[med-svn] [Git][med-team/gffread][master] 8 commits: Add breaks/replaces on cufflinks (<< 2.2.1+dfsg.1-4)

[Michael R. Crusoe]

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 <michael.crusoe at gmail.com>  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 <tille at debian.org>
 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 <michael.crusoe at gmail.com>
+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
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