Bio-Linux compatibility

[tony-travis]

I tried BioMake under Bio-Linux 8.0.8 based on Ubuntu 14.04.5, LTS but encountered problems:

download and install

root@wildcat:/usr/local/src/bioinformatics/BioMake# git clone https://github.com/evoldoers/biomake.git apt install swi-prolog prolog --version SWI-Prolog version 6.6.4 for amd64

test

root@wildcat:/usr/local/src/bioinformatics/BioMake/biomake# make |& tee make.log git clean -fd t/target || true /usr/local/src/bioinformatics/BioMake/biomake/bin/swipl_wrap -q -t test -l prolog/test/test ERROR: /usr/lib/swi-prolog/library/prolog_stack.pl:458: dynamic/1: No permission to modify static procedure `prolog_exception_hook/4' Defined at /usr/local/src/bioinformatics/BioMake/biomake/prolog/test/test.pl:23 [8] backtrace(99) at /usr/lib/swi-prolog/library/prolog_stack.pl:376 [7] prolog_exception_hook(error(...,...),_G810,97,none) at /usr/local/src/bioinformatics/BioMake/biomake/prolog/test/test.pl:25 [6] [5] string_chars([70|...],_G867) [4] announce([70|...]) at /usr/local/src/bioinformatics/BioMake/biomake/prolog/test/test.pl:319 [3] test at /usr/local/src/bioinformatics/BioMake/biomake/prolog/test/test.pl:36 ERROR: announce/1: Undefined procedure: string_chars/2 Exception: (5) string_chars([70, 65, 73, 76, 85, 82, 69, 32|...], _G775) ? EOF: exit

check versions of SWI-Prolog available in Ubuntu repo's

root@wildcat:/usr/local/src/bioinformatics/BioMake/biomake# apt-cache policy swi-prolog swi-prolog: Installed: 6.6.4-2ubuntu1 Candidate: 6.6.4-2ubuntu1 Version table: *** 6.6.4-2ubuntu1 0 500 http://gb.archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages 100 /var/lib/dpkg/status 5.10.4-3ubuntu1 0 500 http://archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages

Any ideas?

Tony.

[cmungall]

I don't believe we've tested under swipl6, swipl7 has been out for a while now.

Does this help? http://www.swi-prolog.org/build/PPA.html

[ihh]

Closing this as it apparently reduces to noncompatibility with older SWIPL