Cygwin: Fix cliquer, giac, meataxe, rw, libbraiding to build shared libraries, using AM_LDFLAGS=-no-undefined

[embray]

Follow-up from #30396, where libtool's fallback to static library build for giac caused linker errors while building sagelib.

This is fixed by passing -no-undefined to the libtool linking flags, by setting AM_LDFLAGS=-no-undefined.

Affected packages can be found as follows:

$ grep "undefined symbols not allowed" logs/pkgs/*
cliquer-1.21.p4.log:libtool: link: warning: undefined symbols not allowed in x86_64-unknown-cygwin shared libraries
giac-1.5.0.87p0.log:libtool: warning: undefined symbols not allowed in x86_64-pc-cygwin shared libraries; building static only
libbraiding-1.0.p0.log:libtool: warning: undefined symbols not allowed in x86_64-unknown-cygwin shared libraries; building static only
rw-0.7.p0.log:libtool: link: warning: undefined symbols not allowed in x86_64-unknown-cygwin shared libraries
singular-4.1.1p2.p0.log:libtool: warning: undefined symbols not allowed in x86_64-unknown-cygwin shared libraries; building static only

In singular, only the gitfan.la library (module) is affected:

Making all in gitfan
...
/usr/bin/bash ../../../libtool  --tag=CXX   --mode=link g++ -std=gnu++11  -O2 -g  -pipe -fno-common -g0 -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -fno-enforce-eh-specs -fconserve-space -funroll-loops -fno-delete-null-pointer-checks -fno-rtti -module -export-dynamic -avoid-version -flat_namespace -weak_reference_mismatches weak -undefined dynamic_lookup -L/cygdrive/d/a/sage/sage/local/lib -Wl,-rpath,/cygdrive/d/a/sage/sage/local/lib  -pipe -fno-common -g0 -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fconserve-space -funroll-loops -fno-delete-null-pointer-checks  -Wl,-Bdynamic -o gitfan.la -rpath /cygdrive/d/a/sage/sage/local/libexec/singular/MOD gitfan_la-gitfan.lo  -lreadline -lncurses -lmpfr -lrt
libtool: warning: undefined symbols not allowed in x86_64-unknown-cygwin shared libraries; building static only
libtool: link: ar cru .libs/gitfan.a  gitfan_la-gitfan.o
libtool: link: ranlib .libs/gitfan.a
libtool: link: ( cd ".libs" && rm -f "gitfan.la" && ln -s "../gitfan.la" "gitfan.la" )

The issue also affects the optional package meataxe.

[meataxe-1.0.p0] /usr/bin/bash ../libtool  --tag=CC   --mode=link gcc  -g -O2  -L/opt/sagemath-9.0/local/lib -Wl,-rpath,/opt/sagemath-9.0/local/lib  -o libmtx.la -rpath /opt/sagemath-9.0/local/lib args.lo berlekmp.lo bsand.lo bscore.lo bsdup.lo bsissub.lo bsmatch.lo bsminus.lo bsop.lo bsor.lo bsprint.lo bsread.lo bswrite.lo cfinfo.lo charpol.lo chbasis.lo error.lo ffio.lo fpcore.lo fpdup.lo fpmul.lo fpmul2.lo fpprint.lo gcd.lo genseed.lo grmaprow.lo grmatcore.lo grtable.lo homcomp.lo imatcore.lo imatread.lo imatwrite.lo init.lo intio.lo issub.lo isisom.lo kernel-0.lo ldiag.lo maddmul.lo mat2vec.lo matadd.lo matclean.lo matcmp.lo maketabF.lo matcopy.lo matcore.lo matcut.lo matdup.lo matech.lo matid.lo matins.lo matinv.lo matmul.lo matnull.lo matorder.lo matpivot.lo matprint.lo matpwr.lo matread.lo mattr.lo mattrace.lo matwrite.lo message.lo mfcore.lo mfread.lo mfreadlong.lo mfwrite.lo mfwritelong.lo minpol.lo mkendo.lo mmulscal.lo mraddgen.lo mrcore.lo mrread.lo mrtranspose.lo mrwrite.lo msclean.lo mscore.lo mtensor.lo mtxobj.lo os.lo permcmp.lo permcore.lo permdup.lo perminv.lo permmul.lo permorder.lo permprint.lo permpwr.lo permread.lo permwrite.lo poladd.lo polcmp.lo polcore.lo polderive.lo poldiv.lo poldup.lo polgcd.lo polmul.lo polprint.lo polread.lo polwrite.lo quotient.lo random.lo rdcfgen.lo saction.lo setcore.lo setinsert.lo settest.lo spinup.lo spinup2.lo split.lo stabpwr.lo stfcore.lo stfread.lo stfwrite.lo string.lo sumint.lo temap.lo tkinfo.lo vec2mat.lo wgen.lo window.lo zcleanrow.lo zcmprow.lo zgap.lo zpermrow.lo zzz2.lo
[meataxe-1.0.p0] libtool:   error: can't build x86_64-unknown-cygwin shared library unless -no-undefined is specified

This is a common issue especially when using libtool to link Windows DLLs and should hopefully be straightforward to fix.

See also:

• nauty: Switch to autotoolized fork so that shared libraries can be built #30271 nauty: Switch to autotoolized fork so that shared libraries can be built

Depends on #31064

Upstream: Reported upstream. No feedback yet.

CC: @simon-king-jena @miguelmarco @dimpase @orlitzky @antonio-rojas @kiwifb @slel @jhpalmieri @vbraun

Component: porting: Cygwin

Author: Matthias Koeppe, Miguel Marco, Simon King

Branch/Commit: 6b6ee5c

Reviewer: Matthias Koeppe, Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/29152

[mkoeppe]

comment:2

The failure can be seen at https://github.com/mkoeppe/sage/runs/641394565

[mkoeppe]

comment:5

Cc'ing mmarco re libbraiding

[mkoeppe]

comment:6

cc'ing dimpase re cliquer, also reported at dimpase/autocliquer#4

[mkoeppe]

Upstream: Reported upstream. No feedback yet.

[mkoeppe]

comment:7

Upstream link in build/pkgs/rw/SPKG.rst no longer works

[mkoeppe]

comment:8

Cc'ing gentoo, arch people to see if new rw upstream is known

[antonio-rojas]

comment:10

I'm getting it from https://sourceforge.net/projects/rankwidth/, but I don't know if there's anybody reading tickets there (there are none filed so far)

[kiwifb]

comment:11

Replying to @antonio-rojas:

I'm getting it from https://sourceforge.net/projects/rankwidth/, but I don't know if there's anybody reading tickets there (there are none filed so far)

Same here in Gentoo https://packages.gentoo.org/packages/sci-mathematics/rw

[orlitzky]

comment:12

What's wrong with rw upstream? The program is more or less "complete," so I wouldn't expect much activity. Last time (a few years ago), we just emailed the guy to ask about contributing an autotools build system.

[mkoeppe]

Branch: u/mkoeppe/cygwin__make_sure_all_packages_build_shared_libraries__using__am_ldflags__no_undefined_

[mkoeppe]

Commit: 45a4167

[mkoeppe]

comment:14

Replying to @orlitzky:

What's wrong with rw upstream?

See ticket description

---

New commits:

45a4167

build/pkgs/rw/SPKG.rst: Update link to upstream project

[miguelmarco]

comment:15

I created a new release for libbraiding:

https://github.com/miguelmarco/libbraiding/releases/tag/1.1

Should I also update the sage package?

IIRC, there is a new way to upload the tarball. Isn't it?

[mkoeppe]

comment:16

Replying to @miguelmarco:

I created a new release for libbraiding:

https://github.com/miguelmarco/libbraiding/releases/tag/1.1

Thanks a lot!

Should I also update the sage package?

Yes please

IIRC, there is a new way to upload the tarball. Isn't it?

No need to upload, but please add upstream_url as explained in https://wiki.sagemath.org/ReleaseTours/sage-9.1#For_developers-1

[miguelmarco]

Changed branch from u/mkoeppe/cygwin__make_sure_all_packages_build_shared_libraries__using__am_ldflags__no_undefined_ to u/mmarco/cygwin__make_sure_all_packages_build_shared_libraries__using__am_ldflags__no_undefined_

[mkoeppe]

Changed commit from 45a4167 to 44839c7

[sagetrac-git]

Changed commit from 9661065 to 4c34a0e

[mkoeppe]

Work Issues: rebase on top of #31064

[sagetrac-git]

Changed commit from 4c34a0e to 58c22df

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:

cea4cd5	ci-cygwin-standard.yml: More stages, continue-on-error: true
cf31b79	Fixup after cherry-pick
73b0e8f	build/pkgs/rw/SPKG.rst: Update link to upstream project
9d724bc	libbraiding version bump
a67a446	build/pkgs/meataxe/distros: Add fedora.txt
c79da6a	build/pkgs/cliquer: Update to 1.22
b5dcb16	build/pkgs/cliquer/SPKG.rst: Update
9e6de0b	build/pkgs/rw: Update to 0.9
32385de	Upgrade SharedMeatAxe, to fix a build problem on Cygwin
58c22df	Add upstream url for SharedMeatAxe

[mkoeppe]

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/412156307, ... to Matthias Koeppe, https://github.com/mkoeppe/sage/actions/runs/432820484, ...

[mkoeppe]

Changed work issues from rebase on top of #31064 to none

[mkoeppe]

Changed dependencies from #30154 to #31064

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

09d1737	Makefile: Add targets ptest-nodoc etc.
0dca776	Merge branch 't/29124/script-packages-prereq-toolchain-bootstrap' into t/31084/makefile__add__ptest__targets_that_do_not_depend_on_the_docbuild
073124c	Merge branch 't/31084/makefile__add__ptest__targets_that_do_not_depend_on_the_docbuild' into t/31064/ci_cygwin__yml__adjust_to_new_script_packages__bootstrap___prereq
8769bd6	.github/workflows/ci-cygwin-*.yml: Separate docbuild and ptest
c2daec7	Merge branch 't/31064/ci_cygwin__yml__adjust_to_new_script_packages__bootstrap___prereq' into t/29152/cygwin__make_sure_all_packages_build_shared_libraries__using__am_ldflags__no_undefined_

[sagetrac-git]

Changed commit from 58c22df to c2daec7

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

78ff9d5	src/sage/misc/package.py: Add one more # optional - build
a44042f	Merge branch 't/30940/src_bin_sage_list_packages__make_it_work_if_sage_root_is_not_available' into t/29124/script-packages-prereq-toolchain-bootstrap
64bde5f	Merge tag '9.3.beta5' into t/30940/src_bin_sage_list_packages__make_it_work_if_sage_root_is_not_available
e9a7572	src/sage/misc/package.py: Improve source formatting
c7bcda9	Merge branch 't/30940/src_bin_sage_list_packages__make_it_work_if_sage_root_is_not_available' into t/29124/script-packages-prereq-toolchain-bootstrap
9988c5f	ci-cygwin*.yml: Adjust to new script packages _bootstrap, _prereq
d65299c	Merge branch 't/29124/script-packages-prereq-toolchain-bootstrap' into t/31064/ci_cygwin__yml__adjust_to_new_script_packages__bootstrap___prereq
ab19133	Merge branch 't/29124/script-packages-prereq-toolchain-bootstrap' into t/30944/tox__improve_local_sudo_ubuntu_standard
a5e4051	Merge branch 't/30944/tox__improve_local_sudo_ubuntu_standard' into t/31064/ci_cygwin__yml__adjust_to_new_script_packages__bootstrap___prereq
76804dc	Merge branch 't/31064/ci_cygwin__yml__adjust_to_new_script_packages__bootstrap___prereq' into t/29152/cygwin__make_sure_all_packages_build_shared_libraries__using__am_ldflags__no_undefined_

[sagetrac-git]

Changed commit from c2daec7 to 76804dc

[mkoeppe]

comment:68

Let's please get this in.

[dimpase]

comment:69

It still doesn't fix all the Cygwin things, no? Anyway, LGTM.

[dimpase]

Changed reviewer from Matthias Koeppe, https://github.com/mkoeppe/sage/actions/runs/432820484, ... to Matthias Koeppe, Dima Pasechnik

[mkoeppe]

comment:70

Thank you!

Follow up for the remaining issues in #30814.

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:

42f4458	Merge tag '9.3.beta7' into t/31064/ci_cygwin__yml__adjust_to_new_script_packages__bootstrap___prereq
6b6ee5c	Merge branch 't/31064/ci_cygwin__yml__adjust_to_new_script_packages__bootstrap___prereq' into t/29152/cygwin__make_sure_all_packages_build_shared_libraries__using__am_ldflags__no_undefined_

[sagetrac-git]

Changed commit from 76804dc to 6b6ee5c

[vbraun]

Changed branch from u/mkoeppe/cygwin__make_sure_all_packages_build_shared_libraries__using__am_ldflags__no_undefined_ to 6b6ee5c