Opened 19 months ago
Closed 10 months ago
#29327 closed defect (invalid)
Meta-ticket: docker-conda-forge-standard, local-ubuntu-conda-forge-standard: Fix build errors with python3, giac, ecl, m4rie, libgd, ...
| Reported by: | mkoeppe | Owned by: | |
|---|---|---|---|
| Priority: | critical | Milestone: | sage-duplicate/invalid/wontfix |
| Component: | porting | Keywords: | |
| Cc: | isuruf, dimpase, saraedum | Merged in: | |
| Authors: | Reviewers: | Matthias Koeppe, Samuel Lelièvre | |
| Report Upstream: | N/A | Work issues: | |
| Branch: | Commit: | ||
| Dependencies: | #29574, #29596, #29597, #29598, #29601, #26287, #29606, #29612, #29618 | Stopgaps: |
Status badges
Description (last modified by )
docker-conda-forge-standard (https://github.com/mkoeppe/sage/runs/506355319):
python3
problem with
_cryptas discussed in #29102,_sqlite,zlib
giac:/opt/conda/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/tuple:1271:29: error: incomplete type 'std::tuple_size<giac::gen (*)(const giac::gen&)>' used in nested name specifier inline constexpr size_t tuple_size_v = tuple_size<_Tp>::value; ^~~~~~~~~~~~ maple.cc: In function 'giac::gen giac::_evalc(const giac::gen&, const giac::context*)': maple.cc:948:24: error: invalid use of 'void' vecteur lp=*apply(l,gen_feuille)._VECTptr; ~~~~~^~~~~~~~~~~~~~~ maple.cc:948:24: error: invalid use of 'void' maple.cc: In function 'giac::gen giac::crsolve(const giac::gen&, const giac::gen&, const giac::gen&, giac::vecteur&, const giac::context*)': maple.cc:2765:19: error: invalid use of 'void' aplatir(*apply(initcond0,equal2diff)._VECTptr,initcond); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ maple.cc:2765:19: error: invalid use of 'void' make[4]: *** [Makefile:790: maple.lo] Error 1
Also libatomic_ops testsuite. (see #28745)
conda-forge-minimal (https://github.com/mkoeppe/sage/runs/506355315):
python3
(see above)
pari### ### Readline library does not seem to work. Maybe install libncurses? ### ### Building without GNU readline support ... /opt/conda/bin/x86_64-conda_cos6-linux-gnu-cc -o gp-dyn -L"/sage/local/var/tmp/sage/build/pari-2.11.2/src/Olinux-x86_64" -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include -Wl,--export-dynamic -L/sage/local/lib -Wl,-rpath,/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib emacs.o gp.o gp_rl.o texmacs.o whatnow.o plotnone.o -Wl,-rpath,"/sage/local/var/tmp/sage/build/pari-2.11.2/src"/Olinux-x86_64:"/sage/local/lib":/sage/local/lib -lpari -lm /opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libgmp.so.23, needed by /sage/local/var/tmp/sage/build/pari-2.11.2/src/Olinux-x86_64/libpari.so, not found (try using -rpath or -rpath-link) /opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /sage/local/var/tmp/sage/build/pari-2.11.2/src/Olinux-x86_64/libpari.so: undefined reference to `__gmpn_divrem_1'
ecl;;; Note: ;;; Invoking external command: ;;; /opt/conda/bin/x86_64-conda_cos6-linux-gnu-cc -o bin/ecl -L/sage/local/var/tmp/sage/build/ecl-16.1.2.p5/src/build/ /sage/local/var/tmp/sage/build/ecl-16.1.2.p5/src/build/eclinitZhjSpA.o -L./ -Wl,--rpath,/sage/local/lib/ -L/sage/local/lib -Wl,-rpath,/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib libecl.so -lgc -ldl -lm /opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libgmp.so.23, needed by libecl.so, not found (try using -rpath or -rpath-link) /opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: libecl.so: undefined reference to `__gmpz_get_si' /opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: libecl.so: undefined reference to `__gmpz_scan1'
m4rie[m4rie-20200115] libtool: link: /opt/conda/bin/x86_64-conda_cos6-linux-gnu-cc -I/include -mmmx -msse -msse2 -msse3 -I.. -O2 -fPIC -Wall -pedantic -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -I/sage/local/include -o test_multiplication test_multiplication.o -L/lib ../.libs/libm4rie.so -lm4ri -lm -Wl,-rpath -Wl,/sage/local/var/tmp/sage/build/m4rie-20200115/src/.libs -Wl,-rpath -Wl,/sage/local/lib [m4rie-20200115] /opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lm4ri
libgdlibtool: link: /opt/conda/bin/x86_64-conda_cos6-linux-gnu-cc -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fvisibility=hidden -Wl,-rpath -Wl,/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath -Wl,/opt/conda/lib -Wl,-rpath-link -Wl,/opt/conda/lib -o .libs/gdcmpgif gdcmpgif.o -L/sage/local/lib -L/opt/conda/lib ./.libs/libgd.so -lz -lm -lpng16 -lfreetype -Wl,-rpath -Wl,/sage/local/lib /opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libbz2.so.1, needed by /sage/local/lib/libfreetype.so, not found (try using -rpath or -rpath-link) /opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /sage/local/lib/libfreetype.so: undefined reference to `BZ2_bzDecompressInit'
To reproduce:
EXTRA_DOCKER_BUILD_ARGS="--build-arg TARGETS=\"build ptest\" --build-arg USE_MAKEFLAGS=\"-k V=0\"" tox -e docker-conda-forge-standard
Attachments (1)
Change History (41)
comment:1 Changed 19 months ago by
- Cc dimpase saraedum added
comment:2 Changed 19 months ago by
- Description modified (diff)
comment:3 Changed 19 months ago by
- Description modified (diff)
comment:4 Changed 19 months ago by
- Description modified (diff)
- Summary changed from Fix build errors with python3, giac, ecl, m4rie, libgd on conda-forge to Fix build errors with python3, giac, ecl, m4rie, libgd on docker-conda-forge-standard
comment:5 Changed 18 months ago by
- Summary changed from Fix build errors with python3, giac, ecl, m4rie, libgd on docker-conda-forge-standard to Fix build errors with python3, giac, ecl, m4rie, libgd on docker-conda-forge-standard and local-ubuntu-conda-forge-standard
comment:6 Changed 18 months ago by
comment:7 Changed 18 months ago by
- Priority changed from major to critical
comment:8 Changed 18 months ago by
Is this on docker only, or on "real" conda the same pops up too?
comment:9 Changed 18 months ago by
I do not have any "real" Linux installation. All my tests on Linux are via Docker and/or on GitHub Actions.
Install on conda on macOS - works completely, with the last remaining bits being #29574 and #29572.
The present ticket is about conda on Linux. I have two types of tests here.
local-ubuntu-conda-forgeruns on anubuntu-latestmachine on GitHub Actions. The conda-forge installation is done bytox -e local-conda-forge, which uses Miniforge. You can run this tox command on any Linux machine to test it.
docker-conda-forgeuses thecontinuumio/miniconda3image and switches to the conda-forge channel.
On both configurations I get similar installation failures, as in the ticket description.
It would be really nice to be able to say that one can install the Sage distribution even if conda is active... but this is not true at the moment because of these failures.
comment:10 follow-up: ↓ 13 Changed 18 months ago by
Most recent runs:
conda-forge-ubuntu-minimalhttps://github.com/mkoeppe/sage/runs/618647294m4rie,pari,python3,eclfail
conda-forge-ubuntu-standardhttps://github.com/mkoeppe/sage/runs/618647333:openblasandsingularfail
conda-forge-ubuntu-standard-python2https://github.com/mkoeppe/sage/runs/618647336python2andpython3fail
comment:11 Changed 18 months ago by
https://trac.sagemath.org/ticket/29596 should fix the pari, ecl, libgd issue.
comment:12 Changed 18 months ago by
https://trac.sagemath.org/ticket/29597 should fix m4rie
comment:13 in reply to: ↑ 10 ; follow-up: ↓ 14 Changed 18 months ago by
Replying to mkoeppe:
conda-forge-ubuntu-standardhttps://github.com/mkoeppe/sage/runs/618647333:
openblasandsingularfail
Do you have the config.log? It fails to find openblas from conda-forge.
comment:14 in reply to: ↑ 13 Changed 18 months ago by
Replying to isuruf:
Replying to mkoeppe:
conda-forge-ubuntu-standardhttps://github.com/mkoeppe/sage/runs/618647333:
openblasandsingularfailDo you have the config.log? It fails to find openblas from conda-forge.
Whole log archive is at https://github.com/mkoeppe/sage/suites/628495286/artifacts/5093478
comment:15 Changed 18 months ago by
## --------------------------------------------------------- ## ## Checking whether SageMath should install SPKG openblas... ## ## --------------------------------------------------------- ## configure:11652: checking BLAS library configure:11671: result: openblas configure:11720: checking whether any of gfortran is installed as or will be installed as SPKG configure:11729: result: no configure:11740: checking for openblas >= 0.2.20 configure:11747: $PKG_CONFIG --exists --print-errors "openblas >= 0.2.20" configure:11750: $? = 0 configure:11764: $PKG_CONFIG --exists --print-errors "openblas >= 0.2.20" configure:11767: $? = 0 configure:12745: result: yes configure:12755: $PKG_CONFIG --exists --print-errors "openblas" configure:12758: $? = 0 configure:12779: checking for cblas_dgemm configure:12779: /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/bin/x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -o conftest -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/lib -Wl,-rpath-link,/home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/lib -L/home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/lib conftest.cpp -L/home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/lib -lopenblas -larb -lflint -lmpfr -lgmp -lm -lntl >&5 /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/lib/libopenblas.a(memory.o): in function `openblas_fork_handler': memory.c:(.text.openblas_fork_handler+0x11): undefined reference to `pthread_atfork' /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/lib/libopenblas.a(blas_server.o): in function `blas_thread_init': blas_server.c:(.text.blas_thread_init+0x12f): undefined reference to `pthread_create' /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/lib/libopenblas.a(blas_server.o): in function `blas_thread_shutdown_': blas_server.c:(.text.blas_thread_shutdown_+0xc9): undefined reference to `pthread_join' collect2: error: ld returned 1 exit status configure:12779: $? = 1
comment:16 Changed 18 months ago by
Thanks. See https://trac.sagemath.org/ticket/29598
comment:17 Changed 18 months ago by
Thanks very much. Running tests with these tickets merged at https://github.com/mkoeppe/sage/actions/runs/88744943
comment:18 Changed 18 months ago by
Singular issue is https://trac.sagemath.org/ticket/29601
comment:19 follow-up: ↓ 20 Changed 18 months ago by
libatomic_ops issue is https://trac.sagemath.org/ticket/29602
comment:20 in reply to: ↑ 19 Changed 18 months ago by
Replying to isuruf:
libatomic_ops issue is https://trac.sagemath.org/ticket/29602
Let's use #26287 (Upgrade to gc 8.0.4 and libatomic 7.6.10)
comment:21 Changed 18 months ago by
New tests run at https://github.com/mkoeppe/sage/actions/runs/89365078
comment:22 Changed 18 months ago by
maxima (via ecl) has an issue with the linker flags too:
; - Loading binary file "binary-ecl/init-cl.fas"
; - Providing system maxima
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: unrecognized option '--sort-common -Wl'
/opt/conda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: use the --help option for usage information
collect2: error: ld returned 1 exit status
An error occurred during initialization:
Error code 1 when executing
(RUN-PROGRAM "/opt/conda/bin/x86_64-conda_cos6-linux-gnu-cc" ("-o"
"binary-ecl/maxima.fas"
"-L/sage/local/lib/"
"/tmp/eclinitM31sB3.o"
"binary-ecl/maxima-package.o"
"binary-ecl/ecl-port.o"
"binary-ecl/autoconf-variables.o"
"binary-ecl/intl.o"
"binary-ecl/nregex.o"
"binary-ecl/cl-info.o"
"binary-ecl/sloop.o"
"binary-ecl/lmdcls.o"
"binary-ecl/letmac.o"
"binary-ecl/generr.o"
"binary-ecl/clmacs.o"
"binary-ecl/commac.o"
"binary-ecl/mormac.o"
"binary-ecl/compat.o"
"binary-ecl/transm.o"
"binary-ecl/getopt.o"
"binary-ecl/command-line.o"
"binary-ecl/defcal.o"
"binary-ecl/maxmac.o"
"binary-ecl/mopers.o"
"binary-ecl/mforma.o"
"binary-ecl/mrgmac.o"
"binary-ecl/rzmac.o"
"binary-ecl/strmac.o"
"binary-ecl/displm.o"
"binary-ecl/safe-recursion.o"
"binary-ecl/ratmac.o"
"binary-ecl/mhayat.o"
"binary-ecl/opers.o"
"binary-ecl/utils.o"
"binary-ecl/sumcon.o"
"binary-ecl/sublis.o"
"binary-ecl/merror.o"
"binary-ecl/mformt.o"
"binary-ecl/mutils.o"
"binary-ecl/outmis.o"
"binary-ecl/ar.o"
"binary-ecl/comm.o"
"binary-ecl/comm2.o"
"binary-ecl/mlisp.o"
"binary-ecl/mmacro.o"
"binary-ecl/buildq.o"
"binary-ecl/numerical/f2cl-package.o"
"binary-ecl/numerical/slatec.o"
"binary-ecl/numerical/f2cl-lib.o"
"binary-ecl/numerical/slatec/fdump.o"
"binary-ecl/numerical/slatec/j4save.o"
"binary-ecl/numerical/slatec/xercnt.o"
"binary-ecl/numerical/slatec/xerhlt.o"
"binary-ecl/numerical/slatec/xgetua.o"
"binary-ecl/numerical/slatec/xerprn.o"
"binary-ecl/numerical/slatec/xersve.o"
"binary-ecl/numerical/slatec/xermsg.o"
"binary-ecl/numerical/slatec/initds.o"
"binary-ecl/numerical/slatec/dcsevl.o"
"binary-ecl/numerical/slatec/d9lgmc.o"
"binary-ecl/numerical/slatec/dgamlm.o"
"binary-ecl/numerical/slatec/dgamma.o"
"binary-ecl/numerical/slatec/dgamln.o"
"binary-ecl/numerical/slatec/dlngam.o"
"binary-ecl/numerical/slatec/d9b0mp.o"
"binary-ecl/numerical/slatec/d9b1mp.o"
"binary-ecl/numerical/slatec/dbesj0.o"
"binary-ecl/numerical/slatec/dbesj1.o"
"binary-ecl/numerical/slatec/djairy.o"
"binary-ecl/numerical/slatec/dasyjy.o"
"binary-ecl/numerical/slatec/dbesj.o"
"binary-ecl/numerical/slatec/dbsi0e.o"
"binary-ecl/numerical/slatec/dbsi1e.o"
"binary-ecl/numerical/slatec/dbesi0.o"
"binary-ecl/numerical/slatec/dbesi1.o"
"binary-ecl/numerical/slatec/dasyik.o"
"binary-ecl/numerical/slatec/dbesi.o"
"binary-ecl/numerical/slatec/zabs.o"
"binary-ecl/numerical/slatec/zdiv.o"
"binary-ecl/numerical/slatec/zexp.o"
"binary-ecl/numerical/slatec/zmlt.o"
"binary-ecl/numerical/slatec/zsqrt.o"
"binary-ecl/numerical/slatec/zasyi.o"
"binary-ecl/numerical/slatec/zuchk.o"
"binary-ecl/numerical/slatec/zlog.o"
"binary-ecl/numerical/slatec/zunik.o"
"binary-ecl/numerical/slatec/zunhj.o"
"binary-ecl/numerical/slatec/zuoik.o"
"binary-ecl/numerical/slatec/zuni1.o"
"binary-ecl/numerical/slatec/zkscl.o"
"binary-ecl/numerical/slatec/zshch.o"
"binary-ecl/numerical/slatec/zbknu.o"
"binary-ecl/numerical/slatec/zmlri.o"
"binary-ecl/numerical/slatec/zs1s2.o"
"binary-ecl/numerical/slatec/zseri.o"
"binary-ecl/numerical/slatec/zacai.o"
"binary-ecl/numerical/slatec/zairy.o"
"binary-ecl/numerical/slatec/zuni2.o"
"binary-ecl/numerical/slatec/zbuni.o"
"binary-ecl/numerical/slatec/zrati.o"
"binary-ecl/numerical/slatec/zwrsk.o"
"binary-ecl/numerical/slatec/zbinu.o"
"binary-ecl/numerical/slatec/zbesi.o"
"binary-ecl/numerical/slatec/zbesj.o"
"binary-ecl/numerical/slatec/dbesy0.o"
"binary-ecl/numerical/slatec/dbesy1.o"
"binary-ecl/numerical/slatec/dbsynu.o"
"binary-ecl/numerical/slatec/dyairy.o"
"binary-ecl/numerical/slatec/dbesy.o"
"binary-ecl/numerical/slatec/zacon.o"
"binary-ecl/numerical/slatec/zunk1.o"
"binary-ecl/numerical/slatec/zunk2.o"
"binary-ecl/numerical/slatec/zbunk.o"
"binary-ecl/numerical/slatec/zbesh.o"
"binary-ecl/numerical/slatec/zbesy.o"
"binary-ecl/numerical/slatec/dbsk0e.o"
"binary-ecl/numerical/slatec/dbesk0.o"
"binary-ecl/numerical/slatec/dbsk1e.o"
"binary-ecl/numerical/slatec/dbesk1.o"
"binary-ecl/numerical/slatec/dbsknu.o"
"binary-ecl/numerical/slatec/dbesk.o"
"binary-ecl/numerical/slatec/zbesk.o"
"binary-ecl/numerical/slatec/d9aimp.o"
"binary-ecl/numerical/slatec/daie.o"
"binary-ecl/numerical/slatec/dai.o"
"binary-ecl/numerical/slatec/dbie.o"
"binary-ecl/numerical/slatec/dbi.o"
"binary-ecl/numerical/slatec/zbiry.o"
"binary-ecl/numerical/slatec/derfc.o"
"binary-ecl/numerical/slatec/derf.o"
"binary-ecl/numerical/slatec/de1.o"
"binary-ecl/numerical/slatec/dei.o"
"binary-ecl/numerical/slatec/d9upak.o"
"binary-ecl/numerical/slatec/dspenc.o"
"binary-ecl/numerical/slatec/dqwgtf.o"
"binary-ecl/numerical/slatec/dqcheb.o"
"binary-ecl/numerical/slatec/dqk15w.o"
"binary-ecl/numerical/slatec/dqwgts.o"
"binary-ecl/numerical/slatec/dqwgtc.o"
"binary-ecl/numerical/slatec/dgtsl.o"
"binary-ecl/numerical/slatec/dqk15.o"
"binary-ecl/numerical/slatec/dqk31.o"
"binary-ecl/numerical/slatec/dqk41.o"
"binary-ecl/numerical/slatec/dqk51.o"
"binary-ecl/numerical/slatec/dqk61.o"
"binary-ecl/numerical/slatec/dqk21.o"
"binary-ecl/numerical/slatec/dqk15i.o"
"binary-ecl/numerical/slatec/dqelg.o"
"binary-ecl/numerical/slatec/dqpsrt.o"
"binary-ecl/numerical/slatec/dqc25s.o"
"binary-ecl/numerical/slatec/dqmomo.o"
"binary-ecl/numerical/slatec/dqc25c.o"
"binary-ecl/numerical/slatec/dqc25f.o"
"binary-ecl/numerical/slatec/dqage.o"
"binary-ecl/numerical/slatec/dqagie.o"
"binary-ecl/numerical/slatec/dqagpe.o"
"binary-ecl/numerical/slatec/dqagp.o"
"binary-ecl/numerical/slatec/dqagse.o"
"binary-ecl/numerical/slatec/dqawoe.o"
"binary-ecl/numerical/slatec/dqawfe.o"
"binary-ecl/numerical/slatec/dqawse.o"
"binary-ecl/numerical/slatec/dqawce.o"
"binary-ecl/numerical/slatec/dqng.o"
"binary-ecl/numerical/slatec/dqag.o"
"binary-ecl/numerical/slatec/dqags.o"
"binary-ecl/numerical/slatec/dqagi.o"
"binary-ecl/numerical/slatec/dqawf.o"
"binary-ecl/numerical/slatec/dqawo.o"
"binary-ecl/numerical/slatec/dqaws.o"
"binary-ecl/numerical/slatec/dqawc.o"
"binary-ecl/numerical/slatec/quadpack.o"
"binary-ecl/simp.o"
"binary-ecl/float.o"
"binary-ecl/csimp.o"
"binary-ecl/csimp2.o"
"binary-ecl/zero.o"
"binary-ecl/logarc.o"
"binary-ecl/rpart.o"
"binary-ecl/numeric.o"
"binary-ecl/server.o"
"binary-ecl/macsys.o"
"binary-ecl/mload.o"
"binary-ecl/suprv1.o"
"binary-ecl/dskfn.o"
"binary-ecl/lesfac.o"
"binary-ecl/factor.o"
"binary-ecl/algfac.o"
"binary-ecl/nalgfa.o"
"binary-ecl/ufact.o"
"binary-ecl/result.o"
"binary-ecl/ifactor.o"
"binary-ecl/rat3a.o"
"binary-ecl/rat3b.o"
"binary-ecl/rat3d.o"
"binary-ecl/rat3c.o"
"binary-ecl/rat3e.o"
"binary-ecl/nrat4.o"
"binary-ecl/ratout.o"
"binary-ecl/transl.o"
"binary-ecl/transs.o"
"binary-ecl/trans1.o"
"binary-ecl/trans2.o"
"binary-ecl/trans3.o"
"binary-ecl/trans4.o"
"binary-ecl/trans5.o"
"binary-ecl/transf.o"
"binary-ecl/troper.o"
"binary-ecl/trutil.o"
"binary-ecl/trmode.o"
"binary-ecl/trdata.o"
"binary-ecl/trpred.o"
"binary-ecl/transq.o"
"binary-ecl/acall.o"
"binary-ecl/fcall.o"
"binary-ecl/evalw.o"
"binary-ecl/trprop.o"
"binary-ecl/mdefun.o"
"binary-ecl/schatc.o"
"binary-ecl/matcom.o"
"binary-ecl/matrun.o"
"binary-ecl/nisimp.o"
"binary-ecl/trigi.o"
"binary-ecl/trigo.o"
"binary-ecl/trgred.o"
"binary-ecl/bessel.o"
"binary-ecl/ellipt.o"
"binary-ecl/airy.o"
"binary-ecl/plasma.o"
"binary-ecl/intpol.o"
"binary-ecl/nparse.o"
"binary-ecl/displa.o"
"binary-ecl/nforma.o"
"binary-ecl/grind.o"
"binary-ecl/spgcd.o"
"binary-ecl/ezgcd.o"
"binary-ecl/option.o"
"binary-ecl/macdes.o"
"binary-ecl/inmis.o"
"binary-ecl/db.o"
"binary-ecl/compar.o"
"binary-ecl/askp.o"
"binary-ecl/sinint.o"
"binary-ecl/sin.o"
"binary-ecl/risch.o"
"binary-ecl/hayat.o"
"binary-ecl/defint.o"
"binary-ecl/residu.o"
"binary-ecl/specfn.o"
"binary-ecl/mat.o"
"binary-ecl/linnew.o"
"binary-ecl/matrix.o"
"binary-ecl/sprdet.o"
"binary-ecl/newinv.o"
"binary-ecl/newdet.o"
"binary-ecl/tlimit.o"
"binary-ecl/limit.o"
"binary-ecl/solve.o"
"binary-ecl/psolve.o"
"binary-ecl/algsys.o"
"binary-ecl/sqrtdenest.o"
"binary-ecl/polyrz.o"
"binary-ecl/cpoly.o"
"binary-ecl/mtrace.o"
"binary-ecl/mdebug.o"
"binary-ecl/scs.o"
"binary-ecl/asum.o"
"binary-ecl/fortra.o"
"binary-ecl/optim.o"
"binary-ecl/marray.o"
"binary-ecl/mdot.o"
"binary-ecl/irinte.o"
"binary-ecl/series.o"
"binary-ecl/numth.o"
"binary-ecl/laplac.o"
"binary-ecl/pade.o"
"binary-ecl/homog.o"
"binary-ecl/combin.o"
"binary-ecl/nset.o"
"binary-ecl/rand-mt19937.o"
"binary-ecl/maxmin.o"
"binary-ecl/nummod.o"
"binary-ecl/conjugate.o"
"binary-ecl/expintegral.o"
"binary-ecl/gamma.o"
"binary-ecl/mstuff.o"
"binary-ecl/pois2.o"
"binary-ecl/pois3.o"
"binary-ecl/desoln.o"
"binary-ecl/elim.o"
"binary-ecl/invert.o"
"binary-ecl/hypgeo.o"
"binary-ecl/hyp.o"
"binary-ecl/todd-coxeter.o"
"binary-ecl/mactex.o"
"binary-ecl/plot.o"
"binary-ecl/gnuplot_def.o"
"binary-ecl/xmaxima_def.o"
"binary-ecl/autol.o"
"binary-ecl/max_ext.o"
"binary-ecl/share-subdirs.o"
"binary-ecl/init-cl.o"
"-Wl,-rpath-link,/sage/local/lib -L/sage/local/lib -Wl,-rpath,/sage/local/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib"
"-Wl,--rpath,/sage/local/lib/"
"-shared"
"-Wl,-rpath-link,/sage/local/lib"
"-L/sage/local/lib"
"-Wl,-rpath,/sage/local/lib"
"-Wl,-O2"
"-Wl,--sort-common"
"-Wl,--as-needed"
"-Wl,-z,relro"
"-Wl,-z,now"
"-Wl,--disable-new-dtags"
"-Wl,--gc-sections"
"-Wl,-rpath,/opt/conda/lib"
"-Wl,-rpath-link,/opt/conda/lib"
"-L/opt/conda/lib"
"-Wl,-rpath-link,/sage/local/lib"
"-L/sage/local/lib"
"-Wl,-rpath,/sage/local/lib"
"-Wl,-O2"
"-Wl,--sort-common"
"-Wl,--as-needed"
"-Wl,-z,relro"
"-Wl,-z,now"
"-Wl,--disable-new-dtags"
"-Wl,--gc-sections"
"-Wl,-rpath,/opt/conda/lib"
"-Wl,-rpath-link,/opt/conda/lib"
"-L/opt/conda/lib"
"-lecl" "-lgmp"
"-lgc" "-lffi"
"-lgc" "-ldl"
"-lm")).
make[5]: *** [Makefile:1350: binary-ecl/maxima] Error 1
make[5]: Target 'all' not remade because of errors.
make[5]: Leaving directory '/sage/local/var/tmp/sage/build/maxima-5.42.2/src/src'
Making all in lisp-utils
comment:23 Changed 18 months ago by
(This one is from tox -e docker-conda-forge-standard )
comment:24 Changed 18 months ago by
Fixed by #29606 (build/pkgs/maxima/spkg-install.in: Do not pass on LDFLAGS)
comment:25 Changed 18 months ago by
comment:26 Changed 18 months ago by
comment:27 Changed 18 months ago by
docker-conda-forge-standard now builds OK (https://github.com/mkoeppe/sage/runs/624793624), but a large number of doctest failures occurs
sage -t src/sage/categories/primer.py # 1 doctest failed sage -t src/sage/combinat/quickref.py # 1 doctest failed sage -t src/sage/combinat/tutorial.py # 1 doctest failed sage -t src/sage/geometry/cone.py # 5 doctests failed sage -t src/sage/geometry/fan.py # 86 doctests failed sage -t src/sage/geometry/fan_isomorphism.py # 12 doctests failed sage -t src/sage/geometry/fan_morphism.py # 92 doctests failed sage -t src/sage/geometry/lattice_polytope.py # 174 doctests failed sage -t src/sage/geometry/polyhedron/backend_normaliz.py # 1 doctest failed sage -t src/sage/geometry/polyhedron/base_ZZ.py # 2 doctests failed sage -t src/sage/geometry/polyhedron/palp_database.py # 2 doctests failed sage -t src/sage/geometry/polyhedron/base.py # 7 doctests failed sage -t src/sage/geometry/polyhedron/ppl_lattice_polytope.py # 3 doctests failed sage -t src/sage/geometry/toric_plotter.py # 17 doctests failed sage -t src/sage/geometry/triangulation/element.py # 1 doctest failed sage -t src/sage/libs/glpk/error.pyx # 1 doctest failed sage -t src/sage/misc/cython.py # 3 doctests failed sage -t src/sage/modules/filtered_vector_space.py # 5 doctests failed sage -t src/sage/numerical/backends/glpk_backend.pyx # 1 doctest failed sage -t src/sage/rings/number_field/totallyreal_rel.py # 4 doctests failed sage -t src/sage/schemes/generic/algebraic_scheme.py # 13 doctests failed sage -t src/sage/schemes/generic/homset.py # 3 doctests failed sage -t src/sage/schemes/toric/chow_group.py # 159 doctests failed sage -t src/sage/schemes/toric/divisor.py # 234 doctests failed sage -t src/sage/schemes/toric/divisor_class.pyx # 50 doctests failed sage -t src/sage/schemes/toric/fano_variety.py # 137 doctests failed sage -t src/sage/schemes/toric/homset.py # 72 doctests failed sage -t src/sage/schemes/toric/library.py # 74 doctests failed sage -t src/sage/schemes/toric/morphism.py # 194 doctests failed sage -t src/sage/schemes/toric/points.py # 108 doctests failed sage -t src/sage/schemes/toric/sheaf/constructor.py # 29 doctests failed sage -t src/sage/schemes/toric/sheaf/klyachko.py # 101 doctests failed sage -t src/sage/schemes/toric/toric_subscheme.py # 104 doctests failed sage -t src/sage/schemes/toric/variety.py # 229 doctests failed sage -t src/sage/schemes/toric/weierstrass.py # 6 doctests failed sage -t src/sage/schemes/toric/weierstrass_covering.py # 9 doctests failed sage -t src/sage/tests/books/computational-mathematics-with-sagemath/combinat_doctest.py # 1 doctest failed
comment:28 Changed 18 months ago by
docker-conda-forge-minimal (https://github.com/mkoeppe/sage/runs/624793614) got farther too, now has a testsuite failure in symmetrica, and still the build error in python3.
comment:29 Changed 18 months ago by
Most of them are of the form,
2020-04-28T07:35:02.7114886Z File "src/sage/schemes/toric/divisor.py", line 1926, in sage.schemes.toric.divisor.ToricRationalDivisorClassGroup
2020-04-28T07:35:02.7115019Z Failed example:
2020-04-28T07:35:02.7115157Z P2 = toric_varieties.P2()
2020-04-28T07:35:02.7115258Z Exception raised:
2020-04-28T07:35:02.7115360Z Traceback (most recent call last):
2020-04-28T07:35:02.7115725Z File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
2020-04-28T07:35:02.7115858Z self.compile_and_execute(example, compiler, test.globs)
2020-04-28T07:35:02.7116212Z File "/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
2020-04-28T07:35:02.7116337Z exec(compiled, globs)
2020-04-28T07:35:02.7116448Z File "<doctest sage.schemes.toric.divisor.ToricRationalDivisorClassGroup[0]>", line 1, in <module>
2020-04-28T07:35:02.7116576Z P2 = toric_varieties.P2()
2020-04-28T07:35:02.7116910Z File "/sage/local/lib/python3.7/site-packages/sage/schemes/toric/library.py", line 531, in P2
2020-04-28T07:35:02.7117218Z return self._make_CPRFanoToricVariety('P2', names, base_ring)
2020-04-28T07:35:02.7117588Z File "/sage/local/lib/python3.7/site-packages/sage/schemes/toric/library.py", line 267, in _make_CPRFanoToricVariety
2020-04-28T07:35:02.7117724Z points = [tuple(_) for _ in polytope.points()]
2020-04-28T07:35:02.7118071Z File "/sage/local/lib/python3.7/site-packages/sage/geometry/lattice_polytope.py", line 3747, in points
2020-04-28T07:35:02.7118190Z points = read_palp_point_collection(StringIO(result), M)
2020-04-28T07:35:02.7118333Z File "sage/geometry/point_collection.pyx", line 1000, in sage.geometry.point_collection.read_palp_point_collection (build/cythonized/sage/geometry/point_collection.c:8112)
2020-04-28T07:35:02.7118464Z m = int(first_line[0])
2020-04-28T07:35:02.7118763Z ValueError: invalid literal for int() with base 10: 'Bad'
comment:30 Changed 18 months ago by
Is this gfan?
comment:31 Changed 18 months ago by
It's a palp issue. https://trac.sagemath.org/ticket/29612
comment:32 Changed 18 months ago by
Tests (also with #29607; but not with #29612) run at https://github.com/mkoeppe/sage/actions/runs/90914869
comment:33 Changed 18 months ago by
- Dependencies set to #29574, #29596, #29597, #29598, #29601, #26287, #29606, #29612, #29618
- Summary changed from Fix build errors with python3, giac, ecl, m4rie, libgd on docker-conda-forge-standard and local-ubuntu-conda-forge-standard to Meta-ticket: docker-conda-forge-standar, local-ubuntu-conda-forge-standard: Fix build errors with python3, giac, ecl, m4rie, libgd, ...
comment:34 Changed 18 months ago by
- Summary changed from Meta-ticket: docker-conda-forge-standar, local-ubuntu-conda-forge-standard: Fix build errors with python3, giac, ecl, m4rie, libgd, ... to Meta-ticket: docker-conda-forge-standard, local-ubuntu-conda-forge-standard: Fix build errors with python3, giac, ecl, m4rie, libgd, ...
comment:35 Changed 18 months ago by
Failures of some optional packages on conda-forge-macos can be seen at https://github.com/mkoeppe/sage/runs/631927929
comment:36 Changed 18 months ago by
libsemigroups failure is fixed in later releases. Is there a config.log for latte_int failure?
comment:37 Changed 18 months ago by
- Milestone changed from sage-9.1 to sage-duplicate/invalid/wontfix
- Status changed from new to needs_review
Let's close this ticket and revisit optional package at some time in the 9.2 cycle after updates have been done, including probably a latte_int update.
comment:38 Changed 13 months ago by
- Status changed from needs_review to positive_review
Is there a follow-up ticket for this? We're well into the 9.2 cycle.
comment:39 Changed 13 months ago by
- Reviewers set to Matthias Koeppe, Samuel Lelièvre
comment:40 Changed 10 months ago by
- Resolution set to invalid
- Status changed from positive_review to closed
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conda builds on macos work, but on linux all of these errors show up.