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Diffstat (limited to 'reproduce/software/make/r-cran.mk')
| -rw-r--r-- | reproduce/software/make/r-cran.mk | 487 |
1 files changed, 487 insertions, 0 deletions
diff --git a/reproduce/software/make/r-cran.mk b/reproduce/software/make/r-cran.mk new file mode 100644 index 0000000..617b8de --- /dev/null +++ b/reproduce/software/make/r-cran.mk @@ -0,0 +1,487 @@ +# Build the project's R (here called R-CRAN) dependencies. +# +# ------------------------------------------------------------------------ +# !!!!! IMPORTANT NOTES !!!!! +# +# This Makefile will be loaded into 'high-level.mk', which is called by the +# './project configure' script. It is not included into the project +# afterwards. +# +# This Makefile contains instructions to build all the R-CRAN-related +# software within the project. +# +# ------------------------------------------------------------------------ +# +# Copyright (C) 2022 Boud Roukema <boud@cosmo.torun.pl> +# Copyright (C) 2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# +# This Makefile 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 3 of the License, or +# (at your option) any later version. +# +# This Makefile 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 Makefile. If not, see <http://www.gnu.org/licenses/>. + + + + + +# BUGS/IMPROVEMENTS +# ----------------- +# +# As of 2021-06-20, the R system is still very new and has not yet +# been tested on non-Debian-derived systems. Please provide bug +# reports ( https://savannah.nongnu.org/task/?15772 ) or propose fixes +# as git pull requests on a public git server (e.g. on a fork of +# https://codeberg.org/boud/maneage_dev ). + + + + + +# R-CRAN enviroment +# ----------------- +# +# It may be necessary to override host-level R-related environment +# variables that interfere with the Maneage-installed R system. +# systems which might interfere. + +# Ideas for which environment variables might create problems +# and might need to be set to be empty here: +# +# https://stat.ethz.ch/R-manual/R-devel/library/base/html/EnvVar.html + +# These first variables should be set automatically when R starts: +#export R_HOME := $(idir)/lib/R +#export R_INCLUDE_DIR := $(idir)/lib/R/include + + + + + +# R-CRAN-specific installation directories. +r-cran-major-version = $(shell echo $(r-cran-version) \ + | awk 'BEGIN{FS="."} \ + {printf "%d.%d\n", $$1, $$2}') + + + + + +# R-CRAN-specific build rules for 'make' +# ====================================== + +# Double-check an already downloaded R source +# ------------------------------------------- +# +# Check that the tarball with the version in +# 'reproduce/software/conf/versions.conf' has the sha512sum (checksum) +# stated 'reproduce/software/conf/checksums.conf'. This does not do any +# security checks; it only checks that the source file package is the one +# that is expected the last time that someone updated these two files for +# the R package of interest. +# +# Calculate the checksum and exit with a non-zero error code if there's a +# mismatch, after informing the user. +# +# Arguments: +# 1: The expected checksum of the tarball. +# +# Necessary shell variables +# 'tarball': This is the name of the actual tarball file without a +# directory. +double-check-R-source = final=$(tdir)/$$tarball; \ + exp_checksum="$(strip $(1))"; \ + if [ x"$$exp_checksum" = x"NO-CHECK-SUM" ]; then \ + result=0; \ + else \ + if type sha512sum > /dev/null 2>/dev/null; then \ + checksum=$$(sha512sum "$$final" | awk '{print $$1}'); \ + if [ x"$$checksum" = x"$$exp_checksum" ]; then \ + result=0; \ + else \ + echo "ERROR: Non-matching checksum: $$final"; \ + echo "Checksum should be: $$exp_checksum"; \ + echo "Checksum is: $$checksum"; \ + result=1; \ + exit 1; \ + fi; \ + else \ + echo "ERROR: sha512sum is unavailable."; \ + exit 1; \ + fi; \ + fi + +# Default 'make' build rules for an CRAN package +# ----------------------------------------------- +# +# The default 'install.packages' function of R only recognizes 'tar.gz' +# tarballs. But Maneage uses '.tar.lz' format for its archival. So to be +# agnostic to the compression algorithm, we will be using 'tar' externally +# (before entering R), then give the un-compressed directory to +# 'install.packages'. +# +# Parameters: +# 1. package name (without 'r-cran', without the version string) +# 2. version string +# 3. checksum of the package +r_cran_build = \ + pkg=$(strip $(1)); \ + version=$(strip $(2)); \ + checksum=$(strip $(3)); \ + $(call import-source, \ + https://cran.r-project.org/src/contrib, \ + $$checksum, \ + $$tarball, \ + https://cran.r-project.org/src/contrib/00Archive/$$pkg); \ + cd "$(ddir)"; \ + tar -xf $(tdir)/$$tarball; \ + unpackdir=$$pkg-$$version; \ + (printf "install.packages(c(\"$(ddir)/$$unpackdir\"),"; \ + printf 'lib="$(ilibrcrandir)",'; \ + printf 'repos=NULL,'; \ + printf 'type="source")\n'; \ + printf 'quit()\n'; \ + printf 'n\n') | R --no-save; \ + rm -rf $$unpackdir; \ + if [ $$pkg = r-pkgconfig ]; then iname=pkgconfig; \ + else iname=$$pkg; fi; \ + if [ -e "$(ilibrcrandir)"/$$iname/Meta/nsInfo.rds ]; then \ + $(call double-check-R-source, $$checksum) \ + && echo "$$pkg $$version" > $@; \ + else \ + printf "r-cran-$$pkg failed: Meta/nsInfo.rds missing.\n"; \ + exit 1; \ + fi + + + + + +# Necessary programs and libraries +# -------------------------------- +# +# While this Makefile is for R programs, in some cases, we need certain +# programs (like R itself), or libraries for the modules. Comment on +# building R without GUI support ('--without-tcltlk') +# +# Tcl/Tk are a set of tools to provide Graphic User Interface (GUI) support +# in some software. But they are not yet natively built within Maneage, +# primarily because we have higher-priority work right now (if anyone is +# interested, they can ofcourse contribute!). GUI tools in general aren't +# high on our priority list right now because they are generally good for +# human interaction (which is contrary to the reproducible philosophy: +# there will always be human-error and frustration, for example in GUI +# tools the best level of reproducibility is statements like this: "move +# your mouse to button XXX, then click on menu YYY and etc"). A robust +# reproducible solution must be done automatically. +# +# If someone wants to use R's GUI functionalities while investigating for +# their analysis, they can do the GUI part on their host OS +# implementation. Later, they can bring the finalized source into Maneage +# to be automatically run in Maneage. This will also be the recommended way +# to deal with GUI tools later when we do install them within Maneage. +$(ibidir)/r-cran-$(r-cran-version): \ + $(itidir)/texlive \ + $(ibidir)/icu-$(icu-version) \ + $(ibidir)/pcre-$(pcre-version) \ + $(ibidir)/cairo-$(cairo-version) \ + $(ibidir)/libpng-$(libpng-version) \ + $(ibidir)/libjpeg-$(libjpeg-version) \ + $(ibidir)/libtiff-$(libtiff-version) \ + $(ibidir)/libpaper-$(libpaper-version) + +# Prepare the tarball, unpack it and enter the directory. + tarball=R-$(r-cran-version).tar.lz + $(call import-source, $(r-cran-url), $(r-cran-checksum)) + cd $(ddir) + tar -xf $(tdir)/$$tarball + unpackdir=R-$(r-cran-version) + cd $$unpackdir + +# We need to manually remove the lines with '~autodetect~', they +# cause the configure script to crash in version 4.0.2. They are used +# in relation to Java, and we don't use Java anyway. + sed -i -e '/\~autodetect\~/ s/^/#/g' configure + export R_SHELL=$(SHELL) + ./configure --prefix=$(idir) \ + --without-x \ + --with-pcre1 \ + --disable-java \ + --with-readline \ + --without-tcltk \ + --disable-openmp + make -j$(numthreads) + make install + cd .. + rm -rf R-$(r-cran-version) + cp -p $(dtexdir)/r-cran.tex $(ictdir)/ + echo "R $(r-cran-version) \citep{RIhakaGentleman1996}" > $@ + + + + + +# Non-Maneage'd tarballs +# ---------------------- +# +# CRAN tarballs differ in two aspects from Maneage'd tarballs: +# - CRAN uses '.tar.gz', while Maneage uses 'tar.lz'. +# - CRAN uses 'name_version', while Maneage uses 'name-version'. +# +# So if you add a new R package, or update the version of an existing one +# (that is not yet in Maneage's archive), you need to use the CRAN naming +# format for the 'tarball' variable. + + + + + +# R-CRAN modules +# --------------- +# +# The rules for downloading, compiling and installing any R-CRAN modules +# that are needed should be provided here. Each target (before the colon) +# is first shown with its dependence on prerequisites (which are listed +# after the colon. The default macro 'r_cran_build' will install the +# package without checking on dependencies. + +$(ircrandir)/r-cran-cli-$(r-cran-cli-version): \ + $(ibidir)/r-cran-$(r-cran-version) \ + $(ircrandir)/r-cran-glue-$(r-cran-glue-version) + tarball=cli-$(r-cran-cli-version).tar.lz + $(call r_cran_build, cli, $(r-cran-cli-version), \ + $(r-cran-cli-checksum)) + +$(ircrandir)/r-cran-colorspace-$(r-cran-colorspace-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=colorspace-$(r-cran-colorspace-version).tar.lz + $(call r_cran_build, colorspace, $(r-cran-colorspace-version), \ + $(r-cran-colorspace-checksum)) + +$(ircrandir)/r-cran-cowplot-$(r-cran-cowplot-version): \ + $(ibidir)/r-cran-$(r-cran-version) \ + $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \ + $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version) \ + $(ircrandir)/r-cran-scales-$(r-cran-scales-version) \ + $(ircrandir)/r-cran-ggplot2-$(r-cran-ggplot2-version) + tarball=cowplot-$(r-cran-cowplot-version).tar.lz + $(call r_cran_build, cowplot, $(r-cran-cowplot-version), \ + $(r-cran-cowplot-checksum)) + +$(ircrandir)/r-cran-crayon-$(r-cran-crayon-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=crayon-$(r-cran-crayon-version).tar.lz + $(call r_cran_build, crayon, $(r-cran-crayon-version), \ + $(r-cran-crayon-checksum)) + +$(ircrandir)/r-cran-digest-$(r-cran-digest-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=digest-$(r-cran-digest-version).tar.lz + $(call r_cran_build, digest, $(r-cran-digest-version), \ + $(r-cran-digest-checksum)) + +$(ircrandir)/r-cran-farver-$(r-cran-farver-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=farver-$(r-cran-farver-version).tar.lz + $(call r_cran_build, farver, $(r-cran-farver-version), \ + $(r-cran-farver-checksum)) + +$(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version): \ + $(ibidir)/r-cran-$(r-cran-version) \ + $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) + tarball=ellipsis-$(r-cran-ellipsis-version).tar.lz + $(call r_cran_build, ellipsis, $(r-cran-ellipsis-version), \ + $(r-cran-ellipsis-checksum)) + +$(ircrandir)/r-cran-fansi-$(r-cran-fansi-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=fansi-$(r-cran-fansi-version).tar.lz + $(call r_cran_build, fansi, $(r-cran-fansi-version), \ + $(r-cran-fansi-checksum)) + +$(ircrandir)/r-cran-ggplot2-$(r-cran-ggplot2-version): \ + $(ibidir)/r-cran-$(r-cran-version) \ + $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \ + $(ircrandir)/r-cran-mgcv-$(r-cran-mgcv-version) \ + $(ircrandir)/r-cran-MASS-$(r-cran-MASS-version) \ + $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \ + $(ircrandir)/r-cran-withr-$(r-cran-withr-version) \ + $(ircrandir)/r-cran-digest-$(r-cran-digest-version) \ + $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version) \ + $(ircrandir)/r-cran-scales-$(r-cran-scales-version) \ + $(ircrandir)/r-cran-tibble-$(r-cran-tibble-version) \ + $(ircrandir)/r-cran-isoband-$(r-cran-isoband-version) + tarball=ggplot2-$(r-cran-ggplot2-version).tar.lz + $(call r_cran_build, ggplot2, $(r-cran-ggplot2-version), \ + $(r-cran-ggplot2-checksum)) + +$(ircrandir)/r-cran-glue-$(r-cran-glue-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=glue-$(r-cran-glue-version).tar.lz + $(call r_cran_build, glue, $(r-cran-glue-version), \ + $(r-cran-glue-checksum)) + +$(ircrandir)/r-cran-gridExtra-$(r-cran-gridExtra-version): \ + $(ibidir)/r-cran-$(r-cran-version) \ + $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version) + tarball=gridExtra-$(r-cran-gridExtra-version).tar.lz + $(call r_cran_build, gridExtra, $(r-cran-gridExtra-version), \ + $(r-cran-gridExtra-checksum)) + +$(ircrandir)/r-cran-gtable-$(r-cran-gtable-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=gtable-$(r-cran-gtable-version).tar.lz + $(call r_cran_build, gtable, $(r-cran-gtable-version), \ + $(r-cran-gtable-checksum)) + +$(ircrandir)/r-cran-isoband-$(r-cran-isoband-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=isoband-$(r-cran-isoband-version).tar.lz + $(call r_cran_build, isoband, $(r-cran-isoband-version), \ + $(r-cran-isoband-checksum)) + +$(ircrandir)/r-cran-labeling-$(r-cran-labeling-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=labeling-$(r-cran-labeling-version).tar.lz + $(call r_cran_build, labeling, $(r-cran-labeling-version), \ + $(r-cran-labeling-checksum)) + +$(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version): \ + $(ibidir)/r-cran-$(r-cran-version) \ + $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \ + $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) + tarball=lifecycle-$(r-cran-lifecycle-version).tar.lz + $(call r_cran_build, lifecycle, $(r-cran-lifecycle-version), \ + $(r-cran-lifecycle-checksum)) + +$(ircrandir)/r-cran-magrittr-$(r-cran-magrittr-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=magrittr-$(r-cran-magrittr-version).tar.lz + $(call r_cran_build, magrittr, $(r-cran-magrittr-version), \ + $(r-cran-magrittr-checksum)) + +$(ircrandir)/r-cran-MASS-$(r-cran-MASS-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=MASS-$(r-cran-MASS-version).tar.lz + $(call r_cran_build, MASS, $(r-cran-MASS-version), \ + $(r-cran-MASS-checksum)) + +# The base R-2.0.4 install includes nlme and Matrix. +# https://cran.r-project.org/web/packages/mgcv/index.html +$(ircrandir)/r-cran-mgcv-$(r-cran-mgcv-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=mgcv-$(r-cran-mgcv-version).tar.lz + $(call r_cran_build, mgcv, $(r-cran-mgcv-version), \ + $(r-cran-mgcv-checksum)) + +$(ircrandir)/r-cran-munsell-$(r-cran-munsell-version): \ + $(ibidir)/r-cran-$(r-cran-version) \ + $(ircrandir)/r-cran-colorspace-$(r-cran-colorspace-version) + tarball=munsell-$(r-cran-munsell-version).tar.lz + $(call r_cran_build, munsell, $(r-cran-munsell-version), \ + $(r-cran-munsell-checksum)) + +#TODO: https://cran.r-project.org/web/packages/pillar/index.html +$(ircrandir)/r-cran-pillar-$(r-cran-pillar-version): \ + $(ibidir)/r-cran-$(r-cran-version) \ + $(ircrandir)/r-cran-cli-$(r-cran-cli-version) \ + $(ircrandir)/r-cran-utf8-$(r-cran-utf8-version) \ + $(ircrandir)/r-cran-fansi-$(r-cran-fansi-version) \ + $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \ + $(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version) \ + $(ircrandir)/r-cran-crayon-$(r-cran-crayon-version) \ + $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version) \ + $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version) + tarball=pillar-$(r-cran-pillar-version).tar.lz + $(call r_cran_build, pillar, $(r-cran-pillar-version), \ + $(r-cran-pillar-checksum)) + +# Since we have other software packages with the name 'pkgconfig', to avoid +# confusion with those tarballs, we have put a 'r-' prefix in the tarball +# name. If you want to use the CRAN tarball, please correct the name +# accordingly (as described in the comment above this group of rules). +$(ircrandir)/r-cran-pkgconfig-$(r-cran-pkgconfig-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=r-pkgconfig-$(r-cran-pkgconfig-version).tar.lz + $(call r_cran_build, r-pkgconfig, $(r-cran-pkgconfig-version), \ + $(r-cran-pkgconfig-checksum)) + +$(ircrandir)/r-cran-RColorBrewer-$(r-cran-RColorBrewer-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=RColorBrewer-$(r-cran-RColorBrewer-version).tar.lz + $(call r_cran_build, RColorBrewer, $(r-cran-RColorBrewer-version), \ + $(r-cran-RColorBrewer-checksum)) + +$(ircrandir)/r-cran-R6-$(r-cran-R6-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=R6-$(r-cran-R6-version).tar.lz + $(call r_cran_build, R6, $(r-cran-R6-version), $(r-cran-R6-checksum)) + +$(ircrandir)/r-cran-rlang-$(r-cran-rlang-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=rlang-$(r-cran-rlang-version).tar.lz + $(call r_cran_build, rlang, $(r-cran-rlang-version), \ + $(r-cran-rlang-checksum)) + +# https://cran.r-project.org/web/packages/scales/index.html +$(ircrandir)/r-cran-scales-$(r-cran-scales-version): \ + $(ibidir)/r-cran-$(r-cran-version) \ + $(ircrandir)/r-cran-R6-$(r-cran-R6-version) \ + $(ircrandir)/r-cran-farver-$(r-cran-farver-version) \ + $(ircrandir)/r-cran-munsell-$(r-cran-munsell-version) \ + $(ircrandir)/r-cran-labeling-$(r-cran-labeling-version) \ + $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version) \ + $(ircrandir)/r-cran-viridisLite-$(r-cran-viridisLite-version) \ + $(ircrandir)/r-cran-RColorBrewer-$(r-cran-RColorBrewer-version) + tarball=scales-$(r-cran-scales-version).tar.lz + $(call r_cran_build, scales, $(r-cran-scales-version), \ + $(r-cran-scales-checksum)) + +#https://cran.r-project.org/web/packages/tibble/index.html +$(ircrandir)/r-cran-tibble-$(r-cran-tibble-version): \ + $(ibidir)/r-cran-$(r-cran-version) \ + $(ircrandir)/r-cran-fansi-$(r-cran-fansi-version) \ + $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \ + $(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version) \ + $(ircrandir)/r-cran-pillar-$(r-cran-pillar-version) \ + $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version) \ + $(ircrandir)/r-cran-magrittr-$(r-cran-magrittr-version) \ + $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version) \ + $(ircrandir)/r-cran-pkgconfig-$(r-cran-pkgconfig-version) + tarball=tibble-$(r-cran-tibble-version).tar.lz + $(call r_cran_build, tibble, $(r-cran-tibble-version), \ + $(r-cran-tibble-checksum)) + +$(ircrandir)/r-cran-utf8-$(r-cran-utf8-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=utf8-$(r-cran-utf8-version).tar.lz + $(call r_cran_build, utf8, $(r-cran-utf8-version), \ + $(r-cran-utf8-checksum)) + +$(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version): \ + $(ibidir)/r-cran-$(r-cran-version) \ + $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \ + $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \ + $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version) + tarball=vctrs-$(r-cran-vctrs-version).tar.lz + $(call r_cran_build, vctrs, $(r-cran-vctrs-version), \ + $(r-cran-vctrs-checksum)) + +$(ircrandir)/r-cran-viridisLite-$(r-cran-viridisLite-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=viridisLite-$(r-cran-viridisLite-version).tar.lz + $(call r_cran_build, viridisLite, $(r-cran-viridisLite-version), \ + $(r-cran-viridisLite-checksum)) + +$(ircrandir)/r-cran-withr-$(r-cran-withr-version): \ + $(ibidir)/r-cran-$(r-cran-version) + tarball=withr-$(r-cran-withr-version).tar.lz + $(call r_cran_build, withr, $(r-cran-withr-version), \ + $(r-cran-withr-checksum)) |