Michael R. Crusoe pushed to branch master at Debian Med / gffread
Commits: c63dc927 by Michael R. Crusoe at 2019-09-25T07:16:47Z Add breaks/replaces on cufflinks (<< 2.2.1+dfsg.1-4) - - - - - 4bae3dc5 by Michael R. Crusoe at 2019-09-25T07:17:10Z New upstream version 0.11.5 - - - - - e5144302 by Michael R. Crusoe at 2019-09-25T07:17:10Z Update upstream source from tag 'upstream/0.11.5' Update to upstream version '0.11.5' with Debian dir 8253c6bf8ddaa2e7488e04350dbd548455ba6fed - - - - - 09fd781a by Michael R. Crusoe at 2019-09-25T07:17:10Z New upstream version - - - - - 86ea01c9 by Michael R. Crusoe at 2019-09-25T07:17:14Z Set upstream metadata fields: Name. - - - - - 0a7e4284 by Michael R. Crusoe at 2019-09-25T07:19:06Z update changelog - - - - - 0f80bc9f by Michael R. Crusoe at 2019-09-25T07:28:20Z refresh patch - - - - - 5293edc8 by Michael R. Crusoe at 2019-09-25T07:36:03Z improve hardening - - - - - 7 changed files: - debian/changelog - debian/control - debian/patches/gclib.patch - + debian/patches/hardening - debian/patches/series - debian/upstream/metadata - gffread.cpp Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +gffread (0.11.5-1) UNRELEASED; urgency=medium + + * Team upload. + * New upstream release. + * Add breaks/replaces on cufflinks (<< 2.2.1+dfsg.1-4). (Closes: #940915) + * Set upstream metadata fields: Name. + + -- Michael R. Crusoe <[email protected]> Wed, 25 Sep 2019 09:15:58 +0200 + gffread (0.11.4-2) unstable; urgency=medium [ Helmut Grohne ] ===================================== debian/control ===================================== @@ -14,6 +14,8 @@ Package: gffread Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} +Breaks: cufflinks (<< 2.2.1+dfsg.1-4) +Replaces: cufflinks (<< 2.2.1+dfsg.1-4) Description: GFF/GTF format conversions, region filtering, FASTA sequence extraction Gffread is a GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more. ===================================== debian/patches/gclib.patch ===================================== @@ -2,9 +2,9 @@ Author: Andreas Tille <[email protected]> Last-Update: Thu, 18 Apr 2019 12:40:25 +0200 Description: Fix build against libgclib ---- a/Makefile -+++ b/Makefile -@@ -82,8 +82,8 @@ gffread.o : gff_utils.h $(GCLDIR)/GBase. +--- gffread.orig/Makefile ++++ gffread/Makefile +@@ -83,8 +83,8 @@ gff_utils.o : gff_utils.h $(GCLDIR)/gff.h ${GCLDIR}/gff.o : ${GCLDIR}/gff.h ${GCLDIR}/GFaSeqGet.h ${GCLDIR}/GList.hh ${GCLDIR}/GHash.hh ${GCLDIR}/GFaSeqGet.o : ${GCLDIR}/GFaSeqGet.h ===================================== debian/patches/hardening ===================================== @@ -0,0 +1,15 @@ +From: Michael R. Crusoe <[email protected]> +Subject: Use CPPFLAGS + +Allows Debian to harden the binary with CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 +--- gffread.orig/Makefile ++++ gffread/Makefile +@@ -65,7 +65,7 @@ + #endif + + %.o : %.cpp +- ${CXX} ${CXXFLAGS} -c $< -o $@ ++ ${CXX} ${CPPFLAGS} ${CXXFLAGS} -c $< -o $@ + + # C/C++ linker + ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ gclib.patch +hardening ===================================== debian/upstream/metadata ===================================== @@ -1,5 +1,6 @@ Registry: - - Name: OMICtools - Entry: OMICS_28050 - - Name: conda:bioconda - Entry: gffread +- Name: OMICtools + Entry: OMICS_28050 +- Name: conda:bioconda + Entry: gffread +Name: gffread ===================================== gffread.cpp ===================================== @@ -4,7 +4,7 @@ #define __STDC_FORMAT_MACROS #include <inttypes.h> -#define VERSION "0.11.4" +#define VERSION "0.11.5" #define USAGE "gffread v" VERSION ". Usage:\n\ gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] \n\ @@ -1212,7 +1212,7 @@ int main(int argc, char* argv[]) { openfw(f_x, args, 'x'); openfw(f_y, args, 'y'); - if (f_out==NULL && f_w==NULL && f_x==NULL && f_y==NULL) + if (f_out==NULL && f_w==NULL && f_x==NULL && f_y==NULL && !covInfo) f_out=stdout; //if (f_y!=NULL || f_x!=NULL) wCDSonly=true; //useBadCDS=useBadCDS || (fgtfok==NULL && fgtfbad==NULL && f_y==NULL && f_x==NULL); View it on GitLab: https://salsa.debian.org/med-team/gffread/compare/6e69d38cf1bbe630b8b0824547f380691684e1e7...5293edc8ac00e41d2a8954d19ad5a49459de2e8f -- View it on GitLab: https://salsa.debian.org/med-team/gffread/compare/6e69d38cf1bbe630b8b0824547f380691684e1e7...5293edc8ac00e41d2a8954d19ad5a49459de2e8f You're receiving this email because of your account on salsa.debian.org.
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