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Parasail build error #12

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atks opened this issue Jun 11, 2021 · 7 comments
Open

Parasail build error #12

atks opened this issue Jun 11, 2021 · 7 comments

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@atks
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atks commented Jun 11, 2021 •
edited
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Hi, this is the error log for building parasail. For some reason, version.sh cannot be executed, I'm already running it with sudo.

My system is Ubuntu 20.04.2 LTS.

(NGSpeciesID) cavs@shangri-la:\~$ sudo pip install NGSpeciesID
Processing /root/.cache/pip/wheels/3d/dc/a9/bcf6c04f5e5d51e228683737da3a567ab0ad2ec9d6bcce603b/NGSpeciesID-0.1.1.1-py2.py3-none-any.whl
Requirement already satisfied: edlib>=1.1.2 in /usr/local/lib/python3.8/dist-packages (from NGSpeciesID) (1.3.8.post2)
Collecting parasail==1.1.11
  Using cached parasail-1.1.11.tar.gz (46 kB)
Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from parasail==1.1.11->NGSpeciesID) (1.17.4)
Building wheels for collected packages: parasail
  Building wheel for parasail (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-kxh9lx29/parasail/setup.py'"'"'; __file__='"'"'/tmp/pip-install-kxh9lx29/parasail/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-9ngj359h
       cwd: /tmp/pip-install-kxh9lx29/parasail/
  Complete output (121 lines):
  running bdist_wheel
  parasail/libparasail.so not found, attempting to build
  Downloading latest parasail master
  Unzipping parasail master archive
  fixing executable bits after unzipping
  Unable to find parasail configure script
  Prepending /usr/bin to PATH
  PATH=/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
  Running autoreconf -fi from ./parasail-master
  b'This is perl 5, version 30, subversion 0 (v5.30.0) built for x86_64-linux-gnu-thread-multi'
  b'm4 (GNU M4) 1.4.18'
  b'autoconf (GNU Autoconf) 2.69'
  b'automake (GNU automake) 1.16.1'
  b'libtool (GNU libtool) 2.4.6'
  b'autoreconf (GNU Autoconf) 2.69'
  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
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  sh: 1: ./version.sh: Permission denied
  libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'build-aux'.
  libtoolize: copying file 'build-aux/ltmain.sh'
  libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
  libtoolize: copying file 'm4/libtool.m4'
  libtoolize: copying file 'm4/ltoptions.m4'
  libtoolize: copying file 'm4/ltsugar.m4'
  libtoolize: copying file 'm4/ltversion.m4'
  libtoolize: copying file 'm4/lt~obsolete.m4'
  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
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  sh: 1: ./version.sh: Permission denied
  configure.ac:115: installing 'build-aux/compile'
  configure.ac:74: installing 'build-aux/config.guess'
  configure.ac:74: installing 'build-aux/config.sub'
  configure.ac:66: installing 'build-aux/install-sh'
  configure.ac:66: installing 'build-aux/missing'
  Makefile.am: installing 'build-aux/depcomp'
  parallel-tests: installing 'build-aux/test-driver'
  autoreconf -fi exited with return code 0
  configuring parasail in directory ./parasail-master
  error: [Errno 13] Permission denied: './configure'
  ----------------------------------------
  ERROR: Failed building wheel for parasail
  Running setup.py clean for parasail
Failed to build parasail
Installing collected packages: parasail, NGSpeciesID
    Running setup.py install for parasail ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-kxh9lx29/parasail/setup.py'"'"'; __file__='"'"'/tmp/pip-install-kxh9lx29/parasail/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-8dhyla3b/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.8/parasail
         cwd: /tmp/pip-install-kxh9lx29/parasail/
    Complete output (7 lines):
    running install
    parasail/libparasail.so not found, attempting to build
    Archive 'parasail-master.zip' already downloaded
    Archive 'parasail-master.zip' already unzipped to /tmp/pip-install-kxh9lx29/parasail
    fixing executable bits after unzipping
    configuring parasail in directory ./parasail-master
    error: [Errno 13] Permission denied: './configure'
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-kxh9lx29/parasail/setup.py'"'"'; __file__='"'"'/tmp/pip-install-kxh9lx29/parasail/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-8dhyla3b/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.8/parasail Check the logs for full command output.
@ksahlin
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ksahlin commented Jun 11, 2021

Hi @atks,

It looks like you don't have permission to run sudo. Is there a reason why you can't run pip install NGSpeciesID as specified in the instructions? That is, without the sudo command.

@atks
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atks commented Jun 11, 2021

hi @ksahlin,

I'm the administrator of the machine, so access is not an issue. I definitely have the rights to run sudo. I tried pip install NGSpeciesID too, same error. I list it here as shown here. The previous steps are fine, and NGSpeciesID itself installed fine, so I think the issue is specific to parasail. Do you have any suggestions on a manual install for parasail? Really keen on using your program!

cavs@shangri-la:~$ conda activate NGSpeciesID
(NGSpeciesID) cavs@shangri-la:~$ pip install NGSpeciesID
Collecting NGSpeciesID
  Using cached NGSpeciesID-0.1.1.1-py2.py3-none-any.whl
Collecting edlib>=1.1.2
  Using cached edlib-1.3.8.post2-cp36-cp36m-manylinux2010_x86_64.whl (304 kB)
Collecting parasail==1.1.11
  Using cached parasail-1.1.11.tar.gz (46 kB)
Requirement already satisfied: numpy in ./anaconda3/envs/NGSpeciesID/lib/python3.6/site-packages (from parasail==1.1.11->NGSpeciesID) (1.16.1)
Building wheels for collected packages: parasail
  Building wheel for parasail (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/cavs/anaconda3/envs/NGSpeciesID/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-pd663yl9/parasail_af55dcf4fbd84e07bfcf7e1427414b72/setup.py'"'"'; __file__='"'"'/tmp/pip-install-pd663yl9/parasail_af55dcf4fbd84e07bfcf7e1427414b72/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-de40ibkz
       cwd: /tmp/pip-install-pd663yl9/parasail_af55dcf4fbd84e07bfcf7e1427414b72/
  Complete output (121 lines):
  running bdist_wheel
  parasail/libparasail.so not found, attempting to build
  Downloading latest parasail master
  Unzipping parasail master archive
  fixing executable bits after unzipping
  Unable to find parasail configure script
  Prepending /usr/bin to PATH
  PATH=/usr/bin:/home/cavs/anaconda3/envs/NGSpeciesID/bin:/home/cavs/anaconda3/bin:/home/cavs/anaconda3/bin:/home/cavs/.local/bin:/home/cavs/bin:/home/cavs/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/usr/local/sra-2.11.0/bin:/usr/local/fratools
  Running autoreconf -fi from ./parasail-master
  b'This is perl 5, version 30, subversion 0 (v5.30.0) built for x86_64-linux-gnu-thread-multi'
  b'm4 (GNU M4) 1.4.18'
  b'autoconf (GNU Autoconf) 2.69'
  b'automake (GNU automake) 1.16.1'
  b'libtool (GNU libtool) 2.4.6'
  b'autoreconf (GNU Autoconf) 2.69'
  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
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  sh: 1: ./version.sh: Permission denied
  libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'build-aux'.
  libtoolize: copying file 'build-aux/ltmain.sh'
  libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
  libtoolize: copying file 'm4/libtool.m4'
  libtoolize: copying file 'm4/ltoptions.m4'
  libtoolize: copying file 'm4/ltsugar.m4'
  libtoolize: copying file 'm4/ltversion.m4'
  libtoolize: copying file 'm4/lt~obsolete.m4'
  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
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  sh: 1: ./version.sh: Permission denied
  sh: 1: ./version.sh: Permission denied
  configure.ac:115: installing 'build-aux/compile'
  configure.ac:74: installing 'build-aux/config.guess'
  configure.ac:74: installing 'build-aux/config.sub'
  configure.ac:66: installing 'build-aux/install-sh'
  configure.ac:66: installing 'build-aux/missing'
  Makefile.am: installing 'build-aux/depcomp'
  parallel-tests: installing 'build-aux/test-driver'
  autoreconf -fi exited with return code 0
  configuring parasail in directory ./parasail-master
  error: [Errno 13] Permission denied: './configure'
  ----------------------------------------
  ERROR: Failed building wheel for parasail
  Running setup.py clean for parasail
Failed to build parasail
Installing collected packages: parasail, edlib, NGSpeciesID
  Attempting uninstall: parasail
    Found existing installation: parasail 1.2.4
    Uninstalling parasail-1.2.4:
      Successfully uninstalled parasail-1.2.4
    Running setup.py install for parasail ... error
    ERROR: Command errored out with exit status 1:
     command: /home/cavs/anaconda3/envs/NGSpeciesID/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-pd663yl9/parasail_af55dcf4fbd84e07bfcf7e1427414b72/setup.py'"'"'; __file__='"'"'/tmp/pip-install-pd663yl9/parasail_af55dcf4fbd84e07bfcf7e1427414b72/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-63ku7dzv/install-record.txt --single-version-externally-managed --compile --install-headers /home/cavs/anaconda3/envs/NGSpeciesID/include/python3.6m/parasail
         cwd: /tmp/pip-install-pd663yl9/parasail_af55dcf4fbd84e07bfcf7e1427414b72/
    Complete output (7 lines):
    running install
    parasail/libparasail.so not found, attempting to build
    Archive 'parasail-master.zip' already downloaded
    Archive 'parasail-master.zip' already unzipped to /tmp/pip-install-pd663yl9/parasail_af55dcf4fbd84e07bfcf7e1427414b72
    fixing executable bits after unzipping
    configuring parasail in directory ./parasail-master
    error: [Errno 13] Permission denied: './configure'
    ----------------------------------------
  Rolling back uninstall of parasail
  Moving to /home/cavs/anaconda3/envs/NGSpeciesID/lib/python3.6/site-packages/parasail-1.2.4.dist-info/
   from /home/cavs/anaconda3/envs/NGSpeciesID/lib/python3.6/site-packages/~arasail-1.2.4.dist-info
  Moving to /home/cavs/anaconda3/envs/NGSpeciesID/lib/python3.6/site-packages/parasail/
   from /home/cavs/anaconda3/envs/NGSpeciesID/lib/python3.6/site-packages/~arasail
ERROR: Command errored out with exit status 1: /home/cavs/anaconda3/envs/NGSpeciesID/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-pd663yl9/parasail_af55dcf4fbd84e07bfcf7e1427414b72/setup.py'"'"'; __file__='"'"'/tmp/pip-install-pd663yl9/parasail_af55dcf4fbd84e07bfcf7e1427414b72/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-63ku7dzv/install-record.txt --single-version-externally-managed --compile --install-headers /home/cavs/anaconda3/envs/NGSpeciesID/include/python3.6m/parasail Check the logs for full command output.

@ksahlin
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ksahlin commented Jun 11, 2021 •
edited
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Hmm, looking a bit closer at the error message, it looks like you already have parasail installed.

specifically the lines

Collecting parasail==1.1.11
  Using cached parasail-1.1.11.tar.gz (46 kB)
Requirement already satisfied: numpy in ./anaconda3/envs/NGSpeciesID/lib/python3.6/site-packages (from parasail==1.1.11->NGSpeciesID) (1.16.1)

Check if you can do:

$ conda activate NGSpeciesID
$ python
>>> import parasail

Does it work? If so, then try running NGSpeciesID. You have to run the other part of the install if you have not already, which is:

conda install --yes -c conda-forge -c bioconda medaka=0.11.5 openblas==0.3.3 spoa racon minimap2

Let me know how it goes.

@atks
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atks commented Jun 11, 2021

@ksahlin

(NGSpeciesID) cavs@shangri-la:~$ python
Python 3.6.10 | packaged by conda-forge | (default, Apr 24 2020, 16:44:11) 
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import parasail
>>>

this work.

the following step was ran successfully previously.

(NGSpeciesID) cavs@shangri-la:~$ conda install --yes -c conda-forge -c bioconda medaka=0.11.5 openblas==0.3.3 spoa racon minimap2
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.10.0
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base conda



# All requested packages already installed.

but ...

(NGSpeciesID) cavs@shangri-la:~$ NGSpeciesID --help
-bash: NGSpeciesID: command not found

@ksahlin
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ksahlin commented Jun 11, 2021

Tricky. I guess there is some version conflict with parasail from another environment.

What I can suggest is that you completely remove the NGSpeciesID environment with:

conda deactivate NGSpeciesID
conda env remove --name NGSpeciesID

and start a new install from scratch following the installation.

If that doesn't work. I would suggest try localizing where the other parasail has been installed. For example:

$ python
>>> import parasail
>>>  parasail.__path__
['/Users/kxs624/opt/anaconda3/lib/python3.8/site-packages/parasail']

And figure out why it is installed there and eventually remove it.

@atks
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atks commented Jun 11, 2021

same issues again after starting the install from scratch.

parasail is not installed prior to the installation of NGSpeciesID.

no worries, I'll go try some other solutions. thanks!

@atks atks closed this as completed Jun 11, 2021
@atks
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atks commented Jul 26, 2021 •
edited
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@ksahlin

just FYI, I managed to finally install NGSpeciesID. The issue was with the /tmp partition not allowing execution of files.

just do : sudo mount -o remount,exec /tmp

This should occur relatively often as it is one of the things that Center for Internet Security (CIS) hardening would require.

@atks atks reopened this Jul 26, 2021
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