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ArchLinux incompatibility #5

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kousu opened this issue Jun 16, 2020 · 1 comment
Open

ArchLinux incompatibility #5

kousu opened this issue Jun 16, 2020 · 1 comment

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@kousu
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kousu commented Jun 16, 2020 •
edited
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I'm getting a bizarre error on ArchLinux:

It says

Defaulting to user installation because normal site-packages is not writeable

but then

The installation directory you specified (via --install-dir, --prefix, or
the distutils default setting) was:

/usr/lib/python3.8/site-packages/

$ git clone https://github.com/datalad/datalad-osf
$ cd datalad-osf
$ pip install -e .
Defaulting to user installation because normal site-packages is not writeable
Obtaining file:///home/kousu/datalad-osf
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Requirement already satisfied: datalad>=0.12.0 in /home/kousu/.local/lib/python3.8/site-packages (from datalad-osf==0+untagged.5.gc7ae2aa.dirty) (0.12.7)
Requirement already satisfied: appdirs in /usr/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.4.4)
Requirement already satisfied: chardet>=3.0.4 in /usr/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (3.0.4)
Requirement already satisfied: GitPython>=2.1.12 in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (3.1.3)
Requirement already satisfied: iso8601 in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (0.1.12)
Requirement already satisfied: humanize in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (2.4.0)
Requirement already satisfied: fasteners in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (0.15)
Requirement already satisfied: patool>=1.7 in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.12)
Requirement already satisfied: tqdm in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (4.46.1)
Requirement already satisfied: wrapt in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.12.1)
Requirement already satisfied: boto in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (2.49.0)
Requirement already satisfied: keyring>=8.0 in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (21.2.1)
Requirement already satisfied: keyrings.alt in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (3.4.0)
Requirement already satisfied: msgpack in /usr/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.0.0)
Requirement already satisfied: requests>=1.2 in /usr/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (2.23.0)
Requirement already satisfied: jsmin in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (2.2.2)
Requirement already satisfied: PyGithub in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.51)
Requirement already satisfied: simplejson in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (3.17.0)
Requirement already satisfied: whoosh in /home/kousu/.local/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (2.7.4)
Requirement already satisfied: distro in /usr/lib/python3.8/site-packages (from datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.5.0)
Requirement already satisfied: gitdb<5,>=4.0.1 in /home/kousu/.local/lib/python3.8/site-packages (from GitPython>=2.1.12->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (4.0.5)
Requirement already satisfied: monotonic>=0.1 in /home/kousu/.local/lib/python3.8/site-packages (from fasteners->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.5)
Requirement already satisfied: six in /usr/lib/python3.8/site-packages (from fasteners->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.15.0)
Requirement already satisfied: jeepney>=0.4.2; sys_platform == "linux" in /home/kousu/.local/lib/python3.8/site-packages (from keyring>=8.0->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (0.4.3)
Requirement already satisfied: SecretStorage>=3; sys_platform == "linux" in /home/kousu/.local/lib/python3.8/site-packages (from keyring>=8.0->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (3.1.2)
Requirement already satisfied: idna>=2.5 in /usr/lib/python3.8/site-packages (from requests>=1.2->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (2.9)
Requirement already satisfied: urllib3>=1.21.1 in /usr/lib/python3.8/site-packages (from requests>=1.2->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.25.9)
Requirement already satisfied: deprecated in /home/kousu/.local/lib/python3.8/site-packages (from PyGithub->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.2.10)
Requirement already satisfied: pyjwt in /home/kousu/.local/lib/python3.8/site-packages (from PyGithub->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.7.1)
Requirement already satisfied: smmap<4,>=3.0.1 in /home/kousu/.local/lib/python3.8/site-packages (from gitdb<5,>=4.0.1->GitPython>=2.1.12->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (3.0.4)
Requirement already satisfied: cryptography in /usr/lib/python3.8/site-packages (from SecretStorage>=3; sys_platform == "linux"->keyring>=8.0->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (2.9.2)
Requirement already satisfied: cffi!=1.11.3,>=1.8 in /usr/lib/python3.8/site-packages (from cryptography->SecretStorage>=3; sys_platform == "linux"->keyring>=8.0->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (1.14.0)
Requirement already satisfied: pycparser in /usr/lib/python3.8/site-packages (from cffi!=1.11.3,>=1.8->cryptography->SecretStorage>=3; sys_platform == "linux"->keyring>=8.0->datalad>=0.12.0->datalad-osf==0+untagged.5.gc7ae2aa.dirty) (2.20)
Installing collected packages: datalad-osf
  Running setup.py develop for datalad-osf
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/kousu/datalad-osf/setup.py'"'"'; __file__='"'"'/home/kousu/datalad-osf/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps --user --prefix=
         cwd: /home/kousu/datalad-osf/
    Complete output (28 lines):
    running develop
    WARNING: The user site-packages directory is disabled.
    error: can't create or remove files in install directory
    
    The following error occurred while trying to add or remove files in the
    installation directory:
    
        [Errno 13] Permission denied: '/usr/lib/python3.8/site-packages/test-easy-install-95206.write-test'
    
    The installation directory you specified (via --install-dir, --prefix, or
    the distutils default setting) was:
    
        /usr/lib/python3.8/site-packages/
    
    Perhaps your account does not have write access to this directory?  If the
    installation directory is a system-owned directory, you may need to sign in
    as the administrator or "root" account.  If you do not have administrative
    access to this machine, you may wish to choose a different installation
    directory, preferably one that is listed in your PYTHONPATH environment
    variable.
    
    For information on other options, you may wish to consult the
    documentation at:
    
      https://setuptools.readthedocs.io/en/latest/easy_install.html
    
    Please make the appropriate changes for your system and try again.
    
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/kousu/datalad-osf/setup.py'"'"'; __file__='"'"'/home/kousu/datalad-osf/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps --user --prefix= Check the logs for full command output.

This doesn't happen with other packages, e.g. https://github.com/Lykos153/AnnexRemote is fine. I don't know what's up with this but some help debugging this would be appreciated.

Could this problem be rooted in datalad itself somehow?
@kousu
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kousu commented Jun 16, 2020

A virtualenv is fine.

[kousu@comms2 datalad-osf]$ python -m virtualenv .venv
created virtual environment CPython3.8.3.final.0-64 in 1215ms
  creator CPython3Posix(dest=/home/kousu/datalad-osf/.venv, clear=False, global=False)
  seeder FromAppData(download=False, pip=latest, setuptools=latest, wheel=latest, via=copy, app_data_dir=/home/kousu/.local/share/virtualenv/seed-app-data/v1.0.1)
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator
[kousu@comms2 datalad-osf]$ . .venv/bin/activate
(.venv) [kousu@comms2 datalad-osf]$ pip install -e .
Obtaining file:///home/kousu/datalad-osf
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting datalad>=0.12.0
  Using cached datalad-0.12.7.tar.gz (1.5 MB)
Collecting appdirs
  Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Collecting chardet>=3.0.4
  Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB)
     |████████████████████████████████| 133 kB 8.5 MB/s 
Collecting GitPython>=2.1.12
  Using cached GitPython-3.1.3-py3-none-any.whl (451 kB)
Collecting iso8601
  Using cached iso8601-0.1.12-py2.py3-none-any.whl (12 kB)
Collecting humanize
  Using cached humanize-2.4.0-py3-none-any.whl (62 kB)
Collecting fasteners
  Using cached fasteners-0.15-py2.py3-none-any.whl (23 kB)
Collecting patool>=1.7
  Using cached patool-1.12-py2.py3-none-any.whl (77 kB)
Collecting tqdm
  Using cached tqdm-4.46.1-py2.py3-none-any.whl (63 kB)
Collecting wrapt
  Using cached wrapt-1.12.1.tar.gz (27 kB)
Collecting boto
  Using cached boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Collecting keyring>=8.0
  Using cached keyring-21.2.1-py3-none-any.whl (31 kB)
Collecting keyrings.alt
  Using cached keyrings.alt-3.4.0-py2.py3-none-any.whl (31 kB)
Collecting msgpack
  Downloading msgpack-1.0.0-cp38-cp38-manylinux1_x86_64.whl (303 kB)
     |████████████████████████████████| 303 kB 13.2 MB/s 
Collecting requests>=1.2
  Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB)
     |████████████████████████████████| 58 kB 6.2 MB/s 
Collecting jsmin
  Using cached jsmin-2.2.2.tar.gz (12 kB)
Collecting PyGithub
  Using cached PyGithub-1.51-py3-none-any.whl (260 kB)
Collecting simplejson
  Using cached simplejson-3.17.0.tar.gz (83 kB)
Collecting whoosh
  Using cached Whoosh-2.7.4-py2.py3-none-any.whl (468 kB)
Collecting distro
  Downloading distro-1.5.0-py2.py3-none-any.whl (18 kB)
Collecting gitdb<5,>=4.0.1
  Using cached gitdb-4.0.5-py3-none-any.whl (63 kB)
Collecting six
  Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting monotonic>=0.1
  Using cached monotonic-1.5-py2.py3-none-any.whl (5.3 kB)
Collecting SecretStorage>=3; sys_platform == "linux"
  Using cached SecretStorage-3.1.2-py3-none-any.whl (14 kB)
Collecting jeepney>=0.4.2; sys_platform == "linux"
  Using cached jeepney-0.4.3-py3-none-any.whl (21 kB)
Collecting idna<3,>=2.5
  Downloading idna-2.9-py2.py3-none-any.whl (58 kB)
     |████████████████████████████████| 58 kB 3.2 MB/s 
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
  Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB)
     |████████████████████████████████| 126 kB 6.3 MB/s 
Collecting certifi>=2017.4.17
  Downloading certifi-2020.4.5.2-py2.py3-none-any.whl (157 kB)
     |████████████████████████████████| 157 kB 15.4 MB/s 
Collecting pyjwt
  Using cached PyJWT-1.7.1-py2.py3-none-any.whl (18 kB)
Collecting deprecated
  Using cached Deprecated-1.2.10-py2.py3-none-any.whl (8.7 kB)
Collecting smmap<4,>=3.0.1
  Using cached smmap-3.0.4-py2.py3-none-any.whl (25 kB)
Collecting cryptography
  Downloading cryptography-2.9.2-cp35-abi3-manylinux2010_x86_64.whl (2.7 MB)
     |████████████████████████████████| 2.7 MB 18.6 MB/s 
Collecting cffi!=1.11.3,>=1.8
  Downloading cffi-1.14.0-cp38-cp38-manylinux1_x86_64.whl (409 kB)
     |████████████████████████████████| 409 kB 15.6 MB/s 
Collecting pycparser
  Downloading pycparser-2.20-py2.py3-none-any.whl (112 kB)
     |████████████████████████████████| 112 kB 31.6 MB/s 
Building wheels for collected packages: datalad, wrapt, jsmin, simplejson
  Building wheel for datalad (setup.py) ... done
  Created wheel for datalad: filename=datalad-0.12.7-py3-none-any.whl size=1473537 sha256=cfe0426b0b338f01e72de49f5b80d0625ee93d2321623ef48b8d1579ebc243a7
  Stored in directory: /home/kousu/.cache/pip/wheels/37/56/33/b3a79b0529cab51fab9801d6a5bfe47d40f41940b415fec982
  Building wheel for wrapt (setup.py) ... done
  Created wheel for wrapt: filename=wrapt-1.12.1-cp38-cp38-linux_x86_64.whl size=75757 sha256=8863a1dabc1b1c478202a6cd9e564e75edd8227f8607a7c288cd4f5fe151c416
  Stored in directory: /home/kousu/.cache/pip/wheels/5f/fd/9e/b6cf5890494cb8ef0b5eaff72e5d55a70fb56316007d6dfe73
  Building wheel for jsmin (setup.py) ... done
  Created wheel for jsmin: filename=jsmin-2.2.2-py3-none-any.whl size=13918 sha256=9d361b7fe6e561e40182019c26a01d87aac5e8ee0122d5999419206569d2cf02
  Stored in directory: /home/kousu/.cache/pip/wheels/65/b7/04/fc4b059d177fd88f3ca362ad372a15e364b0c5433121c7b135
  Building wheel for simplejson (setup.py) ... done
  Created wheel for simplejson: filename=simplejson-3.17.0-cp38-cp38-linux_x86_64.whl size=132592 sha256=5a71e77e61e50d2603b1573a8fd6aa899099d02894569979b3221cc523a397b6
  Stored in directory: /home/kousu/.cache/pip/wheels/79/a1/9f/a28ec96c5663fca58b4c735c54b202b4ae08fc4f7624bddb06
Successfully built datalad wrapt jsmin simplejson
Installing collected packages: appdirs, chardet, smmap, gitdb, GitPython, iso8601, humanize, six, monotonic, fasteners, patool, tqdm, wrapt, boto, jeepney, pycparser, cffi, cryptography, SecretStorage, keyring, keyrings.alt, msgpack, idna, urllib3, certifi, requests, jsmin, pyjwt, deprecated, PyGithub, simplejson, whoosh, distro, datalad, datalad-osf
  Running setup.py develop for datalad-osf
Successfully installed GitPython-3.1.3 PyGithub-1.51 SecretStorage-3.1.2 appdirs-1.4.4 boto-2.49.0 certifi-2020.4.5.2 cffi-1.14.0 chardet-3.0.4 cryptography-2.9.2 datalad-0.12.7 datalad-osf deprecated-1.2.10 distro-1.5.0 fasteners-0.15 gitdb-4.0.5 humanize-2.4.0 idna-2.9 iso8601-0.1.12 jeepney-0.4.3 jsmin-2.2.2 keyring-21.2.1 keyrings.alt-3.4.0 monotonic-1.5 msgpack-1.0.0 patool-1.12 pycparser-2.20 pyjwt-1.7.1 requests-2.23.0 simplejson-3.17.0 six-1.15.0 smmap-3.0.4 tqdm-4.46.1 urllib3-1.25.9 whoosh-2.7.4 wrapt-1.12.1
(.venv) [kousu@comms2 datalad-osf]$

DorienHuijser added a commit that referenced this issue Jun 18, 2020
@DorienHuijser
Merge pull request #5 from datalad/master
b4d7a0e 
Update own branch again
mih pushed a commit that referenced this issue Jun 18, 2020
@TheDragon246
Merge pull request #5 from TheDragon246/TheDragon246-patch-1
829c5e4 
update zenodo.json
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