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  • 04:46
    beckermr closed #3735
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    beckermr commented #3735
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  • Dec 12 19:26

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    docs for pr 3832 (compare)

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    Added note about using Docker Merge pull request #3832 from r… (compare)

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    conda-bot on gh-pages

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    cla-bot[bot] commented #3831
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    bdice opened #3831
  • Dec 11 22:45
    Dellaviola opened #3830
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    rrigdon closed #3698
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  • Dec 11 16:21
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  • Dec 11 16:15
    marscher opened #3829
  • Dec 11 07:03
    marcelotrevisani commented #3828
Matthew R. Becker
@beckermr
OTOH, I put in a custom shim in my build that solved this particular issue
Matthew R. Becker
@beckermr
@jjhelmus there does seem to be some interest in a config option to turn off the replacement
should I make an issue?
Matthew R. Becker
@beckermr
I made an issue on this
deepali-c
@deepali-c

I see below error while building a recipe:

Fixing permissions execute(sys.argv[1:]) File "<mypath>/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 430, in execute verify=args.verify, variants=args.variants) File "<mypath>/lib/python2.7/site-packages/conda_build/api.py", line 201, in build notest=notest, need_source_download=need_source_download, variants=variants) File "<mypath>/lib/python2.7/site-packages/conda_build/build.py", line 2275, in build_tree notest=notest, File "<mypath>/lib/python2.7/site-packages/conda_build/build.py", line 1654, in build newly_built_packages = bundlers[output_d.get('type', 'conda')](output_d, m, env, stats) File "<mypath>/lib/python2.7/site-packages/conda_build/build.py", line 972, in bundle_conda output['checksums'] = create_info_files(metadata, files, prefix=metadata.config.host_prefix) File "<mypath>/lib/python2.7/site-packages/conda_build/build.py", line 665, in create_info_files copy_recipe(m) File "<mypath>/lib/python2.7/site-packages/conda_build/build.py", line 301, in copy_recipe _copy_output_recipe(m, recipe_dir) File "<mypath>/lib/python2.7/site-packages/conda_build/build.py", line 270, in _copy_output_recipe _copy_top_level_recipe(src_dir, m.config, dest_dir, 'parent') File "<mypath>/lib/python2.7/site-packages/conda_build/build.py", line 264, in _copy_top_level_recipe locking=config.locking, clobber=True) File "<mypath>/lib/python2.7/site-packages/conda_build/utils.py", line 502, in copy_into _copy_with_shell_fallback(src, dst_fn) File "<mypath>/lib/python2.7/site-packages/conda_build/utils.py", line 435, in _copy_with_shell_fallback raise OSError("Failed to copy {} to {}. Error was: {}".format(src, dst, e)) OSError: Failed to copy <path>/meta.yaml to <envpath>/info/recipe/parent/meta.yaml. Error was: Command 'cp -a <path>/meta.yaml <envpath>/info/recipe/parent/meta.yaml' returned non-zero exit status 1
Any hints on how to get to the cause of this? I have just shortened the paths here.

Duncan Macleod
@duncanmmacleod
should conda-build be adding ${CONDA_PREFIX}/sbin to path, or is there some other recommendation?
Duncan Macleod
@duncanmmacleod
sorry, this is more of a conda question, not a conda build question
deepali-c
@deepali-c
so shall I post in the conda gitter
Duncan Macleod
@duncanmmacleod
@deepali-c, my question was totally unrelated to yours, sorry for any confusion
Nehal J Wani
@nehaljwani
@duncanmmacleod you should build the package in a manner such that all binaries end up in bin. Any particular reason why you want to use sbin ?
Duncan Macleod
@duncanmmacleod
@nehaljwani, I am just building an existing package that includes daemon scripts that naturally belong in sbin
I understand that sbin is mainly for administrator control, I was just wondering if ‘don’t use sbin’ is a conda policy, or just nobody has tried it until now
Nehal J Wani
@nehaljwani
Conda doesn't add sbin to PATH on activation
Duncan Macleod
@duncanmmacleod
Sorry, my original question was badly worded, I am wondering if that very fact is a choice that was long-considered or just an oversight
Nehal J Wani
@nehaljwani

My understanding is that the sbin folder on Linux systems is for segregating binaries meant to be run by privileged users. (generally speaking, sysadmins)

But conda is a generic package manager and doesn't make such distinctions, so the need for segregating binaries doesn't make much sense here.

Anthony Scopatz
@scopatz
Hi All, is missing_dso_whitelist undocumented?
Seems so
Anthony Scopatz
@scopatz
Yeah that is what I was looking for
or at, rather
Nehal J Wani
@nehaljwani
It is definitely supported though. Are you repackaging something?
Anthony Scopatz
@scopatz
yeah, a haskel package
Anthony Scopatz
@scopatz
here is the existing issue: conda/conda-build#3360
Anthony Scopatz
@scopatz
So does rpaths not add entries to the RPATH for things in the bin/ directory?
Nehal J Wani
@nehaljwani
What entries did you list in rpaths? I thought CB used patchelf on binaries in bin for adding those paths.
Anthony Scopatz
@scopatz
x86_64-conda_cos6-linux-gnu/sysroot/lib/ and ../lib
Nehal J Wani
@nehaljwani
It is relative to $PREFIX I think, not $PREFIX/bin
Anthony Scopatz
@scopatz
yeah that is what I thought too
Nehal J Wani
@nehaljwani
Not sure what adding sysroot to the RPATH would achieve?
If you simply want --error-overlinking to pass, just add the C compiler and any links to glibc libs will stop complaining about missing deps
Anthony Scopatz
@scopatz
Right, yes, but there is no need for the compiler, since this is a haskell binary repackage
Nehal J Wani
@nehaljwani
If every component is being repackaged and 0 compilation, you can add '*' in the missing_dso_whitelist section
It allows patterns
Every CDT package recipe has that
Anthony Scopatz
@scopatz
Agreed, but the problem is deeped than just skipping the overlinking check. On the conda-forge CI, it fails the tests because it actually can't find the libraries
Probably because haskell links them to /lib64/
Nehal J Wani
@nehaljwani
Ah, so you need to force the rpath entries. Do you have a link?
Nehal J Wani
@nehaljwani
Oh no elm-format: /lib64/libc.so.6: version GLIBC_2.14 not found (required by elm-format) this is basically saying that it has been built with glibc 2.14 and the system you are running on, is perhaps centos6 based, which is glibc 2.12
Anthony Scopatz
@scopatz
Yeah, it is.
Nehal J Wani
@nehaljwani
So you can't run the tests, sorry.
Anthony Scopatz
@scopatz
damn, ok
Nehal J Wani
@nehaljwani
Why not build it from source? We already have a haskell compiler, don't we?
Anthony Scopatz
@scopatz
I didn't think we did
conda-forge just has ghc for linux, which I guess would work here
Nehal J Wani
@nehaljwani
yeah, that one
Anthony Scopatz
@scopatz
I guess I should go down that route
Tadeu Manoel
@tadeu
Hi all, did someone ever see an error like this on macOS, being unable to extract a .zip file in the beginning of the recipe build?
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 449, in main
    execute(sys.argv[1:])
(...)
  File "/usr/local/miniconda/lib/python3.7/site-packages/libarchive/extract.py", line 50, in extract_entries
    write_header(write_p, entry._entry_p)
  File "/usr/local/miniconda/lib/python3.7/site-packages/libarchive/ffi.py", line 91, in check_int
    raise archive_error(args[0], retcode)
  File "/usr/local/miniconda/lib/python3.7/site-packages/libarchive/ffi.py", line 75, in archive_error
    raise ArchiveError(msg, errno(archive_p), retcode, archive_p)
libarchive.exception.ArchiveError: Could not open CGAL-4.14.1 (errno=22, retcode=-30, archive_p=140295874731728)