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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)
Link for the recipe PR: conda-forge/cgal-cpp-feedstock#6
the errno keeps varying, in this build it is 22 (Invalid Argument), but before it was 14 (Invalid File Descriptor)
the file is ok, it's being built correctly in Linux
Tadeu Manoel
@tadeu
ah, I just found out this new issue: conda-forge/libarchive-feedstock#43