From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:41373) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dYr2z-0002b0-IO for guix-patches@gnu.org; Sat, 22 Jul 2017 05:50:07 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dYr2w-0004ra-CM for guix-patches@gnu.org; Sat, 22 Jul 2017 05:50:05 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:49240) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1dYr2w-0004rL-8F for guix-patches@gnu.org; Sat, 22 Jul 2017 05:50:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1dYr2v-0008QK-Su for guix-patches@gnu.org; Sat, 22 Jul 2017 05:50:01 -0400 Subject: bug#27637: [PATCH 5/5] gnu: Add conda Resent-To: guix-patches@gnu.org Resent-Message-ID: References: <20170718083709.5062-1-fredmanglis@gmail.com> <20170718083709.5062-5-fredmanglis@gmail.com> <20170721054858.GE16795@thebird.nl> <87inikamru.fsf@elephly.net> From: Ricardo Wurmus In-reply-to: <87inikamru.fsf@elephly.net> Date: Sat, 22 Jul 2017 11:49:20 +0200 Message-ID: <87h8y4ajj3.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: Pjotr Prins Cc: Muriithi Frederick Muriuki , 27637-done@debbugs.gnu.org Ricardo Wurmus writes: > Pjotr Prins 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 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 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