | source(x) 15 | })) 16 | } 17 | 18 | load_all(".") 19 | rundemos() 20 | 21 | --------------------------------------------------------------------------------