GNU bug report logs - #27637
[PATCH] gnu: Add python-conda

Previous Next

Full log

View this message in rfc822 format

From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#27637: closed ([PATCH] gnu: Add python-conda)
Date: Sat, 22 Jul 2017 09:50:01 +0000

[Message part 1 (text/plain, inline)]

Your message dated Sat, 22 Jul 2017 11:49:20 +0200
with message-id <87h8y4ajj3.fsf <at> elephly.net>
and subject line Re: [bug#27637] [PATCH 5/5] gnu: Add conda
has caused the debbugs.gnu.org bug report #27637,
regarding [PATCH] gnu: Add python-conda
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


-- 
27637: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=27637
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

[Message part 2 (message/rfc822, inline)]

From: Frederick Muriithi <fredmanglis <at> gmail.com>
To: guix-patches <at> gnu.org
Subject: [PATCH] gnu: Add python-conda
Date: Mon, 10 Jul 2017 10:29:29 +0300

[Message part 3 (text/plain, inline)]

This package is dependent on python-ruamel.yaml that was submitted in bug #27558

-- 
Frederick M. Muriithi

[0001-gnu-Add-python-conda.patch (text/x-patch, attachment)]

[Message part 5 (message/rfc822, inline)]

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Pjotr Prins <pjotr.public12 <at> thebird.nl>
Cc: Muriithi Frederick Muriuki <fredmanglis <at> gmail.com>,
 27637-done <at> debbugs.gnu.org
Subject: Re: [bug#27637] [PATCH 5/5] gnu: Add conda
Date: Sat, 22 Jul 2017 11:49:20 +0200

Ricardo Wurmus <rekado <at> elephly.net> writes:

> Pjotr Prins <pjotr.public12 <at> thebird.nl> writes:
>
>> Thanks Fred.
>>
>> Can someone take a look at the tar issue?
>
> The tar thing really looks odd.  I’m ready to push the patches leading
> up to this one.  I still need to experiment a bit to avoid this
> complicated install phase.

I fixed this, but conda still has errors; it tries to write to the
store:

--8<---------------cut here---------------start------------->8---
/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/bin/conda install samtools
Fetching package metadata ...An unexpected error has occurred.
Please consider posting the following information to the
conda GitHub issue tracker at:

    https://github.com/conda/conda/issues



Current conda install:

               platform : linux-64
          conda version : 4.3.16
       conda is private : False
      conda-env version : 4.3.16
    conda-build version : not installed
         python version : 3.5.3.final.0
       requests version : 2.13.0
       root environment : /gnu/store/yd655bpcqrzch4ai1dhs7v39yhm70mdi-python-3.5.3  (read only)
    default environment : /gnu/store/yd655bpcqrzch4ai1dhs7v39yhm70mdi-python-3.5.3
       envs directories : /home/rekado/.conda/envs
                          /gnu/store/yd655bpcqrzch4ai1dhs7v39yhm70mdi-python-3.5.3/envs
          package cache : /gnu/store/yd655bpcqrzch4ai1dhs7v39yhm70mdi-python-3.5.3/pkgs
                          /home/rekado/.conda/pkgs
           channel URLs : https://repo.continuum.io/pkgs/free/linux-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/linux-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/linux-64
                          https://repo.continuum.io/pkgs/pro/noarch
            config file : None
           offline mode : False
             user-agent : conda/4.3.16 requests/2.13.0 CPython/3.5.3 Linux/4.1.42-gnu / glibc/2.25
                UID:GID : 1000:1000



`$ /gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/bin/.conda-real install samtools`




    Traceback (most recent call last):
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/exceptions.py", line 626, in conda_exception_handler
        return_value = func(*args, **kwargs)
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/cli/main.py", line 134, in _main
        exit_code = args.func(args, p)
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/cli/main_install.py", line 80, in execute
        install(args, parser, 'install')
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/cli/install.py", line 221, in install
        unknown=index_args['unknown'], prefix=prefix)
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/index.py", line 92, in get_index
        index = fetch_index(channel_priority_map, use_cache=use_cache)
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/index.py", line 111, in fetch_index
        repodatas = collect_all_repodata(use_cache, tasks)
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/repodata.py", line 74, in collect_all_repodata
        repodatas = _collect_repodatas_serial(use_cache, tasks)
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/repodata.py", line 463, in _collect_repodatas_serial
        for url, schan, pri in tasks]
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/repodata.py", line 463, in <listcomp>
        for url, schan, pri in tasks]
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/repodata.py", line 109, in func
        res = f(*args, **kwargs)
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/repodata.py", line 409, in fetch_repodata
        cache_path = join(cache_dir or create_cache_dir(), cache_fn_url(url))
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/repodata.py", line 497, in create_cache_dir
        cache_dir = join(PackageCache.first_writable(context.pkgs_dirs).pkgs_dir, 'cache')
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/package_cache.py", line 169, in first_writable
        return cls.all_writable(pkgs_dirs)[0]
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/package_cache.py", line 176, in all_writable
        (PackageCache(pd) for pd in pkgs_dirs)))
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/package_cache.py", line 175, in <lambda>
        writable_caches = tuple(filter(lambda c: c.is_writable,
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/core/package_cache.py", line 316, in is_writable
        self._is_writable = create_package_cache_directory(self.pkgs_dir)
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/gateways/disk/create.py", line 302, in create_package_cache_directory
        mkdir_p(pkgs_dir)
      File "/gnu/store/pwl68nzl6s3papdx98hx997iij10r3sn-conda-4.3.16/lib/python3.5/site-packages/conda-4.3.16-py3.5.egg/conda/gateways/disk/create.py", line 160, in mkdir_p
        makedirs(path)
      File "/gnu/store/yd655bpcqrzch4ai1dhs7v39yhm70mdi-python-3.5.3/lib/python3.5/os.py", line 241, in makedirs
        mkdir(name, mode)
    OSError: [Errno 30] Read-only file system: '/gnu/store/yd655bpcqrzch4ai1dhs7v39yhm70mdi-python-3.5.3/pkgs'
--8<---------------cut here---------------end--------------->8---

Wherever it says “/gnu/store/yd655bpcqrzch4ai1dhs7v39yhm70mdi-python-3.5.3/” we should provide sane
defaults.

@Fred: could you please look into this?  This may require patching the
conda sources.

I’m marking this bug done now, because Conda is now in the repository.

-- 
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.