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 <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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