--- Begin Message ---
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Subject: |
Re: [bug#27637] [PATCH 5/5] gnu: Add conda |
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Date: |
Sat, 22 Jul 2017 11:49:20 +0200 |
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User-agent: |
mu4e 0.9.18; emacs 25.2.1 |
Ricardo Wurmus <address@hidden> writes:
> Pjotr Prins <address@hidden> 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
--- End Message ---
0001-gnu-Add-python-conda.patch