[med-svn] [Git][med-team/kalign][master] 3 commits: Fix gcc-10 FTBFS

Nilesh Patra gitlab at salsa.debian.org
Tue Aug 4 22:48:47 BST 2020



Nilesh Patra pushed to branch master at Debian Med / kalign


Commits:
213cf9b5 by Nilesh Patra at 2020-08-05T03:08:19+05:30
Fix gcc-10 FTBFS

- - - - -
9ba28095 by Nilesh Patra at 2020-08-04T21:42:14+00:00
Add manpages

- - - - -
4cf5e8e4 by Nilesh Patra at 2020-08-04T21:43:14+00:00
compat version: 13, run wrap-and-sort

- - - - -


9 changed files:

- debian/control
- + debian/createmanpages
- debian/docs
- + debian/kalign.1
- debian/kalign.examples
- + debian/manpages
- + debian/patches/fix-gcc10-build.patch
- debian/patches/series
- + debian/timescorealn.1


Changes:

=====================================
debian/control
=====================================
@@ -1,11 +1,9 @@
 Source: kalign
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
-           Andreas Tille <tille at debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>, Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
-               libsimde-dev
+Build-Depends: debhelper-compat (= 13), libsimde-dev
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/kalign
 Vcs-Git: https://salsa.debian.org/med-team/kalign.git
@@ -14,11 +12,9 @@ Rules-Requires-Root: no
 
 Package: kalign
 Architecture: any
-Built-Using: ${simde:Built-Using} 
-Depends: ${shlibs:Depends},
-         ${misc:Depends}
-Enhances: t-coffee,
-          bioperl-run
+Built-Using: ${simde:Built-Using}
+Depends: ${misc:Depends}, ${shlibs:Depends}
+Enhances: bioperl-run, t-coffee
 Description: Global and progressive multiple sequence alignment
  Kalign is a command line tool to perform multiple alignment of
  biological sequences. It employs the Muth-Manber string-matching


=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,39 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=kalign
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=timescorealn
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+


=====================================
debian/docs
=====================================
@@ -1,3 +1,3 @@
 README.md
-debian/tests/run-unit-test
 debian/README.test
+debian/tests/run-unit-test


=====================================
debian/kalign.1
=====================================
@@ -0,0 +1,44 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
+.TH KALIGN "1" "August 2020" "kalign 3.2.3" "User Commands"
+.SH NAME
+kalign \- Global and progressive multiple sequence alignment
+.SH SYNOPSIS
+.B kalign-avx2
+\fI\,-i <seq file> -o <out aln>\/\fR
+.SH DESCRIPTION
+Kalign (3.2.3)
+.SH OPTIONS
+.TP
+\fB\-\-format\fR
+: Output format. [Fasta]
+.TP
+\fB\-\-reformat\fR
+: Reformat existing alignment. [NA]
+.TP
+\fB\-\-version\fR (\fB\-V\fR/\-v)
+: Prints version. [NA]
+.SH EXAMPLES
+Passing sequences via stdin:
+.IP
+cat input.fa | kalign \-f fasta > out.afa
+.PP
+Combining multiple input files:
+.IP
+kalign seqsA.fa seqsB.fa seqsC.fa \-f fasta > combined.afa
+.SH COPYRIGHT
+Copyright \(co 2006,2019,2020 Timo Lassmann
+.PP
+This program comes with ABSOLUTELY NO WARRANTY; for details type:
+`kalign \fB\-showw\fR'.
+.br
+This is free software, and you are welcome to redistribute it
+under certain conditions; consult the COPYING file for details.
+.SS "Please cite:"
+.IP
+Lassmann, Timo.
+"Kalign 3: multiple sequence alignment of large data sets."
+Bioinformatics (2019)
+https://doi.org/10.1093/bioinformatics/btz795
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.


=====================================
debian/kalign.examples
=====================================
@@ -1,2 +1,2 @@
 debian/tests/data/*
-dev/data/B*
\ No newline at end of file
+dev/data/B*


=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1


=====================================
debian/patches/fix-gcc10-build.patch
=====================================
@@ -0,0 +1,14 @@
+Author: Nilesh Patra <npatra974 at gmail.com>
+Description: Add extren to fix gcc-10 build.
+Last-Changed: August 5, 2020
+--- a/src/tldevel.h
++++ b/src/tldevel.h
+@@ -564,7 +564,7 @@
+ 
+ /* extern char build_config[]; */
+ 
+-float logsum_lookup[LOGSUM_SIZE];
++extern float logsum_lookup[LOGSUM_SIZE];
+ 
+ 
+ extern int print_program_header(char * const argv[],const char* description);


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 simde
 no-native-build
 hardening
+fix-gcc10-build.patch


=====================================
debian/timescorealn.1
=====================================
@@ -0,0 +1,38 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
+.TH TIMESCOREALN "1" "August 2020" "timescorealn 3.2.3" "User Commands"
+.SH NAME
+timescorealn \- Global and progressive multiple sequence alignment
+.SH SYNOPSIS
+.B timescorealn-avx2
+[\fI\,-options\/\fR]   \fI\,-test <test sequences> -ref <reference alignment> -program <kalign|clustalo|muscle> -o <outfile>\/\fR
+.SH DESCRIPTION
+[2020\-08\-04 21:41:11] :   ERROR : No test file
+.IP
+(time_and_score_aln.c line 111)
+.PP
+NOTE: the program appends results to the output file.
+.SH OPTIONS
+.TP
+\fB\-\-scratch\fR
+: Scratch directory. [NA]
+.PP
+Usage: timescorealn\-avx2 [\-options]   \fB\-test\fR <test sequences> \fB\-ref\fR <reference alignment> \fB\-program\fR <kalign|clustalo|muscle> \fB\-o\fR <outfile>
+.PP
+NOTE: the program appends results to the output file.
+.TP
+\fB\-\-scratch\fR
+: Scratch directory. [NA]
+.PP
+[2020\-08\-04 21:41:11] : WARNING : Something went wrong. Use this program like this:
+.IP
+(time_and_score_aln.c line 154)
+.PP
+Usage: timescorealn\-avx2 [\-options]   \fB\-test\fR <test sequences> \fB\-ref\fR <reference alignment> \fB\-program\fR <kalign|clustalo|muscle> \fB\-o\fR <outfile>
+.PP
+NOTE: the program appends results to the output file.
+.TP
+\fB\-\-scratch\fR
+: Scratch directory. [NA]
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.



View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/85e6175345788be5e6b6598af135888dd082814d...4cf5e8e4b15e39adaf373d9a5b42e2582ca1a67b

-- 
View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/85e6175345788be5e6b6598af135888dd082814d...4cf5e8e4b15e39adaf373d9a5b42e2582ca1a67b
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