flass
commented
2 years ago Hi,
this looks like an issue due to the obsolescence of Python 2. As Pantagruel relies on Python 2.7, it aims to have it installed and so the dependency installation script relied on apt to install the relevant Debian packages. however, with the recent effective retirement of Python 2 in modern Linux operating systems, these packages may not be available anymore.
Can you please specify what operating system you're using? I suspect it is too recent.
Pantagruel has been tested on Ubuntu 18.4 LTS the install script was meant to be used on this system; sorry this was not made clear in the doc.
This was now clarified in the INTALL doc (see ac69b4a).
to solve your issue, I recommend you do one of these things:
- try and install Pantagruel on a machine with Ubuntu 18.4 LTS (this can be easily achieved by spinning a VM with this OS flavour)
- use the Docker image provided on Dockerhub (https://hub.docker.com/repository/docker/flass/pantagruel-dep) to run Pantagruel (this image has been built on Ubuntu 18.4 LTS base).
I hope this helps.
Best wishes,
Florent
Hi
I got the following error while trying to install dependencies
Reading package lists... Done Building dependency tree
Reading state information... Done 11 packages can be upgraded. Run 'apt list --upgradable' to see them. Reading package lists... Done Building dependency tree
Reading state information... Done Note, selecting 'python-is-python2' instead of 'python' Package python-scipy is not available, but is referred to by another package. This may mean that the package is missing, has been obsoleted, or is only available from another source
Package python-pip is not available, but is referred to by another package. This may mean that the package is missing, has been obsoleted, or is only available from another source However the following packages replace it: python3-pip
E: Package 'python-scipy' has no installation candidate E: Unable to locate package python-biopython E: Unable to locate package python-biopython-sql E: Unable to locate package python-igraph E: Package 'python-pip' has no installation candidate E: Unable to locate package linuxbrew-wrapper E: Unable to locate package docker.io ERROR: could not install all required Debian packages: Listing... Error! build-essential/focal-updates,now 12.8ubuntu1.1 amd64 [installed] build-essential/focal-updates 12.8ubuntu1.1 i386 clustalo/focal,now 1.2.4-4build1 amd64 [installed,automatic] cmake/focal 3.16.3-1ubuntu1 amd64 cmake/focal 3.16.3-1ubuntu1 i386 cython/focal 0.29.14-0.1ubuntu3 amd64 cython/focal 0.29.14-0.1ubuntu3 i386 g++/focal,now 4:9.3.0-1ubuntu2 amd64 [installed] g++/focal 4:9.3.0-1ubuntu2 i386 gcc/focal,now 4:9.3.0-1ubuntu2 amd64 [installed] gcc/focal 4:9.3.0-1ubuntu2 i386 gfortran/focal,now 4:9.3.0-1ubuntu2 amd64 [installed,automatic] gfortran/focal 4:9.3.0-1ubuntu2 i386 git/focal-updates,focal-security 1:2.25.1-1ubuntu3.4 amd64 [upgradable from: 1:2.25.1-1ubuntu3.3] git/focal-updates,focal-security 1:2.25.1-1ubuntu3.4 i386 lftp/focal,now 4.8.4-2build3 amd64 [installed] libdw-dev/focal 0.176-1.1build1 amd64 libdw-dev/focal 0.176-1.1build1 i386 libdw1/focal,now 0.176-1.1build1 amd64 [installed,automatic] libdw1/focal 0.176-1.1build1 i386 libgsl-dev/focal,now 2.5+dfsg-6build1 amd64 [installed] libgsl-dev/focal 2.5+dfsg-6build1 i386 libgsl23/focal,now 2.5+dfsg-6build1 amd64 [installed,automatic] libgsl23/focal 2.5+dfsg-6build1 i386 libhmsbeagle1v5/focal 3.1.2+dfsg-7build1 amd64 libmagick++-dev/focal-updates,focal-updates,focal-security,focal-security,now 8:6.9.10.23+dfsg-2.1ubuntu11.4 all [installed] mpi-default-bin/focal 1.13 amd64 mpi-default-bin/focal 1.13 i386 mpi-default-dev/focal 1.13 amd64 mpi-default-dev/focal 1.13 i386 mrbayes-mpi/focal 3.2.6+dfsg-2ubuntu2 amd64 mrbayes/focal 3.2.6+dfsg-2ubuntu2 amd64 openjdk-11-jdk/focal-updates,focal-security 11.0.15+10-0ubuntu0.20.04.1 amd64 openjdk-11-jdk/focal-updates,focal-security 11.0.15+10-0ubuntu0.20.04.1 i386 openjdk-11-jre/focal-updates,focal-security 11.0.15+10-0ubuntu0.20.04.1 amd64 [upgradable from: 11.0.14.1+1-0ubuntu1~20.04] openjdk-11-jre/focal-updates,focal-security 11.0.15+10-0ubuntu0.20.04.1 i386 python-numpy/focal 1:1.16.5-2ubuntu7 amd64 r-base-core/focal-cran40,now 4.1.3-1.2004.0 amd64 [installed] r-cran-ade4/focal 1.7-18-1cran1.2004.0 amd64 r-cran-ape/focal 5.6-2-1cran1.2004.0 amd64 r-cran-dbi/focal,focal 1.1.2-1cran1.2004.0 all r-cran-getopt/focal,focal 1.20.3-2.1~ubuntu20.04.1~ppa1 all r-cran-igraph/focal 1.3.0-1cran1.2004.0 amd64 r-cran-phytools/focal,focal 1.0-3-1cran1.2004.0 all r-cran-rcolorbrewer/focal,focal,now 1.1-3-1cran1.2004.0 all [installed,automatic] r-cran-rsqlite/focal 2.2.12-1cran1.2004.0 amd64 r-cran-vegan/focal 2.5-7-1cran1.2004.0 amd64 r-recommended/focal-cran40,now 4.1.3-1.2004.0 all [installed,automatic] raxml/focal,now 8.2.12+dfsg-4 amd64 [installed,automatic] sqlite3-doc/focal-updates,focal-updates,focal-security,focal-security 3.31.1-4ubuntu0.2 all sqlite3/focal-updates,focal-security 3.31.1-4ubuntu0.2 amd64 sqlite3/focal-updates,focal-security 3.31.1-4ubuntu0.2 i386 E: input:0-10: error: Expected pattern docker.io ^^^^^^^^^^ ERROR: abort installation of Pantagruel