[med-svn] [Git][med-team/tree-puzzle][master] 6 commits: debhelper 11
Andreas Tille
gitlab at salsa.debian.org
Tue Oct 16 10:10:58 BST 2018
Andreas Tille pushed to branch master at Debian Med / tree-puzzle
Commits:
79f003fb by Andreas Tille at 2018-10-16T08:51:06Z
debhelper 11
- - - - -
77f8022f by Andreas Tille at 2018-10-16T08:51:45Z
Point Vcs fields to salsa.debian.org
- - - - -
16e330a3 by Andreas Tille at 2018-10-16T08:51:45Z
Standards-Version: 4.2.1
- - - - -
14434262 by Andreas Tille at 2018-10-16T08:54:27Z
Fix doc location (as per debhelper 11)
- - - - -
c2724d78 by Andreas Tille at 2018-10-16T09:04:16Z
Fix some spelling issues
- - - - -
199cedb4 by Andreas Tille at 2018-10-16T09:08:20Z
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/patches/series
- + debian/patches/spelling.patch
- debian/tree-puzzle-doc.doc-base
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+tree-puzzle (5.2-11) unstable; urgency=medium
+
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.2.1
+ * Fix some spelling issues
+
+ -- Andreas Tille <tille at debian.org> Tue, 16 Oct 2018 11:06:43 +0200
+
tree-puzzle (5.2-10) unstable; urgency=medium
* Do not try parallel builds
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
@@ -4,12 +4,12 @@ Uploaders: Andreas Tille <tille at debian.org>,
Charles Plessy <plessy at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
libopenmpi-dev,
libsprng2-dev
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/tree-puzzle.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/tree-puzzle.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/tree-puzzle
+Vcs-Git: https://salsa.debian.org/med-team/tree-puzzle.git
Homepage: http://www.tree-puzzle.de
Package: tree-puzzle
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
20_no_copy_of_sprng.patch
tests-need-bash.patch
+spelling.patch
=====================================
debian/patches/spelling.patch
=====================================
@@ -0,0 +1,106 @@
+Description: Fix some spelling issues
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 16 Oct 2018 10:51:06 +0200
+
+--- a/src/ml2.c
++++ b/src/ml2.c
+@@ -417,7 +417,7 @@ Node *internalnode(Tree *tr, char **chpp
+
+ if (!strcmp(ident, idcomp)) {
+ if (usedtaxa[i]) {
+- fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurence of sequence '");
++ fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurrence of sequence '");
+ fprintf(STDOUT, "%s' in tree)\n\n\n", ident);
+ # if PARALLEL
+ PP_Finalize();
+--- a/src/puzzle1.c
++++ b/src/puzzle1.c
+@@ -1967,7 +1967,7 @@ void initps(FILE *ofp)
+ /* PS definition of a centered print */
+ fprintf(ofp, "/centershow {\n");
+ fprintf(ofp, " dup stringwidth pop %% get length of string\n");
+- fprintf(ofp, " -2 div %% devide length by -2\n");
++ fprintf(ofp, " -2 div %% divide length by -2\n");
+ fprintf(ofp, " 0 rmoveto %% move half width to left\n");
+ fprintf(ofp, " show\n");
+ fprintf(ofp, "} def\n");
+@@ -3538,7 +3538,7 @@ void writeoutputfile(FILE *ofp, int part
+ i+1, Rates[i], (1.0-fracinv)/(double) numcats);
+ }
+ if (rhetmode == GAMMARATE || rhetmode == MIXEDRATE) {
+- fprintf(ofp, "\nCategories 1-%d approximate a continous ", numcats);
++ fprintf(ofp, "\nCategories 1-%d approximate a continuous ", numcats);
+ fprintf(ofp, "Gamma-distribution with expectation 1\n");
+ fprintf(ofp, "and variance ");
+ if (Geta == 1.0) fprintf(ofp, "infinity");
+@@ -5231,21 +5231,21 @@ void printusagehhh(char *fname)
+ #ifdef HHH
+ /* |<--- 80 characters --->| */
+ fprintf(stderr, " not yet implemented in this version:\n");
+- fprintf(stderr, " -wslb - write site lhs to PREFIX.sitelhb (binary) [not yet]\n");
+- fprintf(stderr, " -wsrb - write site rates to PREFIX.siterateb (binary) [not yet]\n");
+- fprintf(stderr, " -wparam - write params to PREFIX.param [not yet]\n");
+- fprintf(stderr, " -qsupport - prints quartet support for incorporated splits [not yet]\n");
+- fprintf(stderr, " -consth=<#> - consensus threshold, e.g. 50=M_50 consensus [not yet]\n");
+- fprintf(stderr, " -wqnex - write quartets in nexus format [not yet]\n");
+- fprintf(stderr, " -wsnex - write splits in nexus format [not yet]\n");
+- fprintf(stderr, " -wsth=<#> - split threshold, e.g. 50 - splits of the M_50 [not yet]\n");
+- fprintf(stderr, " -wsnex=<#> - write splits with > <#>%% occurence - nexus format[not yet]\n");
+- fprintf(stderr, " -witnex - write intermediate trees in nexus format [not yet]\n");
+- fprintf(stderr, " -quartml - use ML values to evaluate quartets [not yet]\n");
+- fprintf(stderr, " -quartmlapprox - use approximate ML values to evaluate quartets [default]\n");
+- fprintf(stderr, " -quartnj - use NJ to evaluate quartets [not yet]\n");
+- fprintf(stderr, " -quartme - use ME to evaluate quartets [not yet]\n");
+- fprintf(stderr, " -quartpars - use parsimony to evaluate quartets [not yet]\n");
++ fprintf(stderr, " -wslb - write site lhs to PREFIX.sitelhb (binary) [not yet]\n");
++ fprintf(stderr, " -wsrb - write site rates to PREFIX.siterateb (binary) [not yet]\n");
++ fprintf(stderr, " -wparam - write params to PREFIX.param [not yet]\n");
++ fprintf(stderr, " -qsupport - prints quartet support for incorporated splits [not yet]\n");
++ fprintf(stderr, " -consth=<#> - consensus threshold, e.g. 50=M_50 consensus [not yet]\n");
++ fprintf(stderr, " -wqnex - write quartets in nexus format [not yet]\n");
++ fprintf(stderr, " -wsnex - write splits in nexus format [not yet]\n");
++ fprintf(stderr, " -wsth=<#> - split threshold, e.g. 50 - splits of the M_50 [not yet]\n");
++ fprintf(stderr, " -wsnex=<#> - write splits with > <#>%% occurrence - nexus format[not yet]\n");
++ fprintf(stderr, " -witnex - write intermediate trees in nexus format [not yet]\n");
++ fprintf(stderr, " -quartml - use ML values to evaluate quartets [not yet]\n");
++ fprintf(stderr, " -quartmlapprox - use approximate ML values to evaluate quartets [default]\n");
++ fprintf(stderr, " -quartnj - use NJ to evaluate quartets [not yet]\n");
++ fprintf(stderr, " -quartme - use ME to evaluate quartets [not yet]\n");
++ fprintf(stderr, " -quartpars - use parsimony to evaluate quartets [not yet]\n");
+ fprintf(stderr, "\n");
+ #endif /* HHH */
+
+--- a/src/puzzle2.c
++++ b/src/puzzle2.c
+@@ -68,7 +68,7 @@ void readid(FILE *infp, int t)
+ if (Identif[t][j] != Identif[i][j])
+ flag = FALSE;
+ if (flag) {
+- fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurence of sequence name '");
++ fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurrence of sequence name '");
+ fputid(STDOUT, t);
+ fprintf(STDOUT, "')\n\n\n");
+ # if PARALLEL
+--- a/src/treesort.c
++++ b/src/treesort.c
+@@ -601,7 +601,7 @@ treelistitemtype *addtree2list(char
+
+ /**********/
+
+-/* resort list of trees by number of occurences for output */
++/* resort list of trees by number of occurrences for output */
+ void sortbynum(treelistitemtype *list, treelistitemtype **sortlist)
+ {
+ treelistitemtype *tmpptr = NULL;
+@@ -721,9 +721,9 @@ void fprintfsortedpstrees(FILE *output,
+ if (num == 1){
+ fprintf (output, "\n");
+ fprintf (output, "The following tree(s) occured in more than %.2f%% of the %d puzzling steps.\n", cutoff, itemsum);
+- fprintf (output, "The trees are orderd descending by the number of occurences.\n");
++ fprintf (output, "The trees are orderd descending by the number of occurrences.\n");
+ fprintf (output, "\n");
+- fprintf (output, "\n occurences ID Phylip tree\n");
++ fprintf (output, "\n occurrences ID Phylip tree\n");
+ }
+ fprintf (output, "%2d. %5d %6.2f%% %5d ", num++, (*tmpptr).count, percent, (*tmpptr).id);
+ }
=====================================
debian/tree-puzzle-doc.doc-base
=====================================
@@ -6,4 +6,4 @@ Abstract: Maximum likelihood analysis for nucleotide, amino acid, and two-state
Section: Science/Biology
Format: pdf
-Files: /usr/share/doc/tree-puzzle-doc/tree-puzzle.pdf
+Files: /usr/share/doc/tree-puzzle/tree-puzzle.pdf
View it on GitLab: https://salsa.debian.org/med-team/tree-puzzle/compare/dbf2df0a041a621f66d5d60b6c21bbc0dd87d24d...199cedb4c92e5bf05f78f5aa76b5b8d4642706e2
--
View it on GitLab: https://salsa.debian.org/med-team/tree-puzzle/compare/dbf2df0a041a621f66d5d60b6c21bbc0dd87d24d...199cedb4c92e5bf05f78f5aa76b5b8d4642706e2
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