Installation error, python?

[shlomobl]

Hello,

Hope someone still keeps an eye on issues here :-)

I am trying to install ReMatCh in an Ubuntu 20.02 in order to run the INNuca pipeline, but I cannot get through the installation.

Seems like something related to the python version, although I do have 3.9.16 installed.

Appreciate any help with this issue!

shlomo@shlomo-HP-Z840:~/Programs/ReMatCh$ sudo python3 setup.py install
running install
running bdist_egg
running egg_info
writing ReMatCh.egg-info/PKG-INFO
writing dependency_links to ReMatCh.egg-info/dependency_links.txt
writing entry points to ReMatCh.egg-info/entry_points.txt
writing requirements to ReMatCh.egg-info/requires.txt
writing top-level names to ReMatCh.egg-info/top_level.txt
reading manifest file 'ReMatCh.egg-info/SOURCES.txt'
writing manifest file 'ReMatCh.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/.git
copying build/lib/.git/index -> build/bdist.linux-x86_64/egg/.git
copying build/lib/.git/description -> build/bdist.linux-x86_64/egg/.git
copying build/lib/.git/packed-refs -> build/bdist.linux-x86_64/egg/.git
creating build/bdist.linux-x86_64/egg/.git/refs
creating build/bdist.linux-x86_64/egg/.git/refs/heads
copying build/lib/.git/refs/heads/master -> build/bdist.linux-x86_64/egg/.git/refs/heads
creating build/bdist.linux-x86_64/egg/.git/refs/remotes
creating build/bdist.linux-x86_64/egg/.git/refs/remotes/origin
copying build/lib/.git/refs/remotes/origin/HEAD -> build/bdist.linux-x86_64/egg/.git/refs/remotes/origin
copying build/lib/.git/config -> build/bdist.linux-x86_64/egg/.git
creating build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/pre-commit.sample -> build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/applypatch-msg.sample -> build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/prepare-commit-msg.sample -> build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/pre-push.sample -> build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/commit-msg.sample -> build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/pre-receive.sample -> build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/pre-applypatch.sample -> build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/update.sample -> build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/fsmonitor-watchman.sample -> build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/post-update.sample -> build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/pre-merge-commit.sample -> build/bdist.linux-x86_64/egg/.git/hooks
copying build/lib/.git/hooks/pre-rebase.sample -> build/bdist.linux-x86_64/egg/.git/hooks
creating build/bdist.linux-x86_64/egg/.git/info
copying build/lib/.git/info/exclude -> build/bdist.linux-x86_64/egg/.git/info
creating build/bdist.linux-x86_64/egg/.git/objects
creating build/bdist.linux-x86_64/egg/.git/objects/pack
copying build/lib/.git/objects/pack/pack-b59d92059d32c2eedef8c798a9a0a194ec88865d.idx -> build/bdist.linux-x86_64/egg/.git/objects/pack
copying build/lib/.git/objects/pack/pack-b59d92059d32c2eedef8c798a9a0a194ec88865d.pack -> build/bdist.linux-x86_64/egg/.git/objects/pack
creating build/bdist.linux-x86_64/egg/.git/logs
creating build/bdist.linux-x86_64/egg/.git/logs/refs
creating build/bdist.linux-x86_64/egg/.git/logs/refs/heads
copying build/lib/.git/logs/refs/heads/master -> build/bdist.linux-x86_64/egg/.git/logs/refs/heads
creating build/bdist.linux-x86_64/egg/.git/logs/refs/remotes
creating build/bdist.linux-x86_64/egg/.git/logs/refs/remotes/origin
copying build/lib/.git/logs/refs/remotes/origin/HEAD -> build/bdist.linux-x86_64/egg/.git/logs/refs/remotes/origin
copying build/lib/.git/logs/HEAD -> build/bdist.linux-x86_64/egg/.git/logs
copying build/lib/.git/HEAD -> build/bdist.linux-x86_64/egg/.git
creating build/bdist.linux-x86_64/egg/ReMatCh
creating build/bdist.linux-x86_64/egg/ReMatCh/src
creating build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1
creating build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/zoom2sam.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/export2sam.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/ace2sam -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/wgsim_eval.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/plot-bamstats -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/blast2sam.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/seq_cache_populate.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/interpolate_sam.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/samtools -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/soap2sam.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/wgsim -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/samtools.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/psl2sam.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/md5sum-lite -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/md5fa -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/novo2sam.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/sam2vcf.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/varfilter.py -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/bowtie2sam.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/maq2sam-short -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
copying build/lib/ReMatCh/src/samtools-1.3.1/bin/maq2sam-long -> build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin
creating build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-inspect-l -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-build-s -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-inspect-l-debug -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-build-l -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-align-s-debug -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2 -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-inspect-s -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-build -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-inspect -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-build-l-debug -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-align-l-debug -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-align-l -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-build-s-debug -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-align-s -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
copying build/lib/ReMatCh/src/bowtie2-2.2.9/bowtie2-inspect-s-debug -> build/bdist.linux-x86_64/egg/ReMatCh/src/bowtie2-2.2.9
creating build/bdist.linux-x86_64/egg/ReMatCh/src/bcftools-1.3.1
creating build/bdist.linux-x86_64/egg/ReMatCh/src/bcftools-1.3.1/bin
copying build/lib/ReMatCh/src/bcftools-1.3.1/bin/bcftools -> build/bdist.linux-x86_64/egg/ReMatCh/src/bcftools-1.3.1/bin
copying build/lib/ReMatCh/src/bcftools-1.3.1/bin/vcfutils.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/bcftools-1.3.1/bin
copying build/lib/ReMatCh/src/bcftools-1.3.1/bin/plot-vcfstats -> build/bdist.linux-x86_64/egg/ReMatCh/src/bcftools-1.3.1/bin
copying build/lib/ReMatCh/src/bcftools-1.3.1/bin/color-chrs.pl -> build/bdist.linux-x86_64/egg/ReMatCh/src/bcftools-1.3.1/bin
copying build/lib/ReMatCh/__init__.py -> build/bdist.linux-x86_64/egg/ReMatCh
creating build/bdist.linux-x86_64/egg/ReMatCh/utils
copying build/lib/ReMatCh/utils/strip_alignment.py -> build/bdist.linux-x86_64/egg/ReMatCh/utils
copying build/lib/ReMatCh/utils/combine_alignment_consensus.py -> build/bdist.linux-x86_64/egg/ReMatCh/utils
copying build/lib/ReMatCh/utils/gffParser.py -> build/bdist.linux-x86_64/egg/ReMatCh/utils
copying build/lib/ReMatCh/utils/restart_rematch.py -> build/bdist.linux-x86_64/egg/ReMatCh/utils
copying build/lib/ReMatCh/utils/convert_Ns_to_gaps.py -> build/bdist.linux-x86_64/egg/ReMatCh/utils
copying build/lib/ReMatCh/utils/README.md -> build/bdist.linux-x86_64/egg/ReMatCh/utils
copying build/lib/ReMatCh/rematch.py -> build/bdist.linux-x86_64/egg/ReMatCh
creating build/bdist.linux-x86_64/egg/ReMatCh/modules
copying build/lib/ReMatCh/modules/rematch_module.py -> build/bdist.linux-x86_64/egg/ReMatCh/modules
copying build/lib/ReMatCh/modules/__init__.py -> build/bdist.linux-x86_64/egg/ReMatCh/modules
creating build/bdist.linux-x86_64/egg/ReMatCh/modules/mlst_schemas
copying build/lib/ReMatCh/modules/mlst_schemas/haemophilus_influenzae.fasta -> build/bdist.linux-x86_64/egg/ReMatCh/modules/mlst_schemas
copying build/lib/ReMatCh/modules/mlst_schemas/streptococcus_dysgalactiae.fasta -> build/bdist.linux-x86_64/egg/ReMatCh/modules/mlst_schemas
copying build/lib/ReMatCh/modules/mlst_schemas/campylobacter_jejuni.fasta -> build/bdist.linux-x86_64/egg/ReMatCh/modules/mlst_schemas
copying build/lib/ReMatCh/modules/mlst_schemas/listeria_monocytogenes.fasta -> build/bdist.linux-x86_64/egg/ReMatCh/modules/mlst_schemas
copying build/lib/ReMatCh/modules/mlst_schemas/salmonella_enterica.fasta -> build/bdist.linux-x86_64/egg/ReMatCh/modules/mlst_schemas
copying build/lib/ReMatCh/modules/mlst_schemas/escherichia_coli#1.fasta -> build/bdist.linux-x86_64/egg/ReMatCh/modules/mlst_schemas
copying build/lib/ReMatCh/modules/mlst_schemas/streptococcus_pneumoniae.fasta -> build/bdist.linux-x86_64/egg/ReMatCh/modules/mlst_schemas
copying build/lib/ReMatCh/modules/mlst_schemas/streptococcus_pyogenes.fasta -> build/bdist.linux-x86_64/egg/ReMatCh/modules/mlst_schemas
copying build/lib/ReMatCh/modules/mlst_schemas/staphylococcus_aureus.fasta -> build/bdist.linux-x86_64/egg/ReMatCh/modules/mlst_schemas
copying build/lib/ReMatCh/modules/mlst_schemas/streptococcus_agalactiae.fasta -> build/bdist.linux-x86_64/egg/ReMatCh/modules/mlst_schemas
copying build/lib/ReMatCh/modules/utils.py -> build/bdist.linux-x86_64/egg/ReMatCh/modules
copying build/lib/ReMatCh/modules/seqFromWebTaxon.py -> build/bdist.linux-x86_64/egg/ReMatCh/modules
copying build/lib/ReMatCh/modules/checkMLST.py -> build/bdist.linux-x86_64/egg/ReMatCh/modules
copying build/lib/ReMatCh/modules/download.py -> build/bdist.linux-x86_64/egg/ReMatCh/modules
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin/varfilter.py to varfilter.cpython-38.pyc
  File "build/bdist.linux-x86_64/egg/ReMatCh/src/samtools-1.3.1/bin/varfilter.py", line 75
    print '''usage: varfilter.py [options] [cns-pileup]

Options: -Q INT minimum RMS mapping quality for SNPs
         -q INT minimum RMS mapping quality for gaps
         -d INT minimum read depth
         -D INT maximum read depth
         -S INT minimum SNP quality
         -i INT minimum indel quality
         -C INT minimum consensus quality for hom-ref sites

         -G INT min indel score for nearby SNP filtering
         -w INT SNP within INT bp around a gap to be filtered

         -W INT window size for filtering dense SNPs
         -N INT max number of SNPs in a window

         -l INT window size for filtering adjacent gaps

         -p print filtered variants'''
          ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print('''usage: varfilter.py [options] [cns-pileup]

Options: -Q INT minimum RMS mapping quality for SNPs
         -q INT minimum RMS mapping quality for gaps
         -d INT minimum read depth
         -D INT maximum read depth
         -S INT minimum SNP quality
         -i INT minimum indel quality
         -C INT minimum consensus quality for hom-ref sites

         -G INT min indel score for nearby SNP filtering
         -w INT SNP within INT bp around a gap to be filtered

         -W INT window size for filtering dense SNPs
         -N INT max number of SNPs in a window

         -l INT window size for filtering adjacent gaps

         -p print filtered variants''')?

byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/__init__.py to __init__.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/utils/strip_alignment.py to strip_alignment.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/utils/combine_alignment_consensus.py to combine_alignment_consensus.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/utils/gffParser.py to gffParser.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/utils/restart_rematch.py to restart_rematch.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/utils/convert_Ns_to_gaps.py to convert_Ns_to_gaps.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/rematch.py to rematch.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/modules/rematch_module.py to rematch_module.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/modules/__init__.py to __init__.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/modules/utils.py to utils.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/modules/seqFromWebTaxon.py to seqFromWebTaxon.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/modules/checkMLST.py to checkMLST.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/ReMatCh/modules/download.py to download.cpython-38.pyc
installing package data to build/bdist.linux-x86_64/egg
running install_data
copying LICENSE -> build/bdist.linux-x86_64/egg/
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying ReMatCh.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying ReMatCh.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying ReMatCh.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying ReMatCh.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying ReMatCh.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying ReMatCh.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
ReMatCh.modules.__pycache__.rematch_module.cpython-38: module references __file__
ReMatCh.modules.__pycache__.utils.cpython-38: module references __file__
creating 'dist/ReMatCh-4.1.0-py3.8.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing ReMatCh-4.1.0-py3.8.egg
removing '/usr/local/lib/python3.8/dist-packages/ReMatCh-4.1.0-py3.8.egg' (and everything under it)
creating /usr/local/lib/python3.8/dist-packages/ReMatCh-4.1.0-py3.8.egg
Extracting ReMatCh-4.1.0-py3.8.egg to /usr/local/lib/python3.8/dist-packages
  File "/usr/local/lib/python3.8/dist-packages/ReMatCh-4.1.0-py3.8.egg/ReMatCh/src/samtools-1.3.1/bin/varfilter.py", line 75
    print '''usage: varfilter.py [options] [cns-pileup]

Options: -Q INT minimum RMS mapping quality for SNPs
         -q INT minimum RMS mapping quality for gaps
         -d INT minimum read depth
         -D INT maximum read depth
         -S INT minimum SNP quality
         -i INT minimum indel quality
         -C INT minimum consensus quality for hom-ref sites

         -G INT min indel score for nearby SNP filtering
         -w INT SNP within INT bp around a gap to be filtered

         -W INT window size for filtering dense SNPs
         -N INT max number of SNPs in a window

         -l INT window size for filtering adjacent gaps

         -p print filtered variants'''
          ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print('''usage: varfilter.py [options] [cns-pileup]

Options: -Q INT minimum RMS mapping quality for SNPs
         -q INT minimum RMS mapping quality for gaps
         -d INT minimum read depth
         -D INT maximum read depth
         -S INT minimum SNP quality
         -i INT minimum indel quality
         -C INT minimum consensus quality for hom-ref sites

         -G INT min indel score for nearby SNP filtering
         -w INT SNP within INT bp around a gap to be filtered

         -W INT window size for filtering dense SNPs
         -N INT max number of SNPs in a window

         -l INT window size for filtering adjacent gaps

         -p print filtered variants''')?

ReMatCh 4.1.0 is already the active version in easy-install.pth
Installing rematch.py script to /usr/local/bin

Installed /usr/local/lib/python3.8/dist-packages/ReMatCh-4.1.0-py3.8.egg
Processing dependencies for ReMatCh==4.1.0
Searching for numpy
Reading https://pypi.org/simple/numpy/
Downloading https://files.pythonhosted.org/packages/78/23/f78fd8311e0f710fe1d065d50b92ce0057fe877b8ed7fd41b28ad6865bfc/numpy-1.26.1.tar.gz#sha256=c8c6c72d4a9f831f328efb1312642a1cafafaa88981d9ab76368d50d07d93cbe
Best match: numpy 1.26.1
Processing numpy-1.26.1.tar.gz
Writing /tmp/easy_install-wopuhyiq/numpy-1.26.1/setup.cfg
Running numpy-1.26.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-wopuhyiq/numpy-1.26.1/egg-dist-tmp-7azhybpr
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 154, in save_modules
    yield saved
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 250, in run_setup
    _execfile(setup_script, ns)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 45, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-wopuhyiq/numpy-1.26.1/setup.py", line 22, in <module>
    version='{}'.format(VERSION),
RuntimeError: Python version >= 3.9 required.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "setup.py", line 20, in <module>
    setup(
  File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 144, in setup
    return distutils.core.setup(**attrs)
  File "/usr/lib/python3.8/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/lib/python3.8/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/lib/python3/dist-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/usr/lib/python3/dist-packages/setuptools/command/install.py", line 117, in do_egg_install
    cmd.run(show_deprecation=False)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 450, in run
    self.easy_install(spec, not self.no_deps)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 693, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 740, in install_item
    self.process_distribution(spec, dist, deps)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 784, in process_distribution
    distros = WorkingSet([]).resolve(
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 781, in resolve
    dist = best[req.key] = env.best_match(
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1066, in best_match
    return self.obtain(req, installer)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1078, in obtain
    return installer(requirement)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 712, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 738, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 923, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1191, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1177, in run_setup
    run_setup(setup_script, args)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 253, in run_setup
    raise
  File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
    self.gen.throw(type, value, traceback)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
    self.gen.throw(type, value, traceback)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 166, in save_modules
    saved_exc.resume()
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 141, in resume
    six.reraise(type, exc, self._tb)
  File "/usr/lib/python3/dist-packages/setuptools/_vendor/six.py", line 685, in reraise
    raise value.with_traceback(tb)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 154, in save_modules
    yield saved
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 250, in run_setup
    _execfile(setup_script, ns)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 45, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-wopuhyiq/numpy-1.26.1/setup.py", line 22, in <module>
    version='{}'.format(VERSION),
RuntimeError: Python version >= 3.9 required.

[ramirma]

Dear shlomobl, Thank you for your interest in INNuca. Development in ReMatch has been slow but we will try to look into this. In the meantime, if possble for you, you coul run INNuca from the Docker image. If you do, please use the 4.2.3-06 tag. Best Regards, Mario

[shlomobl]

Thanks for your reply. I could not install Docker on my system.

On Thu, Nov 2, 2023 at 11:56 AM ramirma @.***> wrote:

Dear shlomobl https://github.com/shlomobl, Thank you for your interest in INNuca. Development in ReMatch has been slow but we will try to look into this. In the meantime, if possble for you, you coul run INNuca from the Docker image https://hub.docker.com/r/ummidock/innuca. If you do, please use the 4.2.3-06 https://hub.docker.com/layers/ummidock/innuca/4.2.3-06/images/sha256-79f4cafa0fcf82a74d548f78985722b49f4d86a3fd4a03b9698f2d00539529aa?context=explore tag. Best Regards, Mario

— Reply to this email directly, view it on GitHub https://github.com/B-UMMI/ReMatCh/issues/30#issuecomment-1790410177, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABKL3XMP2SJNLWOXLGTWGCDYCNU3JAVCNFSM6AAAAAA6U4YXLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJQGQYTAMJXG4 . You are receiving this because you authored the thread.Message ID: @.***>

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