[med-svn] [Git][med-team/lighter][master] 4 commits: Fix FTBFS
Andreas Tille
gitlab at salsa.debian.org
Tue Jul 21 13:52:22 BST 2020
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 <tille at debian.org> 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 <helmut at subdivi.de>
+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 <tille at debian.org>
+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
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