#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 mkoeppe)

docker-conda-forge-standard (https://github.com/mkoeppe/sage/runs/506355319):

  • python3

problem with _crypt as 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
    
  • libgd
    libtool: 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)

config.log (379.7 KB) - added by mkoeppe 18 months ago.
local-conda-forge-ubuntu-standard config.log

Download all attachments as: .zip

Change History (41)

comment:1 Changed 19 months ago by mkoeppe

  • Cc dimpase saraedum added

comment:2 Changed 19 months ago by mkoeppe

  • Description modified (diff)

comment:3 Changed 19 months ago by mkoeppe

  • Description modified (diff)

comment:4 Changed 19 months ago by mkoeppe

  • 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 mkoeppe

  • 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 mkoeppe

conda builds on macos work, but on linux all of these errors show up.

comment:7 Changed 18 months ago by mkoeppe

  • Priority changed from major to critical

comment:8 Changed 18 months ago by dimpase

Is this on docker only, or on "real" conda the same pops up too?

comment:9 Changed 18 months ago by mkoeppe

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-forge runs on an ubuntu-latest machine on GitHub Actions. The conda-forge installation is done by tox -e local-conda-forge, which uses Miniforge. You can run this tox command on any Linux machine to test it.
  • docker-conda-forge uses the continuumio/miniconda3 image 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: Changed 18 months ago by mkoeppe

Most recent runs:

Last edited 18 months ago by mkoeppe (previous) (diff)

comment:11 Changed 18 months ago by isuruf

https://trac.sagemath.org/ticket/29596 should fix the pari, ecl, libgd issue.

comment:13 in reply to: ↑ 10 ; follow-up: Changed 18 months ago by isuruf

Replying to mkoeppe:

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 mkoeppe

Replying to isuruf:

Replying to mkoeppe:

Do 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

Changed 18 months ago by mkoeppe

local-conda-forge-ubuntu-standard config.log

comment:15 Changed 18 months ago by mkoeppe

## --------------------------------------------------------- ##
## 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:17 Changed 18 months ago by mkoeppe

Thanks very much. Running tests with these tickets merged at https://github.com/mkoeppe/sage/actions/runs/88744943

comment:19 follow-up: Changed 18 months ago by isuruf

comment:20 in reply to: ↑ 19 Changed 18 months ago by mkoeppe

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:22 Changed 18 months ago by mkoeppe

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 mkoeppe

(This one is from tox -e docker-conda-forge-standard )

comment:24 Changed 18 months ago by mkoeppe

Fixed by #29606 (build/pkgs/maxima/spkg-install.in: Do not pass on LDFLAGS)

comment:27 Changed 18 months ago by mkoeppe

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 mkoeppe

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 isuruf

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'
Last edited 18 months ago by isuruf (previous) (diff)

comment:30 Changed 18 months ago by mkoeppe

Is this gfan?

comment:32 Changed 18 months ago by mkoeppe

Last edited 18 months ago by mkoeppe (previous) (diff)

comment:33 Changed 18 months ago by mkoeppe

  • 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 mkoeppe

  • 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 mkoeppe

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 isuruf

libsemigroups failure is fixed in later releases. Is there a config.log for latte_int failure?

comment:37 Changed 18 months ago by mkoeppe

  • 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 slelievre

  • 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 slelievre

  • Reviewers set to Matthias Koeppe, Samuel Lelièvre

comment:40 Changed 10 months ago by mkoeppe

  • Resolution set to invalid
  • Status changed from positive_review to closed
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