Package being built even though aliDoctor reports that it can be used from the system.

[olantwin]

Using aliBuild 1.5.5, on slc7_x86-64(using aliBuild in docker on the cern/cc7-base image), I find myself in a situation in which aliDoctor and aliBuild disagree on which packages can be used from the system (output below). This is not a duplicate of #479, as I use the same defaults in both cases.

These are run in an identical environment with the same shipdist (our equivalent of alidist) and same defaults.

Any ideas what could be going wrong or suggestions to troubleshoot?

AliDoctor

 aliDoctor -c shipdist/ --defaults fairship Python

==> In order to improve user experience, aliBuild would like to gather analytics about your builds.
    You can find all the details at:
    
      https://github.com/alisw/alibuild/blob/master/ANALYTICS.md
    
Is that ok for you [YES/no]? no
WARNING: Package Python cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; python3 -c 'import sys; import sqlite3; sys.exit(1 if sys.version_info < (3, 5) else 0)' && pip3 --help > /dev/null && printf '#include "pyconfig.h"' | cc -c $(python-config --includes) -xc -o /dev/null -; if [ $? -ne 0 ]; then printf "Python, the Python development packages, and pip must be installed on your system.\nUsually those packages are called python, python-devel (or python-dev) and python-pip.\n"; exit 1; fi
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: Python: /bin/bash: python3: command not found
WARNING: Python: Python, the Python development packages, and pip must be installed on your system.
WARNING: Python: Usually those packages are called python, python-devel (or python-dev) and python-pip.
WARNING: Python: 
WARNING: 
SUCCESS: Package FreeType will be picked up from the system.
SUCCESS: Package libpng will be picked up from the system.
SUCCESS: Package sqlite will be picked up from the system.
WARNING: Package GCC-Toolchain cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING: 
WARNING: brew() { true; }; set -e
WARNING: which gfortran || { echo "gfortran missing"; exit 1; }
WARNING: which cc && test -f $(dirname $(which cc))/c++ && printf "#define GCCVER ((__GNUC__ << 16)+(__GNUC_MINOR__ << 8)+(__GNUC_PATCHLEVEL__))\n#if (GCCVER < 0x060000 || GCCVER > 0x090000)\n#error \"System's GCC cannot be used: we need GCC 6.X. We are going to compile our own version.\"\n#endif\n" | cc -xc++ - -c -o /dev/null
WARNING: 
WARNING: with the following output:
WARNING: 
WARNING: GCC-Toolchain: /usr/bin/gfortran
WARNING: GCC-Toolchain: /usr/bin/cc
WARNING: GCC-Toolchain: <stdin>:3:2: error: #error "System's GCC cannot be used: we need GCC 6.X. We are going to compile our own version."
WARNING: GCC-Toolchain: 
WARNING: 
SUCCESS: Required package curl will be picked up from the system.
SUCCESS: Package autotools will be picked up from the system.
SUCCESS: Required package yacc-like will be picked up from the system.

==> The following packages will be built by aliBuild because
     usage of a system version of it is not allowed or supported, by policy:
    
    - libffi 
    - defaults-release

==> The following packages will be picked up from the system:
    
    - libpng
    - FreeType
    - autotools
    - sqlite
    
    If this is not you want, you have to uninstall / unload them.

==> The following packages will be built by aliBuild because they couldn't be picked up from the system:
    
    - Python
    - GCC-Toolchain
    
    This is not a real issue, but it might take longer the first time you invoke aliBuild.
    Look at the error messages above to get hints on what packages you need to install separately.

AliBuild

aliBuild -c shipdist/ --defaults fairship build Python

==> Packages will be built in the following order:
     - [email protected]
     - [email protected]
     - [email protected]
     - [email protected]
     - [email protected]
     - [email protected]
     - [email protected]
     - [email protected]

[ironMann]

HI, I observe the similar on my development machine. However, I installed a fresh centos7 VM and by following the https://alice-doc.github.io/alice-analysis-tutorial/building/build.html to the letter I get the intended behavior of alibuld: dependencies being downloaded as prebuilt packages.

Can the installed system python versions cause this?
Bad:

aliBuild version; pip --version; python --version
aliBuild version: 1.5.5 (slc7_x86-64)
pip 9.0.3 from /usr/lib/python3.6/site-packages (python 3.6)
Python 2.7.5

Good:

aliBuild version; pip --version; python --version
aliBuild version: 1.5.5 (slc7_x86-64)
pip 19.3.1 from /usr/lib/python2.7/site-packages/pip (python 2.7)
Python 2.7.5

If I understand correctyl, even though aliDoctor is happy with system packages, for centos7 aliBuild will try to download prebuilt binaries of all dependencies.

• intended behavior Allow defaults to customise python modules alidist#1958 (comment)