Andreas Tille pushed to branch master at Debian Med / kmer
Commits: 7d897abd by Andreas Tille at 2018-08-05T03:47:52Z debhelper 11 - - - - - 9684aa8a by Andreas Tille at 2018-08-05T03:52:18Z Point Vcs fields to salsa.debian.org - - - - - b182bacb by Andreas Tille at 2018-08-05T03:52:19Z Standards-Version: 4.1.5 - - - - - 65485582 by Andreas Tille at 2018-08-05T05:20:32Z Fix Perl interpreter path - - - - - 2e9b7337 by Andreas Tille at 2018-08-05T09:01:22Z Fix spelling - - - - - 4129d4c8 by Andreas Tille at 2018-08-05T09:22:03Z More paths to fix - - - - - 3349d1f8 by Andreas Tille at 2018-08-05T09:34:45Z More spelling issues - - - - - 6 changed files: - debian/changelog - debian/compat - debian/control - debian/patches/series - + debian/patches/spelling.patch - debian/rules Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,14 @@ +kmer (0~20150903+r2013-4) UNRELEASED; urgency=medium + + * Team upload. + * debhelper 11 + * Point Vcs fields to salsa.debian.org + * Standards-Version: 4.1.5 + * Fix Perl interpreter path + * Fix spelling + + -- Andreas Tille <[email protected]> Sun, 05 Aug 2018 05:47:52 +0200 + kmer (0~20150903+r2013-3) unstable; urgency=medium * Rename source package to match upstream name and primary binary package ===================================== debian/compat ===================================== --- a/debian/compat +++ b/debian/compat @@ -1 +1 @@ -10 +11 ===================================== debian/control ===================================== --- a/debian/control +++ b/debian/control @@ -3,15 +3,14 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Afif Elghraoui <[email protected]> Section: science Priority: optional -Build-Depends: - debhelper (>= 10), - dh-exec, +Build-Depends: debhelper (>= 11~), + dh-exec, # For ATAC - dh-python, - python-all-dev, -Standards-Version: 3.9.8 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/kmer.git -Vcs-Git: https://anonscm.debian.org/git/debian-med/kmer.git + dh-python, + python-all-dev +Standards-Version: 4.1.5 +Vcs-Browser: https://salsa.debian.org/med-team/kmer +Vcs-Git: https://salsa.debian.org/med-team/kmer.git Homepage: http://kmer.sourceforge.net Package: kmer @@ -20,7 +19,7 @@ Depends: ${misc:Depends}, meryl, leaff, sim4db, - atac, + atac Description: suite of tools for DNA sequence analysis The kmer package is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); @@ -117,15 +116,14 @@ Description: batch spliced alignment of cDNA sequences to a target genome Package: atac Architecture: any -Depends: - ${shlibs:Depends}, - ${misc:Depends}, - ${python:Depends}, - ${perl:Depends}, - libfile-which-perl, - leaff, - meryl, - gnuplot, +Depends: ${shlibs:Depends}, + ${misc:Depends}, + ${python:Depends}, + ${perl:Depends}, + libfile-which-perl, + leaff, + meryl, + gnuplot Description: genome assembly-to-assembly comparison atac computes a one-to-one pairwise alignment of large DNA sequences. It first finds the unique k-mers in each sequence, chains them to larger blocks, and ===================================== debian/patches/series ===================================== --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ allow-freebsd-build.patch atac-helper-script-paths.patch atac-readme.patch +spelling.patch ===================================== debian/patches/spelling.patch ===================================== --- /dev/null +++ b/debian/patches/spelling.patch @@ -0,0 +1,48 @@ +Description: Fix spelling +Author: Andreas Tille <[email protected]> +Last-Update: Sun, 05 Aug 2018 05:47:52 +0200 + +--- a/libutil/bitPackedFile.C ++++ b/libutil/bitPackedFile.C +@@ -157,7 +157,7 @@ bitPackedFile::bitPackedFile(char const + } else if ((at == uint64Swap(ac)) && (bt == uint64Swap(bc))) { + endianess_flipped = true; + } else { +- fprintf(stderr, "bitPackedFile::bitPackedFile()-- '%s' looked like a bitPackedFile, but failed the endianess check, not opened.\n", _name); ++ fprintf(stderr, "bitPackedFile::bitPackedFile()-- '%s' looked like a bitPackedFile, but failed the endianness check, not opened.\n", _name); + exit(1); + } + } else { +--- a/libkmer/driver-existDB.C ++++ b/libkmer/driver-existDB.C +@@ -178,7 +178,7 @@ const char *usage = + "\n" + " -testexhaustive some.fasta some.meryl\n" + " -- Build an existDB table from some.fasta, check _EVERY_ mer\n" +-" for existance. Complain if a mer exists in the table but\n" ++" for existence. Complain if a mer exists in the table but\n" + " not in the meryl database. Assumes 'some.meryl' is the\n" + " mercount of some.fasta.\n" + "\n"; +--- a/libutil/palloc.c ++++ b/libutil/palloc.c +@@ -133,7 +133,7 @@ palloc2(size_t size, void *handle) { + root->_cn = root->_nl; + + if (root->_dbg > 0) +- fprintf(stderr, "palloc()-- Inital block of "sizetFMT" bytes at %p.\n", root->_bs, root->_cn); ++ fprintf(stderr, "palloc()-- Initial block of "sizetFMT" bytes at %p.\n", root->_bs, root->_cn); + + root->_cn->_cp = 0; + root->_cn->_dt = (char *)really_allocate(root->_bs); +--- a/sim4dbutils/parseSNP.C ++++ b/sim4dbutils/parseSNP.C +@@ -491,7 +491,7 @@ main(int argc, char **argv) { + fprintf(stderr, " default, and if posTag is not found.\n"); + fprintf(stderr, "\n"); + fprintf(stderr, " TAGS: The number immediately after the first\n"); +- fprintf(stderr, " occurance of the tag will be used.\n"); ++ fprintf(stderr, " occurrence of the tag will be used.\n"); + fprintf(stderr, "\n"); + fprintf(stderr, " -o offset An additive offset to the SNP position.\n"); + fprintf(stderr, " The default is 0.\n"); ===================================== debian/rules ===================================== --- a/debian/rules +++ b/debian/rules @@ -34,5 +34,11 @@ override_dh_auto_clean: $(MAKE) real-clean rm -rf installdir +override_dh_install: + dh_install + for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` `grep -l '#!/usr/bin/env \+perl' debian/*/usr/lib/atac/bin/*` ; do \ + sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' $${perlscript} ; \ + done + get-orig-source: DEB_VERSION_UPSTREAM=$(DEB_VERSION_UPSTREAM) debian/get-orig-source View it on GitLab: https://salsa.debian.org/med-team/kmer/compare/de16f7df09c5ba18ca28af09269c8ef3bc61968e...3349d1f8dd802f85f27e588919f2274cf115098d -- View it on GitLab: https://salsa.debian.org/med-team/kmer/compare/de16f7df09c5ba18ca28af09269c8ef3bc61968e...3349d1f8dd802f85f27e588919f2274cf115098d You're receiving this email because of your account on salsa.debian.org.
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