[med-svn] [Git][med-team/ampliconnoise][master] 4 commits: Fix the sequence of function definitions to make sure UpdateMinCacheForRow()...
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Apr 11 09:00:01 BST 2024
Andreas Tille pushed to branch master at Debian Med / ampliconnoise
Commits:
ab76939a by Andreas Tille at 2024-04-11T09:12:37+02:00
Fix the sequence of function definitions to make sure UpdateMinCacheForRow() is known before its first usage
Adjust DEP3 headers and add Forwarded: No (orphaned upstream)
- - - - -
8706a32d by Andreas Tille at 2024-04-11T09:55:33+02:00
Add missing header file
- - - - -
e70f593d by Andreas Tille at 2024-04-11T09:55:54+02:00
routine-update: Standards-Version: 4.7.0
- - - - -
42b9afe3 by Andreas Tille at 2024-04-11T09:57:31+02:00
routine-update: Ready to upload to unstable
- - - - -
10 changed files:
- debian/changelog
- debian/control
- debian/patches/clang-ftbfs.patch
- debian/patches/fix-path-for-data.patch
- debian/patches/fix-segfault-on-non-fasta-input.patch
- + debian/patches/fix_missing_header.patch
- + debian/patches/fix_sequence_of_function_definitions.patch
- debian/patches/hardening.patch
- debian/patches/mayhem.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+ampliconnoise (1.29-11) unstable; urgency=medium
+
+ * Fix the sequence of function definitions to make sure
+ UpdateMinCacheForRow() is known before its first usage
+ Closes: #1066300
+ * Adjust DEP3 headers and add Forwarded: No (orphaned upstream)
+ * Add missing header file
+ * Standards-Version: 4.7.0 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Thu, 11 Apr 2024 09:56:08 +0200
+
ampliconnoise (1.29-10) unstable; urgency=medium
* Fix watchfile to detect new versions on github
=====================================
debian/control
=====================================
@@ -8,7 +8,7 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
libgsl-dev,
libopenmpi-dev
-Standards-Version: 4.6.0
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/ampliconnoise
Vcs-Git: https://salsa.debian.org/med-team/ampliconnoise.git
Homepage: https://github.com/lanzen/ampliconnoise
=====================================
debian/patches/clang-ftbfs.patch
=====================================
@@ -2,6 +2,7 @@ Author: Arthur Marble <arthur at info9.net>
Last-Update: Mon, 24 Feb 2014 19:06:10 -0600
Bug-Debian: http://bugs.debian.org/740029
Description: Fix FTBFS with clang instead of gcc
+Forwarded: No (orphaned upstream)
--- a/FCluster/FCluster.c
+++ b/FCluster/FCluster.c
=====================================
debian/patches/fix-path-for-data.patch
=====================================
@@ -2,12 +2,13 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
Origin: Specific to package
Bug: None
Last-Update: 2011-04-28
-
-The upstream software is built so as to run from the build environment and look for
-data in ../Data. In Debian the binaries belong in /usr/bin and the data belongs
-in /usr/share. With this patch the binaries will run from any directory.
-A better fix would be to allow setting of the Data directory via an environment variable
-or a variable passed to MAKE at build time. This could be contributed back to upstream.
+Forwarded: No (orphaned upstream)
+Description:
+ The upstream software is built so as to run from the build environment and look for
+ data in ../Data. In Debian the binaries belong in /usr/bin and the data belongs
+ in /usr/share. With this patch the binaries will run from any directory.
+ A better fix would be to allow setting of the Data directory via an environment variable
+ or a variable passed to MAKE at build time. This could be contributed back to upstream.
--- a/SeqNoise/SeqNoise.h
+++ b/SeqNoise/SeqNoise.h
=====================================
debian/patches/fix-segfault-on-non-fasta-input.patch
=====================================
@@ -1,7 +1,11 @@
-Some apps segfault when non-FASTA data is inputted, and this is flagged as a security
-concern. I suspect there are still ways to segfault this app, but at least this fixes
-an obvious crash.
-Also fixes https://code.google.com/p/ampliconnoise/issues/detail?id=10
+Description: Some apps segfault when non-FASTA data is inputted, and this is flagged as a security
+ concern. I suspect there are still ways to segfault this app, but at least this fixes
+ an obvious crash.
+ Also fixes https://code.google.com/p/ampliconnoise/issues/detail?id=10
+Forwarded: No (orphaned upstream)
+Author: Tim Booth
+Last-Update: 2013-06-27 17:33:31 +0000
+
--- a/FastaUnique/FastaUnique.c
+++ b/FastaUnique/FastaUnique.c
@@ -39,6 +39,13 @@ void readData(t_Data *ptData, t_Params *
=====================================
debian/patches/fix_missing_header.patch
=====================================
@@ -0,0 +1,53 @@
+Description: Add missing header file
+Bug-Debian: https://bugs.debian.org/1066300
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 11 Apr 2024 09:06:57 +0200
+Forwarded: No (orphaned upstream)
+
+--- a/NDist/NDist.c
++++ b/NDist/NDist.c
+@@ -10,6 +10,7 @@ Output has been verified to be unaffecte
+ #include <string.h>
+ #include <float.h>
+ #include <assert.h>
++#include <ctype.h>
+ #include <math.h>
+ #include <mpi.h>
+
+--- a/SeqDist/SeqDist.c
++++ b/SeqDist/SeqDist.c
+@@ -10,6 +10,7 @@
+ #include <string.h>
+ #include <float.h>
+ #include <assert.h>
++#include <ctype.h>
+ #include <math.h>
+ #include <mpi.h>
+
+--- a/SeqNoise/SeqNoise.c
++++ b/SeqNoise/SeqNoise.c
+@@ -1,3 +1,4 @@
++#include <ctype.h>
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
+--- a/Perseus/Perseus.c
++++ b/Perseus/Perseus.c
+@@ -8,6 +8,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
++#include <ctype.h>
+ #include <float.h>
+ #include <assert.h>
+ #include <math.h>
+--- a/PerseusD/PerseusD.c
++++ b/PerseusD/PerseusD.c
+@@ -8,6 +8,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
++#include <ctype.h>
+ #include <float.h>
+ #include <assert.h>
+ #include <math.h>
=====================================
debian/patches/fix_sequence_of_function_definitions.patch
=====================================
@@ -0,0 +1,51 @@
+Description: Fix the sequence of function definitions to make sure
+ UpdateMinCacheForRow() is known before its first usage
+Bug-Debian: https://bugs.debian.org/1066300
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 11 Apr 2024 09:06:57 +0200
+Forwarded: No (orphaned upstream)
+
+--- a/FCluster/FCluster.c
++++ b/FCluster/FCluster.c
+@@ -219,20 +219,6 @@ void UpdateMinCacheWithNewValue(struct t
+ }
+ };
+
+-// Recalculate cached data for all rows
+-UpdateMinCacheForMarkedRows(struct t_Min* asMin,float** aafDistMatrix,int nN)
+-{
+- int i;
+- for (i = 1; i < nN; i++)
+- {
+- if( asMin[i].reCalc == 1)
+- {
+- UpdateMinCacheForRow(asMin,i,aafDistMatrix);
+- }
+- asMin[i].reCalc = 0;
+- }
+-};
+-
+ // Update the cached data for a row
+ UpdateMinCacheForRow(struct t_Min* asMin,int i,float** aafDistMatrix)
+ {
+@@ -254,6 +240,20 @@ UpdateMinCacheForRow(struct t_Min* asMin
+ asMin[i].indexOfMinNode = nj;
+ };
+
++// Recalculate cached data for all rows
++UpdateMinCacheForMarkedRows(struct t_Min* asMin,float** aafDistMatrix,int nN)
++{
++ int i;
++ for (i = 1; i < nN; i++)
++ {
++ if( asMin[i].reCalc == 1)
++ {
++ UpdateMinCacheForRow(asMin,i,aafDistMatrix);
++ }
++ asMin[i].reCalc = 0;
++ }
++};
++
+ // Initialise min cache per group
+ void InitMinCacheData(int nN, struct t_Min* asMin, float** aafDistMatrix)
+ {
=====================================
debian/patches/hardening.patch
=====================================
@@ -1,6 +1,7 @@
Author: Andreas Tille <tille at debian.org>
LastChanged: Tue, 30 Jul 2013 09:49:02 +0200
Description: Propagate hardening options
+Forwarded: No (orphaned upstream)
--- a/FCluster/makefile
+++ b/FCluster/makefile
=====================================
debian/patches/mayhem.patch
=====================================
@@ -4,6 +4,7 @@ Bug-Debian: https://bugs.debian.org/715593
https://bugs.debian.org/715594
Description: Fix Mayhem issues by
making reading fasta files more robust
+Forwarded: No (orphaned upstream)
--- a/Perseus/Perseus.c
+++ b/Perseus/Perseus.c
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,5 @@ fix-segfault-on-non-fasta-input.patch
hardening.patch
clang-ftbfs.patch
mayhem.patch
+fix_sequence_of_function_definitions.patch
+fix_missing_header.patch
View it on GitLab: https://salsa.debian.org/med-team/ampliconnoise/-/compare/4627579ab6a95bca426a7d74e91a0520c1748ba1...42b9afe37fcabc749e9a6d07b9e42cbb611ee0b7
--
View it on GitLab: https://salsa.debian.org/med-team/ampliconnoise/-/compare/4627579ab6a95bca426a7d74e91a0520c1748ba1...42b9afe37fcabc749e9a6d07b9e42cbb611ee0b7
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