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 <[email protected]> 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 <[email protected]>, Charles Plessy <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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