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Meta-ticket: docker-conda-forge-standard, local-ubuntu-conda-forge-standard: Fix build errors with python3, giac, ecl, m4rie, libgd, ... #29327

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mkoeppe opened this issue Mar 13, 2020 · 36 comments
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Meta-ticket: docker-conda-forge-standard, local-ubuntu-conda-forge-standard: Fix build errors with python3, giac, ecl, m4rie, libgd, ... #29327

mkoeppe opened this issue Mar 13, 2020 · 36 comments
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c: porting r: invalid t: bug

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@mkoeppe
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mkoeppe commented Mar 13, 2020

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

  • python3
    problem with _crypt as discussed in fflas_ffpack installation error on new CPUs with old compilers #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

Depends on #29574
Depends on #29596
Depends on #29597
Depends on #29598
Depends on #29601
Depends on #26287
Depends on #29606
Depends on #29612
Depends on #29618

CC: @isuruf @dimpase @saraedum

Component: porting

Reviewer: Matthias Koeppe, Samuel Lelièvre

Issue created by migration from https://trac.sagemath.org/ticket/29327
@mkoeppe mkoeppe added this to the sage-9.1 milestone Mar 13, 2020
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@mkoeppe mkoeppe changed the title Fix build errors with python3, giac, ecl, m4rie, libgd on conda-forge Fix build errors with python3, giac, ecl, m4rie, libgd on docker-conda-forge-standard Mar 29, 2020
@mkoeppe mkoeppe changed the title Fix build errors with python3, giac, ecl, m4rie, libgd on docker-conda-forge-standard Fix build errors with python3, giac, ecl, m4rie, libgd on docker-conda-forge-standard and local-ubuntu-conda-forge-standard Apr 14, 2020
@mkoeppe
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mkoeppe commented Apr 24, 2020

comment:6

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

@dimpase
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dimpase commented Apr 24, 2020

comment:8

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

@mkoeppe
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mkoeppe commented Apr 27, 2020

comment:9

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.

@mkoeppe
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mkoeppe commented Apr 27, 2020

comment:10

Most recent runs:

@isuruf
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isuruf commented Apr 27, 2020

comment:11

#29596 should fix the pari, ecl, libgd issue.

@isuruf
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isuruf commented Apr 27, 2020

comment:12

#29597 should fix m4rie

@isuruf
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isuruf commented Apr 27, 2020

comment:13

Replying to @mkoeppe:

Do you have the config.log? It fails to find openblas from conda-forge.

@mkoeppe
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mkoeppe commented Apr 27, 2020

comment:14

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

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mkoeppe commented Apr 27, 2020

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

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mkoeppe commented Apr 27, 2020

comment:15

Attachment: config.log

## --------------------------------------------------------- ##
## 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

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isuruf commented Apr 27, 2020

comment:16

Thanks. See #29598

@mkoeppe
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mkoeppe commented Apr 27, 2020

comment:17

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

@isuruf
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isuruf commented Apr 27, 2020

comment:18

Singular issue is #29601

@isuruf
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isuruf commented Apr 27, 2020

comment:19

libatomic_ops issue is #29602

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mkoeppe commented Apr 27, 2020

comment:20

Replying to @isuruf:

libatomic_ops issue is #29602

Let's use #26287 (Upgrade to gc 8.0.4 and libatomic 7.6.10)

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mkoeppe commented Apr 27, 2020

comment:21

New tests run at https://github.com/mkoeppe/sage/actions/runs/89365078

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mkoeppe commented Apr 27, 2020

comment:22

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"
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                                                              "binary-ecl/numerical/slatec/dqk15w.o"
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                                                              "-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

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mkoeppe commented Apr 27, 2020

comment:23

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

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mkoeppe commented Apr 27, 2020

comment:24

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

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mkoeppe commented Apr 28, 2020

comment:25

New tests at https://github.com/mkoeppe/sage/actions/runs/89649733

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mkoeppe commented Apr 28, 2020

comment:26

New tests at https://github.com/mkoeppe/sage/actions/runs/89771836

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mkoeppe commented Apr 28, 2020

comment:27

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

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mkoeppe commented Apr 28, 2020

comment:28

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.

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isuruf commented Apr 28, 2020

comment:29

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'

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mkoeppe commented Apr 28, 2020

comment:30

Is this gfan?

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isuruf commented Apr 28, 2020

comment:31

It's a palp issue. #29612

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mkoeppe commented Apr 29, 2020

comment:32

Tests (also with #29607; but not with #29612) run at https://github.com/mkoeppe/sage/actions/runs/90914869

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mkoeppe commented Apr 29, 2020

Dependencies: #29574, #29596, #29597, #29598, #29601, #26287, #29606, #29612, #29618

@mkoeppe mkoeppe changed the title Fix build errors with python3, giac, ecl, m4rie, libgd on docker-conda-forge-standard and local-ubuntu-conda-forge-standard Meta-ticket: docker-conda-forge-standar, local-ubuntu-conda-forge-standard: Fix build errors with python3, giac, ecl, m4rie, libgd, ... Apr 29, 2020
@mkoeppe mkoeppe changed the title Meta-ticket: docker-conda-forge-standar, local-ubuntu-conda-forge-standard: Fix build errors with python3, giac, ecl, m4rie, libgd, ... Meta-ticket: docker-conda-forge-standard, local-ubuntu-conda-forge-standard: Fix build errors with python3, giac, ecl, m4rie, libgd, ... Apr 29, 2020
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mkoeppe commented Apr 30, 2020

comment:35

Failures of some optional packages on conda-forge-macos can be seen at https://github.com/mkoeppe/sage/runs/631927929

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isuruf commented Apr 30, 2020

comment:36

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

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mkoeppe commented May 7, 2020

comment:37

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.

@mkoeppe mkoeppe removed this from the sage-9.1 milestone May 7, 2020
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slel commented Oct 5, 2020

comment:38

Is there a follow-up ticket for this? We're well into the 9.2 cycle.

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slel commented Oct 5, 2020

Reviewer: Matthias Koeppe, Samuel Lelièvre

@mkoeppe mkoeppe closed this as completed Dec 27, 2020
@dimpase dimpase mentioned this issue May 2, 2020
Closed
@isuruf isuruf mentioned this issue May 4, 2020
Closed
@mkoeppe mkoeppe mentioned this issue May 4, 2020
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