Conda / BioConda

[Gildas Le Corguillé]

Hi dear Migrate developers,

We are trying to create a Conda package for Migrate : https://github.com/bioconda/bioconda-recipes/pull/21974

We still have error here : https://app.circleci.com/pipelines/github/bioconda/bioconda-recipes/27657/workflows/cfc73d21-cd17-44bb-aed9-625354893c6a/jobs/112255/steps

08:21:32 BIOCONDA INFO (OUT) /opt/conda/conda-bld/migrate-n_1591949937471/_build_env/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: PdfBorderStyle.cc:(.text+0x388): undefined reference to `operator delete(void*, unsigned long)'
08:21:32 BIOCONDA INFO (OUT) /opt/conda/conda-bld/migrate-n_1591949937471/_build_env/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: PdfBorderStyle.cc:(.text+0x39d): undefined reference to `operator delete(void*, unsigned long)'
08:21:32 BIOCONDA INFO (OUT) /opt/conda/conda-bld/migrate-n_1591949937471/_build_env/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: PdfBorderStyle.cc:(.text+0x3bf): undefined reference to `operator delete(void*, unsigned long)'
08:21:32 BIOCONDA INFO (OUT) /opt/conda/conda-bld/migrate-n_1591949937471/_build_env/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: PdfBorderStyle.cc:(.text+0x3cf): undefined reference to `__cxa_end_catch'
08:21:32 BIOCONDA INFO (OUT) /opt/conda/conda-bld/migrate-n_1591949937471/_build_env/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: haru/libharu.a(PdfBorderStyle.o): in function `PdfBorderStyle::~PdfBorderStyle()':
08:21:32 BIOCONDA INFO (OUT) PdfBorderStyle.cc:(.text._ZN14PdfBorderStyleD0Ev[_ZN14PdfBorderStyleD5Ev]+0x1d): undefined reference to `operator delete(void*, unsigned long)'
08:21:32 BIOCONDA INFO (OUT) /opt/conda/conda-bld/migrate-n_1591949937471/_build_env/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: haru/libharu.a(PdfBorderStyle.o):(.data.rel.ro._ZTI14PdfBorderStyle[_ZTI14PdfBorderStyle]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
08:21:32 BIOCONDA INFO (OUT) collect2: error: ld returned 1 exit status
08:21:32 BIOCONDA INFO (OUT) make[2]: *** [migrate-n] Error 1
08:21:32 BIOCONDA INFO (OUT) make[1]: *** [all] Error 2
08:21:32 BIOCONDA INFO (OUT) make: *** [intro] Error 2

Do you have any idea?

Thanks by advance.

[Peter Beerli]

Dear Gildas,

it would be  better you would talk directly to me (Peter Beerli, bee...@fsu.edu) about this. But to start the interaction I am somewhat sore about anaconda/conda for taking over my machine (a macbook), because I use anaconda for python development, and stunting other development environments (clang on commandline). 

Your errors look like you have issues concerning C++ code (the old libharu PDF library) and my usages of it in a C framework. In addition you will need to make sure that you use the right compile environmental variables (without that your project will fail). if you tell me more about how to create a conda project I perhaps can add a target to the makefile.

Peter

 

--
You received this message because you are subscribed to the Google Groups "migrate-support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to migrate-suppo...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/migrate-support/ff0fd829-aa48-4885-b23c-a19d0db1e9c7o%40googlegroups.com.

[Gildas Le Corguillé]

Hi Peter,

Because I have a lake of time, I decided to build a Singularity container.

Here is the def file : https://gitlab.com/ifb-elixirfr/cluster/tools/-/blob/master/tools/migrate-n/4.4.4/image.def

It still be interesting to have a Conda package :)

All the best

Gildas

To view this discussion on the web visit https://groups.google.com/d/msgid/migrate-support/59D71D26-B8EA-429D-BFC6-8559512C18A1%40gmail.com.

[Peter Beerli]

thanks, I will check it out,

I have not forgotten about the conda package, but my time seems more like a puddle evaporating quickly.

Peter

To view this discussion on the web visit https://groups.google.com/d/msgid/migrate-support/CALWYMUhBBHSPvLj0k-xLWeWRPXQYttNpgWe7thSr4CQuQF4bVA%40mail.gmail.com.