gfak::mmap_open opens O_RDWR #65
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The workaround is to make the file writable (but this entails making a copy of the whole file in my case). |
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Yeah we should just patch this. It's not a problem.
…On Tue, Apr 7, 2020 at 4:05 PM Peter Amstutz ***@***.***> wrote:
The workaround is to make the file writable (but this entails making a
copy of the whole file in my case).
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currently fails CI due to ``` | odgi: /opt/conda/conda-bld/odgi_1616839257024/work/deps/gfakluge/src/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion `false' failed. | /tmp/tmpdi1icj3u/job_working_directory/000/2/tool_script.sh: line 22: 7 Aborted (core dumped) odgi build -g '/tmp/tmpdi1icj3u/files/b/0/4/dataset_b04a44e9-eafd-415b-a3a8-0e671b31ff1d.dat' -o '/tmp/tmpdi1icj3u/job_working_directory/000/2/outputs/galaxy_dataset_6817b8a3-8f3d-4f14-a7ad-d73d11568ad8.dat' --sort --to-gfa > '/tmp/tmpdi1icj3u/job_working_directory/000/2/outputs/galaxy_dataset_38a641a6-89d8-4d27-baf0-00a9e665dd58.dat' ``` which is because edawson/gfakluge#65
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gfak::mmap_open calls open with O_RDWR (read/write access). This fails with a cryptic error when the file is read-only:
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