Andreas Tille pushed to branch master at Debian Med / garli
Commits: 48ac431b by Andreas Tille at 2018-09-04T10:38:49Z debhelper 11 - - - - - 9798bf64 by Andreas Tille at 2018-09-04T10:38:53Z Point Vcs fields to salsa.debian.org - - - - - 2883f49d by Andreas Tille at 2018-09-04T10:38:53Z Standards-Version: 4.2.1 - - - - - cba93b1d by Andreas Tille at 2018-09-04T12:09:55Z Fix installation - - - - - c1d7a502 by Andreas Tille at 2018-09-04T12:48:00Z Better documentation of MPI version - - - - - eadfefee by Andreas Tille at 2018-09-04T13:20:25Z Upload to unstable - - - - - 8 changed files: - debian/README.Debian - debian/changelog - debian/compat - debian/control - debian/garli-mpi.1 - + debian/garli-mpi.install - debian/garli.install - debian/rules Changes: ===================================== debian/README.Debian ===================================== @@ -16,4 +16,17 @@ and was reported upstream. Please check this issue on Github for further information. + +The MPI version claims to be 32 bit based on this test in src/garlimain.cpp: + + //I'm not sure that this is dependable or portable, but it is only for screen output, so isn't that important + int ptrSize = sizeof(int *); + if(ptrSize == 8) + is64bit = true; + else + is64bit = false; + +I think that test is simply wrong since compilation is 64 bit on amd64. + + -- Andreas Tille <[email protected]> Tue, 04 Sep 2018 11:09:43 +0200 ===================================== debian/changelog ===================================== @@ -1,12 +1,15 @@ -garli (2.1-3) UNRELEASED; urgency=medium +garli (2.1-3) unstable; urgency=medium * d/rules: Fix random seed before running tests to get (mostly!) reproducible results Addresses: #907905 (since the FTBFS issue is solved severity will be reset to minor but I leave the bug open for further discussion) * Provide additional MPI version in separate package + * debhelper 11 + * Point Vcs fields to salsa.debian.org + * Standards-Version: 4.2.1 - -- Andreas Tille <[email protected]> Tue, 04 Sep 2018 11:09:43 +0200 + -- Andreas Tille <[email protected]> Tue, 04 Sep 2018 15:04:01 +0200 garli (2.1-2) unstable; urgency=medium ===================================== debian/compat ===================================== @@ -1 +1 @@ -10 +11 ===================================== debian/control ===================================== @@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 10), +Build-Depends: debhelper (>= 11~), libncl-dev, libopenmpi-dev, ncl-tools, bc -Standards-Version: 4.1.1 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/garli.git -Vcs-Git: https://anonscm.debian.org/git/debian-med/garli.git +Standards-Version: 4.2.1 +Vcs-Browser: https://salsa.debian.org/med-team/garli +Vcs-Git: https://salsa.debian.org/med-team/garli.git Homepage: https://github.com/Ashod/garli Package: garli @@ -29,7 +29,8 @@ Description: phylogenetic analysis of molecular sequence data using maximum-like Package: garli-mpi Architecture: any Depends: ${shlibs:Depends}, - ${misc:Depends} + ${misc:Depends}, + openmpi-bin Description: phylogenetic analysis of molecular sequence data using maximum-likelihood (MPI) GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees. Using an approach similar to a classical ===================================== debian/garli-mpi.1 ===================================== @@ -3,8 +3,7 @@ .SH NAME garli \- phylogenetic analysis of molecular sequence data using maximum-likelihood (MPI version) .SH SYNOPSIS -.B garli -[\fI\,OPTION\/\fR] [\fI\,config filename\/\fR] +\fBmpirun\fR [\fIMPI OPTIONS\fR] \fBgarli-mpi\fR -[# of times to execute config file] [\fI\,config filename\/\fR] .SH DESCRIPTION GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees. Using an approach similar to a classical ===================================== debian/garli-mpi.install ===================================== @@ -0,0 +1 @@ +debian/mpi/* usr/lib/garli/bin ===================================== debian/garli.install ===================================== @@ -1,2 +1 @@ usr/bin usr/lib/garli -# debian/bin usr ===================================== debian/rules ===================================== @@ -11,8 +11,8 @@ override_dh_auto_configure: # First build MPI version of Garli dh_auto_configure -- --with-ncl=/usr --enable-mpi dh_auto_build - mkdir -p debian/$(DEB_SOURCE)-mpi/usr/lib/$(DEB_SOURCE)/bin - mv src/Garli debian/$(DEB_SOURCE)-mpi/usr/lib/$(DEB_SOURCE)/bin/Garli-mpi + mkdir -p debian/mpi + mv src/Garli debian/mpi/Garli-mpi make distclean # Now build single processor binary dh_auto_configure -- --with-ncl=/usr View it on GitLab: https://salsa.debian.org/med-team/garli/compare/0271bccd209b9f5cd205ff4763c64e0785b7f208...eadfefeef220c5c000fd3e57f33b814c3e29d2eb -- View it on GitLab: https://salsa.debian.org/med-team/garli/compare/0271bccd209b9f5cd205ff4763c64e0785b7f208...eadfefeef220c5c000fd3e57f33b814c3e29d2eb You're receiving this email because of your account on salsa.debian.org.
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