Revision 8161194d68665648b93389adb333e741ba230497 authored by Mohammad Akhlaghi on 22 May 2023, 22:44:20 UTC, committed by Mohammad Akhlaghi on 23 May 2023, 06:42:11 UTC
SUMMARY: no change is necessary in your project, unless you use the Fortran features of WCSLIB in your project. Until now, there were two compilation failures on recent macOS computers with an M1 CPU: Less would crash because it couldn't find the relevant PCRE (perl-compatible regular expression) libraries and WCSLIB would crash because the LLVM compiler's Fortran features could not be built. With this commit, both issues have been fixed by disabling the relevant feature. Extensive comments have been placed in both places in case your project needs these features, so please see the comments in the relevant part of 'reproduce/software/make/basic.mk' for Less and 'reproduce/software/make/high-level.mk' for WCSLIB. In fact the previous solution (where we would not have Fortran features in WCSLIB on macOS systems was problematic and non-reproducibile (the features of WCSLIB depended on the operating system!). Another minor change was that for macOS, we now directly use the version-string of WCSLIB to fix the internal linking issue there. As a result, WCSLIB is no longer a "Version-dependent build" software (in 'reproduce/software/config/versions.conf'). Recall that these are software that when changing the version, it is also necessary to inspect their build recipe. These two issues and their fix were discovered and fixed with the help of James Robinson.
1 parent 644a236
r-cran.mk
# 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) 2022-2023 Boud Roukema <boud@cosmo.torun.pl>
# Copyright (C) 2022-2023 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))
Computing file changes ...
