Cygwin: Fix cliquer, giac, meataxe, rw, libbraiding to build shared libraries, using `AM_LDFLAGS=-no-undefined`
Closed this issue · 93 comments
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:
- #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
The failure can be seen at https://github.com/mkoeppe/sage/runs/641394565
Description changed:
---
+++
@@ -1,4 +1,19 @@
-The error occurs when linking:
+Follow-up from #30163, 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
+```
+
+It 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
@@ -6,3 +21,5 @@
```
This is a common issue especially when using libtool to link Windows DLLs and should hopefully be straightforward to fix.
+
+Cc'ing mmarco re libbraiding
cc'ing dimpase re cliquer, also reported at dimpase/autocliquer#4
Upstream: Reported upstream. No feedback yet.
Upstream link in build/pkgs/rw/SPKG.rst no longer works
Cc'ing gentoo, arch people to see if new rw upstream is known
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)
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
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.
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?
Replying to @miguelmarco:
I created a new release for libbraiding:
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
Description changed:
---
+++
@@ -22,4 +22,6 @@
This is a common issue especially when using libtool to link Windows DLLs and should hopefully be straightforward to fix.
+See also:
+- #30271 `nauty`: Switch to autotoolized fork so that shared libraries can be built
Author: Matthias Koeppe, Miguel Marco
Description changed:
---
+++
@@ -1,4 +1,4 @@
-Follow-up from #30163, where libtool's fallback to static library build for `giac` caused linker errors while building sagelib.
+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`.
Fix for meataxe at simon-king-jena/SharedMeatAxe#1
New commits:
b2c0b15 | build/pkgs/meataxe/distros: Add fedora.txt |
Description changed:
---
+++
@@ -13,7 +13,20 @@
singular-4.1.1p2.p0.log:libtool: warning: undefined symbols not allowed in x86_64-unknown-cygwin shared libraries; building static only
```
-It also affects the optional package `meataxe`.
+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.loLooks like the singular gitfan issue may be fixed by upstream commit 2617fca625d047a0b9890e6ffae1c5f8fe755aad
Description changed:
---
+++
@@ -13,20 +13,7 @@
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`.
+It 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.loThe -no-undefined is only needed when building a shared library, so the flag can be appended in e.g.
libfoo_la_LDFLAGS = -no-undefined
rather than the global
AM_LDFLAGS=-no-undefined
that will affect all link operations (including executables). It probably doesn't hurt much, but I remember vaguely that --as-needed was nicer than --no-undefined if you were going to apply it globally.
I also think most projects should have LT_INIT([disable-static]) in configure.ac these days, to disable the static libraries by default. They can still be enabled with --enable-static, but for most people they're a waste of time/space.
Putting back the description I clobbered...
Description changed:
---
+++
@@ -13,7 +13,19 @@
singular-4.1.1p2.p0.log:libtool: warning: undefined symbols not allowed in x86_64-unknown-cygwin shared libraries; building static only
```
-It also affects the optional package `meataxe`.
+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.loReplying to @orlitzky:
The
-no-undefinedis only needed when building a shared library, so the flag can be appended in e.g.libfoo_la_LDFLAGS = -no-undefinedrather than the global
AM_LDFLAGS=-no-undefinedthat will affect all link operations
I agree, that would be a little bit cleaner. But I don't think it's worth going back for this
Replying to @orlitzky:
I also think most projects should have
LT_INIT([disable-static])in configure.ac these days, to disable the static libraries by default. They can still be enabled with--enable-static, but for most people they're a waste of time/space.
I agree, but I want to keep the upstream patches minimal. We have #28890 for the task of sending --disable-static to all our packages
Replying to @mkoeppe:
cc'ing dimpase re cliquer, also reported at dimpase/autocliquer#4
OK, done and dusted, thanks for the PR, see
https://github.com/dimpase/autocliquer/releases/download/v1.22/cliquer-1.22.tar.gz
Branch pushed to git repo; I updated commit sha1. New commits:
1e94f7a | build/pkgs/cliquer: Update to 1.22 |
could you also add
--- a/build/pkgs/cliquer/SPKG.rst
+++ b/build/pkgs/cliquer/SPKG.rst
@@ -5,8 +5,8 @@ Description
-----------
Cliquer is a set of C routines for finding cliques in an arbitrary
-weighted graph. It uses an exact branch-and-bound algorithm recently
-developed by Patr Ostergard.
+weighted graph. It uses an exact branch-and-bound algorithm
+developed by Patric Östergård.
License
-------
@@ -28,4 +28,5 @@ Dependencies
Patches
-------
-- autotoolized - see https://github.com/dimpase/autocliquer
+- minor config updates (v1.22)
+- autotoolized - see https://github.com/dimpase/autocliquer (v1.21)Branch pushed to git repo; I updated commit sha1. New commits:
f2632eb | build/pkgs/cliquer/SPKG.rst: Update |
Branch pushed to git repo; I updated commit sha1. New commits:
9c1ee37 | build/pkgs/rw: Update to 0.9 |
Branch pushed to git repo; I updated commit sha1. New commits:
e662986 | Merge tag '9.2.beta14' into t/29152/cygwin__make_sure_all_packages_build_shared_libraries__using__am_ldflags__no_undefined_ |
I am about to release a new minor version of SharedMeatAxe based on Matthias' suggestions, and my plan was to upgrade it in Sage now. But since it is "needs review" already: Did Matthias did the meataxe upgrade in Sage already?
Work Issues: Upgrade shared_meataxe to v1.0.1
Aparently the upgrade of meataxe hasn't been done yet. So, it should be "needs work".
Changed work issues from Upgrade shared_meataxe to v1.0.1 to none
SharedMeatAxe is upgraded as well. See https://github.com/simon-king-jena/SharedMeatAxe/releases/tag/v1.0.1
I changed the compression from gz to bz2, since the latter gives a smaller tar ball. Self tests pass, I'm running "make test" now.
New commits:
54c2584 | Upgrade SharedMeatAxe, to fix a build problem on Cygwin |
Changed author from Matthias Koeppe, Miguel Marco to Matthias Koeppe, Miguel Marco, Simon King
Tests pass for me. However, the point of this ticket is to fix things on cygwin, which I'm not using.
Hence, no positive review.
A question: Is it still the case that the issues are "Reported upstream. No feedback yet.", or can this be changed to "Fixed upstream"?
Thanks very much, Simon. Could you add an upstream_url field to checksums.ini please (as explained in https://wiki.sagemath.org/ReleaseTours/sage-9.1#For_developers-1)
Branch pushed to git repo; I updated commit sha1. New commits:
cd74ef3 | Add upstream url for SharedMeatAxe |
Hope that upstream_url for SharedMeatAxe is fine.
Replying to @mkoeppe:
You added a URL as reviewer. Is that intended?
Actually it is not clear to me what is stated there. Do I understand correctly that tests on different versions of Cygwin pass, except "cygwin-stage-ii-a (standard)"? And the failed package in this Cygwin version is scipy?
Replying to @simon-king-jena:
Replying to @mkoeppe:
You added a URL as reviewer. Is that intended?
Yes, it's a trick that I have been using recently. The URL shows in ticket lists such as https://trac.sagemath.org/report/92?asc=1&page=1 and this reminds me (or other developers) to inspect these automatic builds when they are done.
They will be replaced by actual reviewer names when ready.
Actually it is not clear to me what is stated there. Do I understand correctly that tests on different versions of Cygwin pass, except "cygwin-stage-ii-a (standard)"? And the failed package in this Cygwin version is scipy?
The build on Cygwin takes very long because of various overheads compared to a build on Linux. On GH Actions there is a time limit of 6 hours per job. Therefore I have split the build into several jobs ("stages"), some of which run in parallel. The linked build https://github.com/mkoeppe/sage/actions/runs/285244461 is the cygwin-standard build, which means that I install binary packages from the Cygwin distribution first and then start the build of Sage.
stage-i-a and stage-i-b ran in parallel and succeeded. What they install in SAGE_LOCAL is carried forward to stage-ii. The 5 jobs stage-ii-a to stage-ii-e all ran in parallel, building various packages.
As you observed, stage-ii-a failed because of scipy. This is a bug unrelated to the present ticket; it is tracked in #30643.
Unfortunately this bug blocks the following stages (stage-iii would go on to build the Sage library), and so because of this we cannot really check that the current ticket is working correctly.
Replying to @mkoeppe:
Unfortunately this bug blocks the following stages (
stage-iiiwould go on to build the Sage library), and so because of this we cannot really check that the current ticket is working correctly.
We cannot test automatically (on github), but a developer with a cygwin machine certainly could...
Replying to @simon-king-jena:
We cannot test automatically (on github), but a developer with a cygwin machine certainly could...
We seem to be in short supply of these...
I have modified the CI script so that the scipy failure does not stop the whole build.
The resulting build logs (https://github.com/mkoeppe/sage/suites/1285136303/artifacts/20016238) show that cliquer, giac, meataxe, and rw, i.e., all packages mentioned in the ticket description except for libbraiding (for which the branch contains an update) and singular (for which the branch does not contain a change) are OK now.
Some optional packages were not built previously. In total, we now have the following remaining issues:
egret:~/Downloads/logs-commit-e41329adfa1f1e69653ba127d6460d2bd7aaaf00-cygwin-standard$ grep "undefined symbols not allowed" pkgs/*
pkgs/barvinok-0.41.1.log:libtool: warning: undefined symbols not allowed in x86_64-unknown-cygwin shared libraries; building static only
pkgs/e_antic-0.1.8.log:libtool: warning: undefined symbols not allowed in x86_64-pc-cygwin shared libraries; building static only
pkgs/isl-0.20.log:libtool: warning: undefined symbols not allowed in x86_64-unknown-cygwin shared libraries; building static only
pkgs/libbraiding-1.1.log:libtool: warning: undefined symbols not allowed in x86_64-pc-cygwin shared libraries; building static only
pkgs/polylib-5.22.5.log:libtool: link: warning: undefined symbols not allowed in x86_64-unknown-cygwin shared libraries
pkgs/singular-4.1.1p2.p0.log:libtool: warning: undefined symbols not allowed in x86_64-unknown-cy(base) eg(ba(base) egr(ba(base) egret(ba(base) (base)(base)(bas(b(bas(base)(((b((
New commits:
e41329a | ci-cygwin-standard.yml: More stages, continue-on-error: true |
Let's get this in so that other tickets can use it as a dependency.
Follow up for the remaining issues in #30814.
Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/287249195 to https://github.com/mkoeppe/sage/actions/runs/287249195, ...
Needs review
there seems to be some problem with building of scipy
In file included from /usr/include/sys/config.h:5,
from /usr/include/_ansi.h:11,
from /usr/include/sys/reent.h:13,
from /usr/include/math.h:5,
from /usr/lib/gcc/x86_64-pc-cygwin/10/include/c++/cmath:45,
from scipy/spatial/ckdtree/src/query.cxx:1:
/usr/include/sys/features.h:255: note: this is the location of the previous definition
255 | #define __BSD_VISIBLE 0
|
In file included from /cygdrive/d/a/sage/sage/local/include/python3.8/pyport.h:219,
from /cygdrive/d/a/sage/sage/local/include/python3.8/Python.h:63,
from /cygdrive/d/a/sage/sage/local/lib/python3.8/site-packages/numpy/core/include/numpy/npy_common.h:11,
from scipy/spatial/ckdtree/src/ckdtree_decl.h:10,
from scipy/spatial/ckdtree/src/query.cxx:13:
/usr/include/sys/time.h:106:34: error: 'u_int' has not been declared
106 | bintime_mul(struct bintime *_bt, u_int _x)
| ^~~~~
g++: scipy/spatial/ckdtree/src/build.cxx
Branch pushed to git repo; I updated commit sha1. New commits:
0bb7fc0 | Merge tag '9.3.beta3' into t/29152/cygwin__make_sure_all_packages_build_shared_libraries__using__am_ldflags__no_undefined_ |
7244a9d | ci-cygwin-standard.yml: Use tar --listed-incremental |
5ccf1ea | tar --remove-files and --listed-incremental are not compatible |
9661065 | Merge branch 't/30154/gh_actions__cygwin__use_incremental_archives_for_the_sage_local_artifact' into t/29152/cygwin__make_sure_all_packages_build_shared_libraries__using__am_ldflags__no_undefined_ |
Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/287249195, ... to https://github.com/mkoeppe/sage/actions/runs/412156307, ...
Branch pushed to git repo; I updated commit sha1. New commits:
4c34a0e | Update ci-cygwin-minimal.yml |
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 |
Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/412156307, ... to Matthias Koeppe, https://github.com/mkoeppe/sage/actions/runs/432820484, ...
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_ |
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_ |
Let's please get this in.
It still doesn't fix all the Cygwin things, no? Anyway, LGTM.
Changed reviewer from Matthias Koeppe, https://github.com/mkoeppe/sage/actions/runs/432820484, ... to Matthias Koeppe, Dima Pasechnik
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_ |