cygwin-standard: sagelib build fails

[mkoeppe]

https://github.com/sagemath/sage/runs/1003662756

  [sagelib-9.2.beta9]   gcc -shared -Wl,--enable-auto-image-base -L/cygdrive/d/a/sage/sage/local/lib -Wl,-rpath,/cygdrive/d/a/sage/sage/local/lib build/temp.cygwin-3.1.6-x86_64-3.7/build/cythonized/sage/ext/interpreters/wrapper_rr.o -L/cygdrive/d/a/sage/sage/local/lib/python3.7/config -L/usr/lib -lmpfr -lgmp -lpython3.7m -o build/lib.cygwin-3.1.6-x86_64-3.7/sage/ext/interpreters/wrapper_rr.cpython-37m-x86_64-cygwin.dll -lpari
  [sagelib-9.2.beta9]   g++ -shared -Wl,--enable-auto-image-base -L/cygdrive/d/a/sage/sage/local/lib -Wl,-rpath,/cygdrive/d/a/sage/sage/local/lib build/temp.cygwin-3.1.6-x86_64-3.7/build/cythonized/sage/symbolic/expression.o -L/cygdrive/d/a/sage/sage/local/lib/python3.7/config -L/usr/lib -lgmp -lpynac -lpython3.7m -o build/lib.cygwin-3.1.6-x86_64-3.7/sage/symbolic/expression.cpython-37m-x86_64-cygwin.dll -lpari
  [sagelib-9.2.beta9]   error: command 'gcc' failed with exit status 1

CC: @embray @frederichan-IMJPRG @sagetrac-parisse @kiwifb @jhpalmieri @dimpase

Component: porting: Cygwin

Author: Matthias Koeppe

Branch/Commit: e673110

Reviewer: Darij Grinberg, Travis Scrimshaw

Issue created by migration from https://trac.sagemath.org/ticket/30396

[embray]

comment:1

Without an error message I wouldn't even know how to begin interpreting this. Is it something you can reproduce locally? Did anything change recently in that file?

[mkoeppe]

comment:2

That's exactly my problem as well. Very consistently in these builds I get this error but no error message.

[mkoeppe]

comment:3

Local replication of this failure would already be a step forward. (I don't have a Windows machine.)

[vbraun]

comment:4

Realistically that can't be a release blocker then

[darijgr]

comment:5

I have what appears to be the same error. 9.2.beta12, after distclean.
Last lines after what appears to be a full compilation of sagelib:

[sagelib-9.2.beta12] error: command 'g++' failed with exit status 1
[sagelib-9.2.beta12]
[sagelib-9.2.beta12] real       191m8.476s
[sagelib-9.2.beta12] user       176m28.216s
[sagelib-9.2.beta12] sys        5m47.132s
make[4]: *** [Makefile:2161: sagelib-no-deps] Error 1
make[3]: *** [Makefile:2161: /home/skraeling/sage/local/var/lib/sage/installed/sagelib-9.2.beta12] Error 2
make[2]: *** [Makefile:1769: all-build] Error 2
make[2]: Leaving directory '/home/skraeling/sage/build/make'

Full log: https://www.dropbox.com/s/jjmgib33r9z0359/install.log?dl=0

[mkoeppe]

comment:7

Thanks for checking this.

I see this error:

[sagelib-9.2.beta12] gcc -shared -Wl,--enable-auto-image-base -L/home/skraeling/sage/local/lib -Wl,-rpath,/home/skraeling/sage/local/lib build/temp.cygwin-3.1.6-x86_64-3.6/build/cythonized/sage/misc/sage_ostools.o -L/home/skraeling/sage/local/lib/python3.6/config -L/usr/lib -lpython3.6m -o build/lib.cygwin-3.1.6-x86_64-3.6/sage/misc/sage_ostools.cpython-36m-x86_64-cygwin.dll
[sagelib-9.2.beta12] /usr/lib/gcc/x86_64-pc-cygwin/9.3.0/../../../../x86_64-pc-cygwin/bin/ld: build/temp.cygwin-3.1.6-x86_64-3.6/build/cythonized/sage/misc/sage_ostools.o: in function `__pyx_pf_4sage_4misc_12sage_ostools_5fix_for_ticket_30157':
[sagelib-9.2.beta12] /home/skraeling/sage/build/pkgs/sagelib/src/build/cythonized/sage/misc/sage_ostools.c:4052: undefined reference to `sqlite3_initialize'
[sagelib-9.2.beta12] /home/skraeling/sage/build/pkgs/sagelib/src/build/cythonized/sage/misc/sage_ostools.c:4052:(.text+0xe05): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `sqlite3_initialize'
[sagelib-9.2.beta12] collect2: error: ld returned 1 exit status

[mkoeppe]

comment:8

Could you rerun make build one more time after this failure and post the log?

Could you also post your config.log?

[mkoeppe]

comment:9

Looks like this is coming from #30157

[mkoeppe]

Branch: u/mkoeppe/cygwin_standard__sagelib_build_fails

[mkoeppe]

Commit: d133f2c

[mkoeppe]

comment:11

Here's a possible fix

---

New commits:

d133f2c

src/sage/misc/sage_ostools.pyx: Add distutils header

[darijgr]

comment:12

Sadly, doesn't help.
https://www.dropbox.com/s/z2ayo5teqhfqvoa/install-last.log?dl=0

Where do I find config.log?

[mkoeppe]

comment:13

Replying to @darijgr:

Where do I find config.log?

Root of the sage tree

[darijgr]

comment:14

Interesting. The file is supposedly there but actually isn't. But this reminds me of the fact that I have not used ./configure. Maybe I should try again....

[mkoeppe]

comment:15

Replying to @darijgr:

Sadly, doesn't help.

It did, actually, now other errors are preventing the build.

[sagelib-9.2.beta12] g++ -shared -Wl,--enable-auto-image-base -L/home/skraeling/sage/local/lib -Wl,-rpath,/home/skraeling/sage/local/lib build/temp.cygwin-3.1.6-x86_64-3.6/build/cythonized/sage/libs/giac/giac.o -L/home/skraeling/sage/local/lib/python3.6/config -L/usr/lib -lgmp -lgiac -lpython3.6m -o build/lib.cygwin-3.1.6-x86_64-3.6/sage/libs/giac/giac.cpython-36m-x86_64-cygwin.dll -lpari
[sagelib-9.2.beta12] /usr/lib/gcc/x86_64-pc-cygwin/9.3.0/../../../../x86_64-pc-cygwin/bin/ld: /home/skraeling/sage/local/lib/libgiac.a(moyal.o): in function `giac::Airy_Ai(giac::gen const&, giac::context const*)':
[sagelib-9.2.beta12] /home/skraeling/sage/local/var/tmp/sage/build/giac-1.5.0.87p0/src/src/moyal.cc:243: undefined reference to `gsl_sf_airy_Ai'
[sagelib-9.2.beta12] /home/skraeling/sage/local/var/tmp/sage/build/giac-1.5.0.87p0/src/src/moyal.cc:243:(.text+0x63b): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `gsl_sf_airy_Ai'
....

Looks like libgiac is underlinked

[mkoeppe]

comment:16

(This comes from #29171)

[sagetrac-git]

Changed commit from d133f2c to a36d00a

[sagetrac-git]

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

a36d00a

src/sage/libs/giac/giac.pyx: Add libraries to work around underlinked libgiac on cygwin

[mkoeppe]

comment:18

Try with this one please

[darijgr]

comment:19

config.log (just ran ./configure): https://www.dropbox.com/s/lv2r3wq2qz55th3/config.log?dl=0

---

New commits:

a36d00a

src/sage/libs/giac/giac.pyx: Add libraries to work around underlinked libgiac on cygwin

[darijgr]

comment:20

New failure, with your new commit: https://www.dropbox.com/s/lv2r3wq2qz55th3/config.log?dl=0

[darijgr]

comment:21

Oops, wrong link.
https://www.dropbox.com/s/1lsao5jh7l8i67y/install3.log?dl=0

[darijgr]

comment:46

This errors out again again:
https://www.dropbox.com/s/do329gofsaxxw3w/install6.log?dl=0
Note that I have not run "make distclean" after pulling; I've just done the ./configure you suggested and tried to make build again.

[sagetrac-git]

comment:47

Attachment: giac-1.5.0.87p2.tar.bz2.gz

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

c47b078

build/pkgs/giac: Fixup: Ensure shared library build on cygwin

[sagetrac-git]

Changed commit from d48a91a to c47b078

[mkoeppe]

comment:48

Thanks for testing. Here's a better version

[mkoeppe]

Changed reviewer from Darij Grinberg to Darij Grinberg, https://github.com/mkoeppe/sage/actions/runs/250810927

[darijgr]

comment:50

Smaller install.log, still failing (don't mind the interrupt; I had to turn off my PC in the process). Again it's sagelib that's failing, not giac.
https://www.dropbox.com/s/xhzrzwzt27643wf/install7.log?dl=0

[mkoeppe]

comment:51

Thanks for testing, we are getting closer.

[giac-1.5.0.87p2] /usr/bin/bash ../libtool  --tag=CXX   --mode=link g++ -std=gnu++11  -g -O2  -fno-strict-aliasing -DGIAC_GENERIC_CONSTANTS -no-undefined -L/home/skraeling/sage/local/lib -Wl,-rpath,/home/skraeling/sage/local/lib  -o libgiac.la -rpath /home/skraeling/sage/local/lib input_lexer.lo sym2poly.lo gausspol.lo threaded.lo moyal.lo maple.lo ti89.lo mathml.lo misc.lo permu.lo quater.lo desolve.lo input_parser.lo symbolic.lo index.lo modpoly.lo modfactor.lo ezgcd.lo derive.lo solve.lo intg.lo intgab.lo risch.lo lin.lo series.lo subst.lo vecteur.lo sparse.lo csturm.lo tex.lo global.lo ifactor.lo alg_ext.lo gauss.lo isom.lo plot.lo plot3d.lo rpn.lo prog.lo pari.lo cocoa.lo unary.lo usual.lo identificateur.lo gen.lo tinymt32.lo first.lo TmpLESystemSolver.lo TmpFGLM.lo help.lo lpsolve.lo optimization.lo signalprocessing.lo graphe.lo graphtheory.lo nautywrapper.lo markup.lo kdisplay.lo kadd.lo -lntl  -lpari -lgsl -lopenblas -lm  -lopenblas  -lopenblas  -lintl -lrt -lpthread -lnauty -lcurl -lglpk -ldl -lm -lecm -lmpfi -lmpfr -lgmp 
[giac-1.5.0.87p2] 
[giac-1.5.0.87p2] *** Warning: linker path does not have real file for library -lnauty.
[giac-1.5.0.87p2] *** I have the capability to make that library automatically link in when
[giac-1.5.0.87p2] *** you link to this library.  But I can only do this if you have a
[giac-1.5.0.87p2] *** shared version of the library, which you do not appear to have
[giac-1.5.0.87p2] *** because I did check the linker path looking for a file starting
[giac-1.5.0.87p2] *** with libnauty and none of the candidates passed a file format test
[giac-1.5.0.87p2] *** using a file magic. Last file checked: /home/skraeling/sage/local/lib/libnauty.a
[giac-1.5.0.87p2] *** The inter-library dependencies that have been dropped here will be
[giac-1.5.0.87p2] *** automatically added whenever a program is linked with this library
[giac-1.5.0.87p2] *** or is declared to -dlopen it.
[giac-1.5.0.87p2] 
[giac-1.5.0.87p2] *** Since this library must not contain undefined symbols,
[giac-1.5.0.87p2] *** because either the platform does not support them or
[giac-1.5.0.87p2] *** it was explicitly requested with -no-undefined,
[giac-1.5.0.87p2] *** libtool will only create a static version of it.
[giac-1.5.0.87p2] libtool: link: ar cru .libs/libgiac.a  input_lexer.o sym2poly.o gausspol.o threaded.o moyal.o maple.o ti89.o mathml.o misc.o permu.o quater.o desolve.o input_parser.o symbolic.o index.o modpoly.o modfactor.o ezgcd.o derive.o solve.o intg.o intgab.o risch.o lin.o series.o subst.o vecteur.o sparse.o csturm.o tex.o global.o ifactor.o alg_ext.o gauss.o isom.o plot.o plot3d.o rpn.o prog.o pari.o cocoa.o unary.o usual.o identificateur.o gen.o tinymt32.o first.o TmpLESystemSolver.o TmpFGLM.o help.o lpsolve.o optimization.o signalprocessing.o graphe.o graphtheory.o nautywrapper.o markup.o kdisplay.o kadd.o
[giac-1.5.0.87p2] libtool: link: ranlib .libs/libgiac.a
[giac-1.5.0.87p2] libtool: link: ( cd ".libs" && rm -f "libgiac.la" && ln -s "../libgiac.la" "libgiac.la" )
[giac-1.5.0.87p2] /usr/bin/bash ../libtool  --tag=CXX   --mode=link g++ -std=gnu++11  -g -O2  -fno-strict-aliasing -DGIAC_GENERIC_CONSTANTS -no-undefined -L/home/skraeling/sage/local/lib -Wl,-rpath,/home/skraeling/sage/local/lib  -o libxcas.la  History.lo Input.lo Xcas1.lo Equation.lo Print.lo Tableur.lo Editeur.lo Graph.lo Graph3d.lo Help1.lo Cfg.lo Flv_CStyle.lo Flve_Check_Button.lo Flve_Input.lo Flv_Style.lo Flv_Data_Source.lo Flve_Combo.lo Flv_List.lo Flv_Table.lo gl2ps.lo libgiac.la  -lintl -lrt -lpthread -lnauty -lcurl -lglpk -ldl -lm -lecm -lmpfi -lmpfr -lgmp 

[sagetrac-git]

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

e673110

build/pkgs/giac/spkg-install.in [Cygwin]: Disable linking with libnauty.a

[sagetrac-git]

Changed commit from c47b078 to e673110

[mkoeppe]

comment:53

Please try this one

[darijgr]

comment:54

Compiles and runs this time. Good job! (That said, I haven't "make distclean"ed.)

[mkoeppe]

comment:55

Great! Thanks very much for testing.

[mkoeppe]

Changed reviewer from Darij Grinberg, https://github.com/mkoeppe/sage/actions/runs/250810927 to Darij Grinberg

[darijgr]

comment:57

pats laptop on the back

[mkoeppe]

comment:59

Build from scratch at https://github.com/mkoeppe/sage/runs/1106904182 succeeded in building sagelib too

[tscrim]

comment:60

This now works for me on Ubuntu.

[mkoeppe]

comment:61

Positive review?

[tscrim]

Changed reviewer from Darij Grinberg to Darij Grinberg, Travis Scrimshaw

[tscrim]

comment:62

In terms of things working, yes, but I don't think having new tarballs of a tweaked giac are the way to go. The standard ways are something released from upstream or you include the patch(es) you applied in the $SAGE_ROOT/build/pkgs/giac/patches/ folder with a change in the patch level to 1.5.0.87p1 in the package-version.txt file. (It would also be good to remove the patched bzips from trac to avoid clutter that way.)

[mkoeppe]

comment:63

The new patch modifies autotools source files and therefore the tarball has to be regenerated. See https://doc.sagemath.org/html/en/developer/packaging.html#when-to-patch-when-to-repackage-when-to-autoconfiscate

[tscrim]

comment:64

I see. Thanks for the explanation.

These are in the nitpick category: Could the patched tarball name have a slightly more descriptive description (the numbering p2 also doesn't make sense once it goes into Sage as well). I would leave it also as .p0 since you are patching that new modified version for the first time.

[mkoeppe]

comment:65

giac-1.5.0.87p2 identifies the patched tarball uniquely on the Sage mirrors (... and in testers' upstream/ directories)

[tscrim]

comment:66

However, it won't have a good history on the mirrors as it feels arbitrary. Anyways, I don't care that strongly about it, so feel free to set a positive review if you want to keep the name.

[mkoeppe]

comment:67

Thanks.

[vbraun]

Changed branch from u/mkoeppe/cygwin_standard__sagelib_build_fails to e673110