diff options
| -rw-r--r-- | README-hacking.md | 15 | ||||
| -rwxr-xr-x | reproduce/analysis/bash/download-multi-try.sh | 59 | ||||
| -rw-r--r-- | reproduce/analysis/make/initialize.mk | 41 | ||||
| -rw-r--r-- | reproduce/analysis/make/top-prepare.mk | 6 | ||||
| -rw-r--r-- | reproduce/software/config/checksums.conf | 3 | ||||
| -rw-r--r-- | reproduce/software/config/servers-backup.conf | 2 | ||||
| -rw-r--r-- | reproduce/software/config/urls.conf | 1 | ||||
| -rw-r--r-- | reproduce/software/config/versions.conf | 8 | ||||
| -rw-r--r-- | reproduce/software/make/basic.mk | 102 | ||||
| -rw-r--r-- | reproduce/software/make/high-level.mk | 61 | ||||
| -rwxr-xr-x | reproduce/software/shell/apptainer.sh | 2 | ||||
| -rwxr-xr-x | reproduce/software/shell/configure.sh | 86 | ||||
| -rwxr-xr-x | reproduce/software/shell/pre-make-build.sh | 18 |
13 files changed, 254 insertions, 150 deletions
diff --git a/README-hacking.md b/README-hacking.md index 6d02976..dc6e623 100644 --- a/README-hacking.md +++ b/README-hacking.md @@ -187,9 +187,9 @@ information like title, DOI and etc, in a unified format (independent of which journal the paper is published in). - Eskandarlou et - al. ([2026](https://scixplorer.org/abs/2026arXiv260322166E), A&A - accepted; - arXiv:[2603.22166](https://arxiv.org/abs/2510.2603.22166)). The + al. ([2026](https://scixplorer.org/abs/2026A%26A...709A.210E), A&A + Volume 709, id.A210, 17 pp; + arXiv:[2603.22166](https://arxiv.org/abs/2603.22166)). The project's version controlled source is on [Gitlab](https://gitlab.com/sepideh.esk/alba), necessary software, outputs and backup of history are available at @@ -1894,6 +1894,15 @@ this section, the development workflow is described: when making a commit should be written as comments within the source (to be preserved during the squash) and not in the commit message. + - Checklist for the maintainer: + + - Make sure all contributors are properly acknowledged. + + - The final commit amend (done to edit the final text of the commit + message) should be like this: `git commit --amend --date=now`. This + helps have a date on the commit that matches the merge (independent of + which development commit was squashed first). + diff --git a/reproduce/analysis/bash/download-multi-try.sh b/reproduce/analysis/bash/download-multi-try.sh index 16950b5..5cc5407 100755 --- a/reproduce/analysis/bash/download-multi-try.sh +++ b/reproduce/analysis/bash/download-multi-try.sh @@ -90,6 +90,37 @@ urlfile=$(echo "$inurl" | awk -F "/" '{print $NF}') +# Function for downloading +download_func () { + + # Set the arguments. + inurl="$1" + + # Attempt downloading the file. Note that the 'downloader' ends with + # the respective option to specify the output name. For example "wget + # -O" (so 'outname', that comes after it) will be the name of the + # downloaded file. + if [ x"$lockfile" = xnolock ]; then + if ! $downloader $outname $inurl; then rm -f $outname; fi + else + flock "$lockfile" sh -c \ + "if ! $downloader $outname \"$inurl\"; then rm -f $outname; fi" + fi + + # Some servers return HTTP 4xx/5xx errors as an HTML page with a 200 + # status, so the downloader exits 0 and saves the HTML body to disk. + # Detect this by checking whether the response starts with an HTML tag + # and treat it as a failed download so backup servers will be tried. + if [ -f "$outname" ] \ + && head -c 500 "$outname" 2>/dev/null | grep -qi '<html'; then + rm -f "$outname" + fi +} + + + + + # Try downloading multiple times before crashing. counter=0 maxcounter=10 @@ -119,30 +150,22 @@ while [ ! -f "$outname" ]; do sleep $tstep fi - # Attempt downloading the file. Note that the 'downloader' ends with - # the respective option to specify the output name. For example "wget - # -O" (so 'outname', that comes after it) will be the name of the - # downloaded file. - if [ x"$lockfile" = xnolock ]; then - if ! $downloader $outname $inurl; then rm -f $outname; fi - else - # Try downloading from the requested URL. - flock "$lockfile" sh -c \ - "if ! $downloader $outname \"$inurl\"; then rm -f $outname; fi" - fi + # First attempt at the download. + download_func "$inurl" # If the download failed, try the backup server(s). if [ ! -f "$outname" ]; then if [ x"$backupservers" != x ]; then for bs in $backupservers; do - # Use this backup server. - if [ x"$lockfile" = xnolock ]; then - if ! $downloader $outname $bs/$urlfile; then rm -f $outname; fi - else - flock "$lockfile" sh -c \ - "if ! $downloader $outname $bs/$urlfile; then rm -f $outname; fi" - fi + # For Zenodo backup servers, append '?download=1' as well. + bsurl="$bs/$urlfile" + case "$bsurl" in + *zenodo.org*) bsurl="${bsurl}?download=1" ;; + esac + + # Download the file. + download_func "$bsurl" # If the file was downloaded, break out of the loop that # parses over the backup servers. diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index 7aefd3f..2752f47 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -685,27 +685,40 @@ $(mtexdir)/initialize.tex: # Calculate the latest Maneage commit used to build this project: # - The project may not have the 'maneage' branch (for example # after cloning from a fork that didn't include it!). In this -# case, we'll print a descriptive warning, telling the user what -# should be done (reporting the last merged commit and its date -# is very useful for the future). +# case, if a PDF is to be created, print a descriptive warning, +# telling the user what should be done (reporting the last merged +# commit and its date is very useful for the future). +# - This is not relevant when no PDF is requested because we only +# use this to print the latest Maneage commit as a LaTeX macro. # - The '--dirty' option (used in 'project-commit-hash') isn't # applicable to "commit-ishes" (direct quote from Git's error -# message!). +# message!), so no need to include it here. if git log maneage -1 &> /dev/null; then c=$$(git merge-base HEAD maneage) v=$$(git describe --always --long $$c) d=$$(git show -s --format=%aD $$v | awk '{print $$2, $$3, $$4}') + +# No 'maneage' branch found else - echo - echo "WARNING: no 'maneage' branch found! Without it, the latest merge of " - echo "this project with Maneage can't be reported in the paper (which is bad " - echo "for your readers; that includes yourself in a few years). Please run " - echo "the commands below to fetch the 'maneage' branch from its own server " - echo "and remove this warning (these commands will not affect your project):" - echo " $ git remote add origin-maneage http://git.maneage.org/project.git" - echo " $ git fetch origin-maneage" - echo " $ git branch maneage --track origin-maneage/maneage" - echo + +# Only print a warning if a PDF is to be created. + if [ x$(pdf-build-final) = xyes ]; then + echo + printf "WARNING: no 'maneage' branch found! Without it, " + printf "the latest merge of this project with Maneage can't " + printf "be reported in the paper (which is bad for your " + printf "readers; that includes yourself in a few years). " + printf "Please run the commands below to fetch the " + printf "'maneage' branch from its own server and remove " + printf "this warning (these commands will not affect your " + printf "project):\n" + printf " $ git remote add origin-maneage " + printf "http://git.maneage.org/project.git\n" + printf " $ git fetch origin-maneage\n" + printf " $ git branch maneage --track " + printf "origin-maneage/maneage\n" + echo + fi v="\textcolor{red}{NO-MANEAGE-BRANCH (see printed warning to fix this)}" d="\textcolor{red}{NO-MANEAGE-DATE}" fi diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk index 8d1c2e0..913a062 100644 --- a/reproduce/analysis/make/top-prepare.mk +++ b/reproduce/analysis/make/top-prepare.mk @@ -42,10 +42,10 @@ else all: @if [ "x$(GROUP-NAME)" = x ]; then \ echo "Project is NOT configured for groups, please run"; \ - echo " $$ ./project prepare"; \ + echo " $$ ./project configure"; \ else \ echo "Project is configured for groups, please run"; \ - echo " $$ ./project prepare --group=$(GROUP-NAME) -j8"; \ + echo " $$ ./project configure --group=$(GROUP-NAME) -j8"; \ fi exit 1 endif @@ -61,7 +61,7 @@ endif # # To ensure that 'prepare' and 'make' have the same basic definitions and # environment and that all 'downloads' are managed in one place, both -# './project prepare' and './project make' will first read 'initialize.mk' +# './project configure' and './project make' will first read 'initialize.mk' # and 'downloads.mk'. makesrc = initialize \ prepare diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index 9e1c437..d3717cb 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -27,7 +27,7 @@ file-checksum = b843b3c25656e8dec52e64eed6f581b29faf36540e0604a803d61c0f0eca830a findutils-checksum = 826c643e7f5c5d6976a47eabcd9807e51350d09ee8fc7dc931f2d9276f938f65aa0bd97e6213aa979742234784c120e1a6850a52207c327e1c1a465feb374053 flock-checksum = f711815035e21b46572bf80e730a55822e5abf4cb29749e476ee6cf4d5027e9a7deeacf5f6b8c37f18f17a0cc7a6d98fb0be3936e97b122707f1cb2306d1e1d9 gawk-checksum = 9013f5cb4c08aa13029ecf0c6b5e02ac93a3b500683b07ae8d34d698f0451dd5146a0a5aef96a249112834e27b379869d8e541f6a1b99accf701ba6a48f58f33 -gcc-checksum = f7386218e0993e19da1092bf625791cb9ec269667f7bdf378fef359a304aa08e4d79cb7b9f56d5d7028b53b29071005707a1cad0fd1b770884ab02310ed7b028 +gcc-checksum = b2191bf7005c21dee7675cc1f9ed615de418eac6afaf8dd6b3fc6022660d2ae63aec66a3fd072f227fa05da1654e04c2d06fb331fd50798c768de7ef1a7d9590 gettext-checksum = dbdc5016a776f12feb7134c05e2568ba9134bfa66b824967b4cc81d2093328c0f3bbcf269ad5a60ff2257625c763ac96c071685ee2b1d397730b06a058f565aa git-checksum = e2a3d2cf272554c0e9fa2abc4cf7b1eff17884911859f17567b76f170996802caa01675a42dbf29af7fc283a07e8dc4a11382ffbd2a03d7d62238e8c598f0b56 gmp-checksum = ad65de00ecb46cf454ed6c40d2a57ce2528f5fa64df1284dfa15036f1e8cf27760a09a4ecdfcc39048faffb71339bba30d99dd365c54173dbc2ba629bee2fad9 @@ -105,6 +105,7 @@ help2man-checksum = 83dca38c2020c85a66da882cd994b4e291eb6a0584149b7b3a74fec14443 icu-checksum = ab14b52a3fdf2dcde6b5160ab7218eac381b850d3c278324379741c49d71fa6040fbacca94c6937e6c9fc15843761121deff302ca6854da5ca1cd5b26a34e839 imagemagick-checksum = 2132614540b7422c9772fcebe7e8e358994efcfb53d8e48fa52992313b09b191847e395bad305322c377a4697014353bb8c15adc4edfd712e038504fc7f17c5e imfit-checksum = 15edd2349232c1c8e611b31d3a46b0700112d274515f54d0a0085bb4bfa6d3d5f8a15cd926516e043a29ce841accf3534ae58dbfb952d858dc9445199c957096 +jq-checksum = f83613b26ed6f4f963865bbc28fdc5246644e0e21287d0707ce62c5d10e84d70e622c7ca7f83147682e6052d96892697a2fe32a47d47bd3f32e3d74548877743 lalsuite-checksum = 330f2576698bd3107621d49596da66c7629d314e5744b3a267b3fa346e7926bb255979506627abaeeba62ff9a776c6091e9150ab5c471c3b4a43bec40a1a5de1 lapack-checksum = ff670e194a1d8c998f05e6143e01a09e6b43176c511217ea3c77742afd9f2566251c50fc23aeb916442401f7118c1d1fe21f0172382a7f4f2c516c1d7d873e24 libbsd-checksum = 5c7d98474000af1271a36ab769e54aba41578e0b0f06e47af2986d6821b6586ac430ec04cc51b7836823834dd9d0aec9f4ab3af088b94f963b89729fa2cc95d8 diff --git a/reproduce/software/config/servers-backup.conf b/reproduce/software/config/servers-backup.conf index 26c992f..04ad406 100644 --- a/reproduce/software/config/servers-backup.conf +++ b/reproduce/software/config/servers-backup.conf @@ -9,6 +9,6 @@ # permitted in any medium without royalty provided the copyright notice and # this notice are preserved. This file is offered as-is, without any # warranty. -http://gitlab.cefca.es/maneage/tarballs-software/-/raw/master/ +http://gitlab.cefca.es/maneage/tarballs-software/-/raw/master http://gitlab.com/maneage/tarballs-software/-/raw/master http://git.maneage.org/tarballs-software.git/plain diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf index f976930..8010c9d 100644 --- a/reproduce/software/config/urls.conf +++ b/reproduce/software/config/urls.conf @@ -111,6 +111,7 @@ #icu-url = https://github.com/unicode-org/icu/releases #imagemagick-url = https://download.imagemagick.org/ImageMagick/download #imfit-url = http://www.mpe.mpg.de/~erwin/resources/imfit +#jq-url = https://jqlang.org/download #lapack-url = http://www.netlib.org/lapack #libbsd-url = http://libbsd.freedesktop.org/releases #libffi-url = https://github.com/libffi/libffi diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index 3e4ec9a..552043f 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -26,6 +26,7 @@ diffutils-version = 3.12 findutils-version = 4.10.0 flock-version = 0.4.0 gawk-version = 5.3.2 +gcc-version = 16.1.0 gettext-version = 1.0 git-version = 2.52.0 grep-version = 3.12 @@ -107,12 +108,6 @@ file-version = 5.46 ncurses-version = 6.5 pkgconfig-version = 0.29.2 -# GCC -# --- -# -# There is a version-specific 'sed -e' fix for a bug in this version of GCC -# that should no longer be necessary in future versions. -gcc-version = 15.2.0 @@ -156,6 +151,7 @@ healpix-version = 3.83-2024Nov13 icu-version = 70.1 imagemagick-version = 7.1.0-13 imfit-version = 1.6.1 +jq-version = 1.8.2 libbsd-version = 0.11.3 libffi-version = 3.4.7 libidn-version = 1.42 diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 92fa8f0..000f62d 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -369,14 +369,17 @@ $(ibidir)/tar-$(tar-version): \ $(ibidir)/zlib-$(zlib-version) \ $(ibidir)/bzip2-$(bzip2-version) -# About the onfigurations: nls and iconv were creating problems with -# the dependencies on MacOs and are not relevant in the context of -# Maneage, hence, they are disabled. +# About the configurations: disabled because they are not relevant in +# the context of Maneage usage. +# - nls: conflicts with iconv on macOS. +# - acl: causing crashes when Tar was compiled with GCC 16.1.1. $(call unsafe-config) tarball=tar-$(tar-version).tar.lz $(call import-source, $(tar-url), $(tar-checksum)) $(call gbuild, tar-$(tar-version), , \ - --disable-nls am_cv_func_iconv=no, \ + --disable-nls \ + --disable-acl \ + am_cv_func_iconv=no, \ -j$(numthreads) V=1) echo "GNU Tar $(tar-version)" > $@ @@ -417,35 +420,56 @@ $(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/tar-$(tar-version) # 'pkg-config' is built first. But when we don't have a clean build # (and 'libiconv' exists) there will be a problem. So before # re-building 'pkg-config', we'll remove any installation of -# 'libiconv'. +# 'libiconv'. This can create a known bug: +# https://savannah.nongnu.org/bugs/?67001 rm -f $(ildir)/libiconv* $(idir)/include/iconv.h -# Some Mac OS systems may have a version of the GNU C Compiler (GCC) -# installed that doesn't support some necessary features of building -# Glib (as part of pkg-config), so we will disable pkg-config's -# internal Glib for Mac systems, and to be further safe, we'll make -# sure it will use LLVM's Clang. -# -# On macOS systems, to ensure that Clang can build pkg-config, take -# the following steps: -# 1. Install the latest Glib via Homebrew: -# brew install glib -# 2. Set these environment variables before configuring Maneage: -# export GLIB_CFLAGS=$(pkg-config --cflags glib-2.0) -# export GLIB_LIBS=$(pkg-config --libs glib-2.0) -# 3. Ensure PKG_CONFIG_PATH includes Homebrew's pkgconfig: -# export PKG_CONFIG_PATH=/opt/homebrew/lib/pkgconfig:$PKG_CONFIG_PATH +# On GNU/Linux no changes necessary, so we'll start with those. If +# the runner is on a macOS, some changes are necessary. + export compiler="" + confsh=./configure if [ x$(on_mac_os) = xyes ]; then - extra_pkgconf="" + +# On macOS we force Clang, because some GCC versions shipped with +# Xcode lack features needed to build Glib. export compiler="CC=clang" - else - export compiler="" - extra_pkgconf="--with-internal-glib" + +# The bundled glib's gatomic.c uses integer-to-pointer conversions +# that newer Clang (Xcode 26+) treats as hard errors on all macOS +# architectures. + CFLAGS="-Wno-int-conversion $$CFLAGS" + +# On macOS ARM64 the bundled glib sub-configure checks for Carbon +# support with the C preprocessor only. Since 'Carbon/Carbon.h' +# exists in the Xcode SDK on Apple Silicon, the check passes and +# '-framework Carbon' is appended to LDFLAGS. But Carbon cannot +# actually be linked on ARM64, so every subsequent linker test in +# glib's configure fails silently and libglib-2.0.la is never +# created. We work around this by passing gbuild a tiny wrapper +# script (instead of ./configure) that patches glib/configure to +# force glib_have_carbon=no before the real configure runs. +# +# NOTE: the initial two SPACES in the SED command are very +# important (see 'glib/configure'): without them, the wrong +# variable will be set. + confsh=$(ddir)/pkg-config-configure + printf '#!/bin/sh\n' > $$confsh + printf 'sed -i.bak "s/^ glib_have_carbon=yes$$/' >> $$confsh + printf ' glib_have_carbon=no/"' >> $$confsh + printf ' glib/configure\n' >> $$confsh + printf 'exec ./configure "$$@"\n' >> $$confsh + chmod +x $$confsh fi + +# Configuration options: +# --with-internal-glib: the internal glib is necessary because +# without it, we have many problems in macOS. export CFLAGS="-std=$(std_c_old) $$CFLAGS" $(call gbuild, pkg-config-$(pkgconfig-version), static, \ - $$compiler $$extra_pkgconf \ - --with-pc-path=$(ildir)/pkgconfig, V=1) + $$compiler \ + --with-internal-glib \ + --with-pc-path=$(ildir)/pkgconfig, V=1, , $$confsh) + if [ -f $$confsh ]; then rm $$confsh; fi # Only on macOS. echo "pkg-config $(pkgconfig-version)" > $@ @@ -1458,32 +1482,6 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) # first look into its own 'include' directory before anything else. export CPPFLAGS="-I$$(pwd)/include $(CPPFLAGS)" -# In the GNU C Library 2.36 (which is more recent than GCC 12.1.0), -# the 'linux/mount.h' (loaded by 'linux/fs.h', which is loaded by -# 'libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp' -# in GCC) conflicts with 'sys/mount.h' which is directly loaded by -# the same file! This is a known conflict in glibc 2.36 (see -# [1]). As described in [1], one solution is the final job done in -# [2]. We therefore do this process here: 1) Not loading -# 'linux/fs.h', and adding the necessary macros directly. -# -# [1] https://sourceware.org/glibc/wiki/Release/2.36#Usage_of_.3Clinux.2Fmount.h.3E_and_.3Csys.2Fmount.h.3E -# [2] https://reviews.llvm.org/D129471 - sed -e's|\#include <linux/fs.h>||' \ - -e"s|FS_IOC_GETFLAGS;|_IOR('f', 1, long);|" \ - -e"s|FS_IOC_GETVERSION;|_IOR('v', 1, long);|" \ - -e"s|FS_IOC_SETFLAGS;|_IOW('f', 2, long);|" \ - -e"s|FS_IOC_SETVERSION;|_IOW('v', 2, long);|" \ - -i libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp - -# Bug in GCC 15.2.0 using glibc 2.43 (see [1]) as fixed in [2]. -# [1] https://patchwork.ozlabs.org/project/gcc/patch/e1679277-d7c9-49aa-8365-a8dca082d9bd@web.de -# [2] https://github.com/johnny-mnemonic/toolchain-autobuilds/commit/9585fdfc - sed -e's|char \*q = strchr (p + 1,|const char \*q = strchr (p + 1,|' \ - libgomp/affinity-fmt.c > affinity-fmt-tmp.c - mv affinity-fmt-tmp.c libgomp/affinity-fmt.c - - # Set the build directory for the processing. mkdir build cd build diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index d059544..281bd84 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -465,7 +465,7 @@ $(ibidir)/cfitsio-$(cfitsio-version): $(call gbuild, cfitsio-$(cfitsio-version), , \ $$confopts \ --disable-curl \ - --disable-fortran \ + --without-fortran \ --enable-reentrant \ --with-bzip2=$(idir), , \ make fpack funpack) @@ -1764,6 +1764,20 @@ $(ibidir)/imfit-$(imfit-version): \ rm -rf $$unpackdir echo "Imfit $(imfit-version) \citep{imfit2015}" > $@ +# jq (to parse JSON files on the command-line) uses the external Oniguruma +# regular expression library that has ended development in 2025-04-24, see +# https://github.com/kkos/oniguruma. If this library ('libonig') is present +# on the host, jq will build with that: causing a leaking of os environment +# into the Maneage'd environment. Fortunately, jq maintains a copy of this +# library in its own source (within its tarball) and will build it with the +# '--with-oniguruma=builtin' configuration option. +$(ibidir)/jq-$(jq-version): + tarball=jq-$(jq-version).tar.lz + $(call import-source, $(jq-url), $(jq-checksum)) + $(call gbuild, jq-$(jq-version), static, \ + --with-oniguruma=builtin, V=1) + echo "jq $(jq-version)" > $@ + # This is the LIGO lscsoft package 'metaio' [1] (to be distinguished from # some other packages with the same name). # @@ -1771,7 +1785,7 @@ $(ibidir)/imfit-$(imfit-version): \ $(ibidir)/metaio-$(metaio-version): tarball=metaio-$(metaio-version).tar.lz $(call import-source, $(metaio-url), $(metaio-checksum)) - $(call gbuild, metaio-$(metaio-version), static) + $(call gbuild, metaio-$(metaio-version), static,, V=1) echo "Lscsoft Metaio $(metaio-version)" > $@ # Minizip 1.x is actually distributed within zlib. It doesn't have its own @@ -2279,14 +2293,45 @@ $(ibidir)/vim-$(vim-version): rm -rf $$unpackdir echo "VIM $(vim-version)" > $@ -$(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version) +$(ibidir)/unzip-$(unzip-version): + +# Prepare the tarball and build directory. tarball=unzip-$(unzip-version).tar.lz $(call import-source, $(unzip-url), $(unzip-checksum)) - $(call gbuild, unzip-$(unzip-version), static,, \ - -f unix/Makefile generic \ - CFLAGS="-DBIG_MEM -DMMAP",,pwd, \ - -f unix/Makefile generic \ - BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 ) + +# Unpack and go into the directory. + export LDFLAGS="$$LDFLAGS -static" + cd $(ddir) + rm -fr unzip-$(unzip-version)/ + tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions + cd unzip-$(unzip-version)/ + +# Remove reference to the old 'gmtime' function and include the +# system's 'time.h instead. + sed -i -e's|struct tm *gmtime(), *localtime();|#include <time.h>|' \ + -e'/gmtime/d; /localtime/d' unix/unxcfg.h + +# The 'NO_DIR' variable causes conflicts: the unzip code has its own +# internal fallback implementation called 'NO_DIR'. The modern Linux +# system already provides a standard implementation using +# 'dirent.h'. These two systems conflict with each other. This causes +# compilation errors such as conflicting types for DIR and invalid +# use of DIR. + sed -i -e's/-DNO_DIR//g' unix/configure + sed -i -e's/#ifdef NO_DIR/#if 0/g' unix/unix.c + sed -i -e's/-DNO_DIR//g' -e's/-U_NO_DIR//g' unix/Makefile + +# Since unzip is no longer maintained, it uses an old C standard. + export CFLAGS="-std=gnu89 -fcommon" + +# Build and install + make SHELL=$(ibdir)/bash -f unix/Makefile generic + make SHELL=$(ibdir)/bash install -f unix/Makefile \ + generic BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 + +# Go back to the top build directory, clean up and finalize. + cd $(ddir) + rm -rf unzip-$(unzip-version)/ echo "Unzip $(unzip-version)" > $@ $(ibidir)/zip-$(zip-version): diff --git a/reproduce/software/shell/apptainer.sh b/reproduce/software/shell/apptainer.sh index 8760db6..eb24e9e 100755 --- a/reproduce/software/shell/apptainer.sh +++ b/reproduce/software/shell/apptainer.sh @@ -343,7 +343,7 @@ From: $base_sif %post cd /home/maneager/source - ./project configure --jobs=$jobs \\ + ./project configure --jobs=$jobs --no-pause \\ --input-dir=/home/maneager/input \\ --build-dir=$intbuild \\ --software-dir=/home/maneager/tarballs-software diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index 3e0163e..e17c9ad 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -375,20 +375,23 @@ if [ $built_container = 0 ]; then fi # On macOS, the way of obtaining the number of cores is different - # between Intel or Apple M1 CPUs. Here we disinguish between Apple - # M1 or others. - maccputype=$(sysctl -n machdep.cpu.brand_string) - if [ x"$maccputype" = x"Apple M1" ] \ - || [ x"$maccputype" = x"Apple M2" ] \ - || [ x"$maccputype" = x"Apple M3" ] \ - || [ x"$maccputype" = x"Apple M4" ] \ - || [ x"$maccputype" = x"Apple M5" ] ; then - address_size_physical=$(sysctl -n machdep.cpu.thread_count) - address_size_virtual=$(sysctl -n machdep.cpu.logical_per_package) - else - address_size_physical=$(sysctl -n machdep.cpu.address_bits.physical) - address_size_virtual=$(sysctl -n machdep.cpu.address_bits.virtual) - fi + # between Intel or Apple Silicon CPUs. Here we distinguish between + # Apple Silicon (any "Apple M*" brand string, e.g. M1, M1 Pro, M1 + # Max, M2, M2 Pro, ...) and Intel-based Macs. Note that the Apple + # Silicon group can be in the formats of "Apple M1" or "Apple M1 + # Pro", so we use a prefix match via a 'case' pattern to include + # both in one check. + maccputype=$(sysctl -n machdep.cpu.brand_string 2>/dev/null) + case "$maccputype" in + "Apple M"*) + address_size_physical=$(sysctl -n machdep.cpu.thread_count) + address_size_virtual=$(sysctl -n machdep.cpu.logical_per_package) + ;; + *) + address_size_physical=$(sysctl -n machdep.cpu.address_bits.physical) + address_size_virtual=$(sysctl -n machdep.cpu.address_bits.virtual) + ;; + esac address_sizes="$address_size_physical bits physical, " address_sizes+="$address_size_virtual bits virtual" else @@ -1781,30 +1784,37 @@ fi # an example, the directory part of the URL for all the other software are # the same). This is not done if the options '--debug' or `--offline` are # used. -zenodourl="" -user_backup_urls="" -zenodocheck="$bdir"/software/zenodo-check.html -if [ $built_container = 0 ]; then - if [ x$debug = x ] && [ x$offline = x ]; then - if $downloader $zenodocheck \ - https://doi.org/10.5281/zenodo.3883409; then - zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \ - | sed -n -e'/http/p' \ - | tr ' ' '\n' \ - | grep http \ - | sed -e 's/href="//' -e 's|/coreutils| |' \ - | awk 'NR==1{print $1}') - fi - fi - rm -f $zenodocheck - - # Add the Zenodo URL to the user's given back software URLs. Since the - # user can specify 'user_backup_urls' (not yet implemented as an option - # in './project'), we'll give preference to their specified servers, - # then add the Zenodo URL afterwards. - user_backup_urls="$user_backup_urls $zenodourl" - elapsed_time_from_prev_step zenodo-url -fi +# +# NOTE on commented region below (starting with '##'): As described [1], +# Zenodo's upload strategy does not allow a repository with more than one +# hundred files. So until the solution there has been implemented, this +# step has been commented. +# +# [1] https://savannah.nongnu.org/task/?16621 +## zenodourl="" +## user_backup_urls="" +## zenodocheck="$bdir"/software/zenodo-check.html +## if [ $built_container = 0 ]; then +## if [ x$debug = x ] && [ x$offline = x ]; then +## if $downloader $zenodocheck \ +## https://doi.org/10.5281/zenodo.3883409; then +## zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \ +## | sed -n -e'/http/p' \ +## | tr ' ' '\n' \ +## | grep http \ +## | sed -e 's/href="//' -e 's|/coreutils| |' \ +## | awk 'NR==1{print $1}') +## fi +## fi +## rm -f $zenodocheck +## +## # Add the Zenodo URL to the user's given back software URLs. Since the +## # user can specify 'user_backup_urls' (not yet implemented as an option +## # in './project'), we'll give preference to their specified servers, +## # then add the Zenodo URL afterwards. +## user_backup_urls="$user_backup_urls $zenodourl" +## elapsed_time_from_prev_step zenodo-url +## fi diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh index 8236247..3163f74 100755 --- a/reproduce/software/shell/pre-make-build.sh +++ b/reproduce/software/shell/pre-make-build.sh @@ -120,16 +120,24 @@ download_tarball() { "$bservers" fi + # Make sure this is the correct tarball. if type sha512sum > /dev/null 2> /dev/null; then - checksum=$(sha512sum "$ucname" | awk '{print $1}') + + # On macOS, sha512sum wraps the hash in two lines. The 'tr -d '\n'' + # part joins them into one before awk extracts the first field. On + # Linux (GNU coreutils) the output is already a single line, so the + # 'tr' command has no effect. + checksum=$(sha512sum "$ucname" | tr -d '\n' | awk '{print $1}') expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' \ "$checksumsfile") - if [ x$checksum = x$expectedchecksum ]; then mv "$ucname" "$maneagetar" + if [ x$checksum = x$expectedchecksum ]; then + mv "$ucname" "$maneagetar" else - echo "ERROR: Non-matching checksum: $tarball" - echo "Checksum should be: $expectedchecksum" - echo "Checksum is: $checksum" + echo "ERROR: Non-matching checksum in $tarball" + echo " Checksum should be: $expectedchecksum" + echo " Checksum is: $checksum" + rm -f "$ucname" exit 1 fi; else mv "$ucname" "$maneagetar" |