[med-svn] [Git][med-team/segemehl][master] 4 commits: d/p/arm64.patch: Fix segfaults on !amd64 and !i386

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / segemehl


Commits:
b27b35fe by Nilesh Patra at 2021-08-24T22:17:58+05:30
d/p/arm64.patch: Fix segfaults on !amd64 and !i386

- - - - -
d8f5807c by Nilesh Patra at 2021-08-24T22:18:25+05:30
Bump Standards-Version to 4.6.0 (no changes needed)

- - - - -
89e1050a by Nilesh Patra at 2021-08-24T22:18:51+05:30
Minor fix

- - - - -
da3cd8dc by Nilesh Patra at 2021-08-24T22:19:25+05:30
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/arm64.patch
- debian/patches/series
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+segemehl (0.3.4-5) unstable; urgency=medium
+
+  * Team Upload.
+  * d/p/arm64.patch: Fix segfaults on !amd64 and !i386
+  * Bump Standards-Version to 4.6.0 (no changes needed)
+
+ -- Nilesh Patra <nilesh at debian.org>  Tue, 24 Aug 2021 22:19:01 +0530
+
 segemehl (0.3.4-4) unstable; urgency=medium
 
   [ Shruti Sridhar ]


=====================================
debian/control
=====================================
@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13),
                libhts-dev,
                libncurses-dev,
                zlib1g-dev
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/med-team/segemehl
 Vcs-Git: https://salsa.debian.org/med-team/segemehl.git
 Homepage: http://www.bioinf.uni-leipzig.de/Software/segemehl/


=====================================
debian/patches/arm64.patch
=====================================
@@ -0,0 +1,75 @@
+Description: Change the signed-ness for several chars to fix segfault
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2021-08-24
+--- a/libs/biofiles.c
++++ b/libs/biofiles.c
+@@ -1916,7 +1916,7 @@
+     Uint max, Uint *minlen, Uint *maxlen, unsigned char *minq, unsigned char *maxq) 
+ {
+ 
+-  char ch;
++  signed char ch;
+   char idchar=0;
+   int ret=0;
+   off_t curseqoffset, lastindexoffset=0;
+@@ -2515,7 +2515,7 @@
+ {
+ 
+   FILE *fp;
+-  char ch;
++  signed char ch;
+   char *buffer;
+   char *descrbuffer = NULL;
+   char *seqbuffer = NULL;
+--- a/libs/fileio.c
++++ b/libs/fileio.c
+@@ -498,7 +498,7 @@
+ void
+ bl_freplacestr(char *filename, char *str, Uint len, char stop){
+   int i = 0;
+-  char ch;
++  signed char ch;
+   FILE *fp;
+ 
+   fp = fopen(filename, "rb+");  
+@@ -523,7 +523,8 @@
+ 
+ int
+ bl_fgets(void *space, FILE *fp, char **str) {
+-  char ch, *buffer;
++  signed char ch;
++  char *buffer;
+   size_t buffersize = MAXBUFFERSIZE;
+   size_t len = 0;
+ 
+@@ -549,7 +550,7 @@
+ char* 
+ readfile(void* space, char* filename, size_t* strlen) {
+ 
+-  char ch;
++  signed char ch;
+   char *buffer;
+   FILE *fp;
+   size_t buffersize = MAXBUFFERSIZE;
+--- a/libs/merge.c
++++ b/libs/merge.c
+@@ -596,7 +596,7 @@
+   if (!file->complete && !file->eof){
+ 
+ #ifndef FILEBUFFEREDMERGE
+-    char ch;
++    signed char ch;
+     Uint buffersize = 1024;
+     buffer = ALLOCMEMORY(NULL, NULL, char, buffersize);
+     len = 0;
+--- a/libs/samheader.c
++++ b/libs/samheader.c
+@@ -460,7 +460,7 @@
+ {
+   FILE *fp;
+   off_t offset = 0;
+-  char ch;
++  signed char ch;
+   char *buffer;
+   //  char *descrbuffer = NULL;
+   //  char *seqbuffer = NULL;


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 rpath.patch
 cross.patch
+arm64.patch


=====================================
debian/tests/run-unit-test
=====================================
@@ -13,8 +13,7 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
 
-#do_stuff_to_test_package#
 segemehl -x index.idx -d seq1.fa
 segemehl -i index.idx -d seq1.fa -q myseq.fa > mymap.sam
 segemehl -S -i index.idx -d seq1.fa -q seq2.fa > my.sngl.bed
-[ -s "mymap.sam" ] && [ -s "index.idx" ] && [ -s "my.sngl.bed" ] || exit 1 && echo "PASS Test"
\ No newline at end of file
+[ -s "mymap.sam" ] && [ -s "index.idx" ] && [ -s "my.sngl.bed" ] || exit 1 && echo "PASS Test"



View it on GitLab: https://salsa.debian.org/med-team/segemehl/-/compare/4f6ddcfa6a68090c8fe98da880bd35c1d80f4263...da3cd8dc17eafc6af2e528a2fd7fdef9cf1a4cc2

-- 
View it on GitLab: https://salsa.debian.org/med-team/segemehl/-/compare/4f6ddcfa6a68090c8fe98da880bd35c1d80f4263...da3cd8dc17eafc6af2e528a2fd7fdef9cf1a4cc2
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