[med-svn] [Git][med-team/soapdenovo2][master] 3 commits: gcc-14.patch: new: fix a lot of issues caught by gcc 14.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Aug 11 17:17:47 BST 2024
Étienne Mollier pushed to branch master at Debian Med / soapdenovo2
Commits:
cb816ffb by Étienne Mollier at 2024-08-11T18:11:44+02:00
gcc-14.patch: new: fix a lot of issues caught by gcc 14.
Closes: #1075524
- - - - -
2adba46b by Étienne Mollier at 2024-08-11T18:12:30+02:00
d/control: declare compliance to standards version 4.7.0.
- - - - -
f432d475 by Étienne Mollier at 2024-08-11T18:17:04+02:00
Ready for upload to unstable.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/gcc-14.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+soapdenovo2 (242+dfsg-4) unstable; urgency=medium
+
+ * Team upload.
+ * gcc-14.patch: new: fix a lot of issues caught by gcc 14. (Closes: #1075524)
+ * d/control: declare compliance to standards version 4.7.0.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 11 Aug 2024 18:16:19 +0200
+
soapdenovo2 (242+dfsg-3) unstable; urgency=medium
* Fix watch file
=====================================
debian/control
=====================================
@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),
libbam-dev,
libaio-dev,
rename
-Standards-Version: 4.6.1
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/soapdenovo2
Vcs-Git: https://salsa.debian.org/med-team/soapdenovo2.git
Homepage: http://soap.genomics.org.cn/soapdenovo.html
=====================================
debian/patches/gcc-14.patch
=====================================
@@ -0,0 +1,200 @@
+Description: fix a lot of issues identified by gcc 14.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075524
+Forwarded: no
+Last-Update: 2024-08-11
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- soapdenovo2.orig/standardPregraph/contig.c
++++ soapdenovo2/standardPregraph/contig.c
+@@ -35,6 +35,13 @@
+ static int M = 1; //merge bubble level
+ static int maxk = 0; //max kmer of multikmer
+
++// These are external functions from iterate.c.
++extern void swapedge ();
++extern void sortedge ();
++extern void freshArc ();
++extern void Iterate ( char *, char *, int, int );
++extern void freshpreGraphBasic ( boolean, int, char * );
++
+ /*************************************************
+ Function:
+ call_heavygraph
+--- soapdenovo2.orig/standardPregraph/cutTipPreGraph.c
++++ soapdenovo2/standardPregraph/cutTipPreGraph.c
+@@ -33,6 +33,9 @@
+ static void Mark1in1outNode ();
+ static void thread_mark ( KmerSet *set, unsigned char thrdID );
+
++// These external functions from from kmer.c.
++extern void PrintKmer ( FILE *, Kmer );
++
+ /*
+ static void printKmer(Kmer kmer)
+ {
+--- soapdenovo2.orig/standardPregraph/hashFunction.c
++++ soapdenovo2/standardPregraph/hashFunction.c
+@@ -102,6 +102,7 @@
+ return ecx;
+ }
+
++#if defined __SSE4_2__
+ static inline int crc32cHardware64 ( uint32_t crc, const char *data, size_t length )
+ {
+ size_t i;
+@@ -114,6 +115,7 @@
+
+ return ( int ) crc;
+ }
++#endif
+
+ static inline int crc32cTable ( uint32_t crc, const char *buf, size_t len )
+ {
+--- soapdenovo2.orig/standardPregraph/loadPreGraph.c
++++ soapdenovo2/standardPregraph/loadPreGraph.c
+@@ -29,6 +29,9 @@
+
+ static void loadPreArcs ( char *graphfile );
+
++// This external function comes from kmer.c.
++extern void PrintKmer ( FILE *, Kmer );
++
+ int cmp_vertex ( const void *a, const void *b )
+ {
+ VERTEX *A, *B;
+--- soapdenovo2.orig/standardPregraph/localAsm.c
++++ soapdenovo2/standardPregraph/localAsm.c
+@@ -36,6 +36,9 @@
+ kmer_t **soFarNode, short *multiOccu1, short *multiOccu2, int *routeLens,
+ char **foundRoutes, char *soFarSeq, long long *soFarLinks, double *avgLinks );
+
++// This external function comes from kmer.c.
++extern void PrintKmer ( FILE *, Kmer );
++
+ #ifdef MER127
+ static Kmer prevKmerLocal ( Kmer next, char ch, int overlap )
+ {
+--- soapdenovo2.orig/standardPregraph/node2edge.c
++++ soapdenovo2/standardPregraph/node2edge.c
+@@ -41,6 +41,9 @@
+ static void merge_linearV2 ( char bal_edge, STACK *nStack, int count, gzFile fp );
+ static int check_iden_kmerList ( STACK *stack1, STACK *stack2 );
+
++// This external function comes from kmer.c.
++extern void PrintKmer ( FILE *, Kmer );
++
+ //for stack
+ static STACK *nodeStack; //the stack for storing linear nodes
+ static STACK *bal_nodeStack; // the stack for storing the reverse complemental nodes ..
+--- soapdenovo2.orig/standardPregraph/output_pregraph.c
++++ soapdenovo2/standardPregraph/output_pregraph.c
+@@ -27,6 +27,9 @@
+ #include <extvab.h>
+ static int outvCounter = 0;
+
++extern void PrintKmer ( FILE *, Kmer );
++extern void print_kmer_gz ( gzFile fp, Kmer kmer, char c );
++
+ //after this LINKFLAGFILTER in the Kmer is destroyed
+ static void output1vt ( kmer_t *node1, FILE *fp )
+ {
+--- soapdenovo2.orig/standardPregraph/prlRead2Ctg.c
++++ soapdenovo2/standardPregraph/prlRead2Ctg.c
+@@ -781,7 +781,7 @@
+ long long i;
+ char *src_name, *next_name, name[256];
+ FILE *fo2;
+- gzFile fo, *outfp1 = NULL, *outfp2 = NULL, *outfp3 = NULL, *outfp4 = NULL;
++ gzFile fo, outfp1 = NULL, outfp2 = NULL, *outfp3 = NULL, outfp4 = NULL;
+ int maxReadNum, libNo, prevLibNo, insSize = 0;
+ boolean flag, pairs = 1;
+ pthread_t threads[thrd_num];
+--- soapdenovo2.orig/standardPregraph/cutTip_graph2.c
++++ soapdenovo2/standardPregraph/cutTip_graph2.c
+@@ -30,6 +30,9 @@
+ static int caseA, caseB, caseC, caseD, caseE;
+ void removeDeadArcs2();
+
++// This function comes from lineraEdge.c.
++extern void linearConcatenate2 ( boolean last );
++
+ //Destroy the edge.
+ void destroyEdge2 ( unsigned int edgeid )
+ {
+--- soapdenovo2.orig/standardPregraph/prlRead2path.c
++++ soapdenovo2/standardPregraph/prlRead2path.c
+@@ -76,6 +76,9 @@
+ static void thread_wait ( pthread_t *threads );
+ static void thread_add1preArc ( unsigned int from_ed, unsigned int to_ed, unsigned int thrdID );
+
++// This external function comes from kmer.c.
++extern void PrintKmer ( FILE *, Kmer );
++
+ static void creatThrds ( pthread_t *threads, PARAMETER *paras )
+ {
+ unsigned char i;
+--- soapdenovo2.orig/standardPregraph/read2edge.c
++++ soapdenovo2/standardPregraph/read2edge.c
+@@ -94,6 +94,9 @@
+ static void creatThrds ( pthread_t *threads, PARAMETER *paras );
+ static void searchKmer1read ( int i, KmerSet2 *kset, int threadID );
+
++extern boolean read1seqInLibpos ( char *src_seq, char *src_name, int *len_seq, // FILE *file,
++ int *file_No, int file_num, char **fileName, int *fileType, int *maxLen, long *pos_seq );
++
+ struct preArc
+ {
+ unsigned int to_ed;
+--- soapdenovo2.orig/standardPregraph/scaffold.c
++++ soapdenovo2/standardPregraph/scaffold.c
+@@ -32,6 +32,9 @@
+ static boolean LINK, SCAFF;
+ static char graphfile[256];
+
++// This external function comes from orderContig.c.
++extern void ScafStat ( int len_cut, char *graphfile );
++
+ /*************************************************
+ Function:
+ call_scaffold
+--- soapdenovo2.orig/standardPregraph/iterate.c
++++ soapdenovo2/standardPregraph/iterate.c
+@@ -47,6 +47,16 @@
+
+ static void forward ( unsigned int index, int first );
+
++extern void destroyEdge2 ( unsigned int edgeid );
++extern void Read2edge ( char *libfile, char *graph, int maxk );
++extern void Read2edge2 ( char *libfile, char *graph, int last, int maxk );
++extern ARC *arcCount2 ( unsigned int edgeid, unsigned int *num );
++extern void copyEdge ( unsigned int source, unsigned int target );
++extern void removeWeakEdges2 ( int lenCutoff, unsigned int multiCutoff, int mink );
++extern void removeLowCovEdges2 ( int lenCutoff, unsigned short covCutoff, int mink, boolean last );
++extern void cutTipsInGraph2 ( int cutLen, boolean strict, boolean last );
++extern void removeDeadArcs2();
++
+ //Fresh preGraphBasic to record the original message and the multikmer message.
+ void freshpreGraphBasic ( boolean iterate, int maxk, char *graph )
+ {
+--- soapdenovo2.orig/standardPregraph/orderContig.c
++++ soapdenovo2/standardPregraph/orderContig.c
+@@ -91,6 +91,8 @@
+ static boolean checkSimple ( DARRAY *ctgArray, int count );
+ static void checkCircle();
+
++int allConnect ( unsigned int ctg, CONNECT *preCNT );
++
+ /*************************************************
+ Function:
+ checkFiles4Scaff
+--- soapdenovo2.orig/fusion/main.c
++++ soapdenovo2/fusion/main.c
+@@ -8,6 +8,7 @@
+ extern int call_align();
+ extern int call_bundle();
+ extern int data_prepare();
++extern void potential();
+
+ #define MAPPING 0
+ #define SCAFF 1
=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ add_hardening
use_debian_zlib
reproducible
gcc-10.patch
+gcc-14.patch
View it on GitLab: https://salsa.debian.org/med-team/soapdenovo2/-/compare/8bcedf55c7e84dc186074fe8b0bf4fd72c17d921...f432d4755a838d4e2581bf8d3baea0a000b99061
--
View it on GitLab: https://salsa.debian.org/med-team/soapdenovo2/-/compare/8bcedf55c7e84dc186074fe8b0bf4fd72c17d921...f432d4755a838d4e2581bf8d3baea0a000b99061
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