Andreas Tille pushed to branch master at Debian Med / lighter
Commits: 57a7a7b5 by Andreas Tille at 2020-07-21T14:47:00+02:00 Fix FTBFS - - - - - bc98dbf2 by Andreas Tille at 2020-07-21T14:47:22+02:00 Fix typo - - - - - 796edf35 by Andreas Tille at 2020-07-21T14:50:01+02:00 Fix spelling - - - - - b8c44ba2 by Andreas Tille at 2020-07-21T14:50:48+02:00 Upload to unstable - - - - - 6 changed files: - debian/changelog - debian/copyright - debian/lighter.1 - + debian/patches/ftbfs.patch - debian/patches/series - + debian/patches/spelling.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,14 @@ +lighter (1.1.2-3) unstable; urgency=medium + + [ Helmut Grohne ] + * Fix FTBFS + Closes: #965228 + + [ Andreas Tille ] + * Fix spelling + + -- Andreas Tille <[email protected]> Tue, 21 Jul 2020 14:50:09 +0200 + lighter (1.1.2-2) unstable; urgency=medium * Rules-Requires-Root: no (routine-update) ===================================== debian/copyright ===================================== @@ -577,7 +577,7 @@ License: MPL-1.1 shall survive. . 8.2. If You initiate litigation by asserting a patent infringement - claim (excluding declatory judgment actions) against Initial Developer + claim (excluding declaratory judgment actions) against Initial Developer or a Contributor (the Initial Developer or Contributor against whom You file such action is referred to as "Participant") alleging that: . ===================================== debian/lighter.1 ===================================== @@ -18,7 +18,7 @@ comparable accuracy. .SH OPTIONS: .SS Required parameters: .TP -\fB\-r\fR seq_file: seq_file is the path to the sequence file. Can use multiple \fB\-r\fR to specifiy multiple sequence files +\fB\-r\fR seq_file: seq_file is the path to the sequence file. Can use multiple \fB\-r\fR to specify multiple sequence files The file can be fasta and fastq, and can be gzip'ed with extension *.gz. When the input file is *.gz, the corresponding output file will also be gzip'ed. .TP ===================================== debian/patches/ftbfs.patch ===================================== @@ -0,0 +1,46 @@ +Date: Fri, 17 Jul 2020 22:36:54 +0200 +From: Helmut Grohne <[email protected]> +Bug-Debian: https://bugs.debian.org/965228 +Description: lighter fails to build from source, because: + . + main.cpp:26:25: error: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ [-Wnarrowing] + . + What happens here is that nucToNum is assigned -1, but it is typed array + of char, which happens to be unsigned (on some architectures). It really + wants a small signed integer type here (representing numbers between -1 + and 3). A very simple fix is using signed char (which isn't architecture + dependent). + +--- lighter-1.1.2.orig/main.cpp ++++ lighter-1.1.2/main.cpp +@@ -20,7 +20,7 @@ + + char LIGHTER_VERSION[] = "Lighter v1.1.2" ; + +-char nucToNum[26] = { 0, -1, 1, -1, -1, -1, 2, ++signed char nucToNum[26] = { 0, -1, 1, -1, -1, -1, 2, + -1, -1, -1, -1, -1, -1, -1, + -1, -1, -1, -1, -1, 3, + -1, -1, -1, -1, -1, -1 } ; +--- lighter-1.1.2.orig/KmerCode.h ++++ lighter-1.1.2/KmerCode.h +@@ -4,7 +4,7 @@ + #include <stdio.h> + #include "utils.h" + +-extern char nucToNum[26] ; ++extern signed char nucToNum[26] ; + extern char numToNuc[26] ; + + const int K_BLOCK_NUM = ( MAX_KMER_LENGTH - 1 ) / ( sizeof( uint64_t ) * 4 ) + 1 ; +--- lighter-1.1.2.orig/ErrorCorrection.cpp ++++ lighter-1.1.2/ErrorCorrection.cpp +@@ -3,7 +3,7 @@ + + //#define DEBUG + +-extern char nucToNum[26] ; ++extern signed char nucToNum[26] ; + extern char numToNuc[26] ; + extern int MAX_CORRECTION ; + extern bool ALLOW_TRIMMING ; ===================================== debian/patches/series ===================================== @@ -1 +1,3 @@ hardening.patch +ftbfs.patch +spelling.patch ===================================== debian/patches/spelling.patch ===================================== @@ -0,0 +1,26 @@ +Description: Fix spelling +Author: Andreas Tille <[email protected]> +Last-Update: Tue, 21 Jul 2020 13:35:04 +0200 + +--- a/README.md ++++ b/README.md +@@ -27,7 +27,7 @@ Lighter is small and portable, with [pth + Usage: ./lighter [OPTIONS] + OPTIONS: + Required parameters: +- -r seq_file: seq_file is the path to the sequence file. Can use multiple -r to specifiy multiple sequence files ++ -r seq_file: seq_file is the path to the sequence file. Can use multiple -r to specify multiple sequence files + The file can be fasta and fastq, and can be gzip'ed with extension *.gz. + When the input file is *.gz, the corresponding output file will also be gzip'ed. + -k kmer_length genome_size alpha +--- a/main.cpp ++++ b/main.cpp +@@ -58,7 +58,7 @@ void PrintHelp() + printf( "Usage: ./lighter [OPTIONS]\n" + "OPTIONS:\n" + "Required parameters:\n" +- "\t-r seq_file: seq_file is the path to the sequence file. Can use multiple -r to specifiy multiple sequence files\n" ++ "\t-r seq_file: seq_file is the path to the sequence file. Can use multiple -r to specify multiple sequence files\n" + "\t The file can be fasta and fastq, and can be gzip\'ed with extension *.gz.\n" + "\t When the input file is *.gz, the corresponding output file will also be gzip\'ed.\n" + "\t-k kmer_length genome_size alpha: (see README for information on setting alpha)\n" View it on GitLab: https://salsa.debian.org/med-team/lighter/-/compare/806500417d3c3d85be74897c2f3400371f845930...b8c44ba2e4386fbfcf5e4cedb4f116dee1d3ff80 -- View it on GitLab: https://salsa.debian.org/med-team/lighter/-/compare/806500417d3c3d85be74897c2f3400371f845930...b8c44ba2e4386fbfcf5e4cedb4f116dee1d3ff80 You're receiving this email because of your account on salsa.debian.org.
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