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

mkoeppe commented 4 years ago

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

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 commented 4 years ago

Description changed:

--- 
+++ 
@@ -62,3 +62,9 @@
     /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 +

mkoeppe commented 4 years ago

Description changed:

--- 
+++ 
@@ -20,6 +20,8 @@
      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):

mkoeppe commented 4 years ago

Description changed:

--- 
+++ 
@@ -1,4 +1,4 @@
-`conda-forge-standard` (https://github.com/mkoeppe/sage/runs/506355319):
+`docker-conda-forge-standard` (https://github.com/mkoeppe/sage/runs/506355319):

 - `python3`  
     problem with `_crypt` as discussed in #29102, `_sqlite`, `zlib`

mkoeppe commented 4 years ago

comment:6

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

dimpase commented 4 years ago

comment:8

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

mkoeppe commented 4 years ago

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 commented 4 years ago

comment:10

Most recent runs:

conda-forge-ubuntu-minimal https://github.com/mkoeppe/sage/runs/618647294
- m4rie, pari, python3, ecl fail
conda-forge-ubuntu-standard https://github.com/mkoeppe/sage/runs/618647333:
- openblas and singular fail
conda-forge-ubuntu-standard-python2 https://github.com/mkoeppe/sage/runs/618647336
- python2 and python3 fail

isuruf commented 4 years ago

comment:11

https://github.com/sagemath/sage-prod/issues/29596 should fix the pari, ecl, libgd issue.

isuruf commented 4 years ago

comment:12

https://github.com/sagemath/sage-prod/issues/29597 should fix m4rie

isuruf commented 4 years ago

comment:13

Replying to @mkoeppe:

conda-forge-ubuntu-standard https://github.com/mkoeppe/sage/runs/618647333:

openblas and singular fail

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

mkoeppe commented 4 years ago

comment:14

Replying to @isuruf:

Replying to @mkoeppe:

conda-forge-ubuntu-standard https://github.com/mkoeppe/sage/runs/618647333:

openblas and singular fail

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

mkoeppe commented 4 years ago

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

mkoeppe commented 4 years ago

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

isuruf commented 4 years ago

comment:16

Thanks. See https://github.com/sagemath/sage-prod/issues/29598

mkoeppe commented 4 years ago

comment:17

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

isuruf commented 4 years ago

comment:18

Singular issue is https://github.com/sagemath/sage-prod/issues/29601

isuruf commented 4 years ago

comment:19

libatomic_ops issue is https://github.com/sagemath/sage-prod/issues/29602

mkoeppe commented 4 years ago

comment:20

Replying to @isuruf:

libatomic_ops issue is https://github.com/sagemath/sage-prod/issues/29602

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

mkoeppe commented 4 years ago

comment:21

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

mkoeppe commented 4 years ago

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"
                                                              "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

mkoeppe commented 4 years ago

comment:23

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

mkoeppe commented 4 years ago

comment:24

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

mkoeppe commented 4 years ago

comment:25

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

mkoeppe commented 4 years ago

comment:26

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

mkoeppe commented 4 years ago

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

mkoeppe commented 4 years ago

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.

isuruf commented 4 years ago

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'

mkoeppe commented 4 years ago

comment:30

Is this gfan?

isuruf commented 4 years ago

comment:31

It's a palp issue. https://github.com/sagemath/sage-prod/issues/29612

mkoeppe commented 4 years ago

comment:32

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

mkoeppe commented 4 years ago

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

mkoeppe commented 4 years ago

comment:35

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

isuruf commented 4 years ago

comment:36

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

mkoeppe commented 4 years ago

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.

slel commented 3 years ago

comment:38

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

slel commented 3 years ago

Reviewer: Matthias Koeppe, Samuel Lelièvre

sagemath / sage

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