Package: guix-patches;
Reported by: Frederick Muriithi <fredmanglis <at> gmail.com>
Date: Mon, 10 Jul 2017 07:32:02 UTC
Severity: normal
Tags: patch
Done: Ricardo Wurmus <rekado <at> elephly.net>
Bug is archived. No further changes may be made.
Message #67 received at 27637-done <at> debbugs.gnu.org (full text, mbox):
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
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