diff -Nru examl-3.0.20/debian/changelog examl-3.0.21/debian/changelog --- examl-3.0.20/debian/changelog 2018-02-10 18:25:43.000000000 +0000 +++ examl-3.0.21/debian/changelog 2018-07-02 09:32:28.000000000 +0000 @@ -1,3 +1,18 @@ +examl (3.0.21-2) unstable; urgency=medium + + * export OMPI_MCA_rmaps_base_oversubscribe=1 in autopkgtest script + Closes: #902848 + + -- Andreas Tille Mon, 02 Jul 2018 11:32:28 +0200 + +examl (3.0.21-1) unstable; urgency=medium + + * New upstream version + * Point Vcs fields to salsa.debian.org + * Standards-Version: 4.1.4 + + -- Andreas Tille Fri, 08 Jun 2018 13:10:46 +0200 + examl (3.0.20-1) unstable; urgency=medium * New upstream version diff -Nru examl-3.0.20/debian/control examl-3.0.21/debian/control --- examl-3.0.20/debian/control 2018-02-10 18:25:43.000000000 +0000 +++ examl-3.0.21/debian/control 2018-07-02 09:32:28.000000000 +0000 @@ -5,9 +5,9 @@ Priority: optional Build-Depends: debhelper (>= 11~), libopenmpi-dev -Standards-Version: 4.1.3 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/examl.git -Vcs-Git: https://anonscm.debian.org/git/debian-med/examl.git +Standards-Version: 4.1.4 +Vcs-Browser: https://salsa.debian.org/med-team/examl +Vcs-Git: https://salsa.debian.org/med-team/examl.git Homepage: https://github.com/stamatak/ExaML Package: examl diff -Nru examl-3.0.20/debian/tests/run-unit-test examl-3.0.21/debian/tests/run-unit-test --- examl-3.0.20/debian/tests/run-unit-test 2018-02-10 18:25:43.000000000 +0000 +++ examl-3.0.21/debian/tests/run-unit-test 2018-07-02 09:32:28.000000000 +0000 @@ -3,6 +3,8 @@ pkg="examl" +export OMPI_MCA_rmaps_base_oversubscribe=1 + if [ "$ADTTMP" = "" ] ; then ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM diff -Nru examl-3.0.20/debian/upstream/metadata examl-3.0.21/debian/upstream/metadata --- examl-3.0.20/debian/upstream/metadata 2018-02-10 18:25:43.000000000 +0000 +++ examl-3.0.21/debian/upstream/metadata 2018-07-02 09:32:28.000000000 +0000 @@ -10,3 +10,10 @@ PMID: 25819675 URL: https://academic.oup.com/bioinformatics/article/31/15/2577/188794/ExaML-version-3-a-tool-for-phylogenomic-analyses eprint: https://academic.oup.com/bioinformatics/article-pdf/31/15/2577/5030920/btv184.pdf +Registry: + - Name: OMICtools + Entry: OMICS_08024 + - Name: bio.tools + Entry: NA + - Name: SciCrunch + Entry: NA \ No newline at end of file diff -Nru examl-3.0.20/parser/parsePartitions.c examl-3.0.21/parser/parsePartitions.c --- examl-3.0.20/parser/parsePartitions.c 2018-01-26 08:37:26.000000000 +0000 +++ examl-3.0.21/parser/parsePartitions.c 2018-05-29 04:39:54.000000000 +0000 @@ -370,7 +370,15 @@ return p - *lineptr; } - +static void nonContiguousError(analdef *adef) +{ + if(adef->compressPatterns == FALSE) + { + printf("\nError: You are not allowed to use interleaved partitions, that is, assign non-contiguous sites\n"); + printf("to the same partition model, when pattern compression is disabled via the -c flag!\n\n"); + exit(-1); + } +} void parsePartitions(analdef *adef, rawdata *rdta, tree *tr) { @@ -499,6 +507,7 @@ if(*ch == ',') { upper = lower; + nonContiguousError(adef); goto SINGLE_NUMBER; } @@ -542,6 +551,7 @@ if(*ch == ',') { ch++; + nonContiguousError(adef); goto numberPairs; } @@ -556,13 +566,8 @@ exit(-1); } - if(adef->compressPatterns == FALSE) - { - printf("\nError: You are not allowed to use interleaved partitions, that is, assign non-contiguous sites\n"); - printf("to the same partition model, when pattern compression is disabled via the -c flag!\n\n"); - exit(-1); - } - + nonContiguousError(adef); + l = 0; while(isNum(*ch)) { @@ -582,6 +587,7 @@ if(*ch == ',') { ch++; + nonContiguousError(adef); goto numberPairs; } } diff -Nru examl-3.0.20/versionHeader/version.h examl-3.0.21/versionHeader/version.h --- examl-3.0.20/versionHeader/version.h 2018-01-26 08:37:26.000000000 +0000 +++ examl-3.0.21/versionHeader/version.h 2018-05-29 04:39:54.000000000 +0000 @@ -1,4 +1,4 @@ #define programName "ExaML" -#define programVersion "3.0.20" -#define programVersionInt 3020 -#define programDate "January 26 2018" +#define programVersion "3.0.21" +#define programVersionInt 3021 +#define programDate "May 29 2018"