[med-svn] [Git][med-team/gmap][master] 2 commits: Refresh patch
Nilesh Patra
gitlab at salsa.debian.org
Sat Aug 29 16:32:07 BST 2020
Nilesh Patra pushed to branch master at Debian Med / gmap
Commits:
25f4be1e by Nilesh Patra at 2020-08-29T20:49:18+05:30
Refresh patch
- - - - -
f587bea9 by Nilesh Patra at 2020-08-29T21:01:03+05:30
Fix gcc-10 FTBFS
- - - - -
3 changed files:
- + debian/patches/fix-gcc10-build.patch
- debian/patches/remove_getopt_code_copy.patch
- debian/patches/series
Changes:
=====================================
debian/patches/fix-gcc10-build.patch
=====================================
@@ -0,0 +1,15 @@
+Description: Fix gcc-10 build failures by adding extern attribute
+Author: Nilesh Patra <npatra974 at gmail.com>
+Bug: https://bugs.debian.org/cgi-bin/bugreport.cgi?archive=no&bug=966863
+Last-Update: 2020-08-29
+--- a/src/dynprog_single.c
++++ b/src/dynprog_single.c
+@@ -91,7 +91,7 @@
+
+ #define T Dynprog_T
+
+-bool homopolymerp;
++extern bool homopolymerp;
+
+ void
+ Dynprog_single_setup (bool homopolymerp_in) {
=====================================
debian/patches/remove_getopt_code_copy.patch
=====================================
@@ -4,7 +4,7 @@ Description: getline belongs to libc - no need to have a copy here
--- a/src/Makefile.am
+++ b/src/Makefile.am
-@@ -194,7 +194,7 @@ GMAP_FILES = bool.h types.h univcoord.h
+@@ -196,7 +196,7 @@
request.c request.h result.c result.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
chimera.c chimera.h datadir.c datadir.h parserange.c parserange.h \
@@ -13,7 +13,7 @@ Description: getline belongs to libc - no need to have a copy here
# Note: dist_ commands get read by bootstrap, and don't follow the flags
-@@ -285,7 +285,7 @@ GMAPL_FILES = bool.h types.h univcoord.h
+@@ -287,7 +287,7 @@
request.c request.h result.c result.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
chimera.c chimera.h datadir.c datadir.h parserange.c parserange.h \
@@ -22,7 +22,7 @@ Description: getline belongs to libc - no need to have a copy here
# Note: dist_ commands get read by bootstrap, and don't follow the flags
-@@ -380,7 +380,7 @@ GSNAP_FILES = bool.h types.h univcoord.h
+@@ -382,7 +382,7 @@
request.c request.h resulthr.c resulthr.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
datadir.c datadir.h mode.h parserange.c parserange.h \
@@ -31,7 +31,7 @@ Description: getline belongs to libc - no need to have a copy here
# Note: dist_ commands get read by bootstrap, and don't follow the flags
-@@ -480,7 +480,7 @@ GSNAPL_FILES = bool.h types.h univcoord.
+@@ -482,7 +482,7 @@
request.c request.h resulthr.c resulthr.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
datadir.c datadir.h mode.h parserange.c parserange.h \
@@ -40,7 +40,7 @@ Description: getline belongs to libc - no need to have a copy here
# Note: dist_ commands get read by bootstrap, and don't follow the flags
-@@ -578,7 +578,7 @@ UNIQSCAN_FILES = bool.h types.h univcoor
+@@ -580,7 +580,7 @@
uint8table_rh.c uint8table_rh.h uinttable_rh.c uinttable_rh.h stage1hr.c stage1hr.h \
resulthr.c resulthr.h \
datadir.c datadir.h mode.h parserange.c parserange.h \
@@ -49,7 +49,7 @@ Description: getline belongs to libc - no need to have a copy here
uniqscan_CC = $(PTHREAD_CC)
uniqscan_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 $(POPCNT_CFLAGS)
-@@ -633,7 +633,7 @@ UNIQSCANL_FILES = bool.h types.h univcoo
+@@ -635,7 +635,7 @@
uint8table_rh.c uint8table_rh.h stage1hr.c stage1hr.h \
resulthr.c resulthr.h \
datadir.c datadir.h mode.h parserange.c parserange.h \
@@ -58,7 +58,7 @@ Description: getline belongs to libc - no need to have a copy here
uniqscanl_CC = $(PTHREAD_CC)
uniqscanl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_STACK_READLENGTH=$(MAX_STACK_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 $(POPCNT_CFLAGS)
-@@ -687,7 +687,7 @@ INDEXDB_CAT_FILES = bool.h types.h univc
+@@ -689,7 +689,7 @@
indexdbdef.h indexdb.c indexdb.h indexdb-write.c indexdb-write.h \
complement.h compress-write.c compress-write.h bzip2.c bzip2.h fopen.c fopen.h \
datadir.c datadir.h parserange.c parserange.h \
@@ -67,7 +67,7 @@ Description: getline belongs to libc - no need to have a copy here
indexdb_cat_CC = $(PTHREAD_CC)
indexdb_cat_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
-@@ -714,7 +714,7 @@ SNPINDEX_FILES = bool.h types.h univcoor
+@@ -716,7 +716,7 @@
chrom.c chrom.h \
complement.h md5.c md5.h bzip2.c bzip2.h fopen.c fopen.h sequence.c sequence.h genome.c genome.h \
datadir.c datadir.h parserange.c parserange.h \
@@ -76,7 +76,7 @@ Description: getline belongs to libc - no need to have a copy here
snpindex_CC = $(PTHREAD_CC)
snpindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
-@@ -742,7 +742,7 @@ CMETINDEX_FILES = bool.h types.h univcoo
+@@ -744,7 +744,7 @@
uintlist.c uintlist.h intlist.c intlist.h \
uint8list.c uint8list.h \
list.c list.h datadir.c datadir.h parserange.c parserange.h \
@@ -85,7 +85,7 @@ Description: getline belongs to libc - no need to have a copy here
cmetindex_CC = $(PTHREAD_CC)
cmetindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
-@@ -770,7 +770,7 @@ ATOIINDEX_FILES = bool.h types.h univcoo
+@@ -772,7 +772,7 @@
uintlist.c uintlist.h intlist.c intlist.h \
uint8list.c uint8list.h \
list.c list.h datadir.c datadir.h parserange.c parserange.h \
@@ -94,7 +94,7 @@ Description: getline belongs to libc - no need to have a copy here
atoiindex_CC = $(PTHREAD_CC)
atoiindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
-@@ -792,7 +792,7 @@ TRINDEX_FILES = fopen.h bool.h types.h u
+@@ -794,7 +794,7 @@
uintlist.c uintlist.h intlist.c intlist.h \
list.c list.h datadir.c datadir.h \
bzip2.c bzip2.h getline.c getline.h \
@@ -103,7 +103,7 @@ Description: getline belongs to libc - no need to have a copy here
trindex_CC = $(PTHREAD_CC)
trindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
-@@ -816,7 +816,7 @@ GET_GENOME_FILES = bool.h types.h univco
+@@ -818,7 +818,7 @@
chrnum.c chrnum.h \
datadir.c datadir.h parserange.c parserange.h \
getline.c getline.h \
@@ -112,7 +112,7 @@ Description: getline belongs to libc - no need to have a copy here
get_genome_CC = $(PTHREAD_CC)
get_genome_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
-@@ -836,7 +836,7 @@ IIT_STORE_FILES = fopen.h bool.h types.h
+@@ -838,7 +838,7 @@
iit-write-univ.c iit-write-univ.h iitdef.h iit-write.c iit-write.h \
tableint.c tableint.h table.c table.h chrom.c chrom.h \
bzip2.c bzip2.h getline.c getline.h \
@@ -121,7 +121,7 @@ Description: getline belongs to libc - no need to have a copy here
iit_store_CC = $(PTHREAD_CC)
iit_store_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
-@@ -856,7 +856,7 @@ IIT_GET_FILES = fopen.h bool.h types.h u
+@@ -858,7 +858,7 @@
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
complement.h parserange.c parserange.h \
bzip2.c bzip2.h getline.c getline.h \
@@ -130,7 +130,7 @@ Description: getline belongs to libc - no need to have a copy here
iit_get_CC = $(PTHREAD_CC)
iit_get_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
-@@ -872,7 +872,7 @@ IIT_DUMP_FILES = fopen.h bool.h types.h
+@@ -874,7 +874,7 @@
stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h parserange.c parserange.h \
@@ -139,7 +139,7 @@ Description: getline belongs to libc - no need to have a copy here
iit_dump_CC = $(PTHREAD_CC)
iit_dump_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
-@@ -888,7 +888,7 @@ IIT_PILEUP_FILES = fopen.h bool.h types.
+@@ -890,7 +890,7 @@
genomicpos.h interval.c interval.h \
intlist.c intlist.h uintlist.c uintlist.h iitdef.h iit-read.c iit-read.h \
univinterval.c univinterval.h iit-read-univ.c iit-read-univ.h parserange.c parserange.h \
@@ -148,7 +148,7 @@ Description: getline belongs to libc - no need to have a copy here
iit_pileup_CC = $(PTHREAD_CC)
iit_pileup_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
-@@ -910,7 +910,7 @@ SAM_SORT_FILES = bool.h types.h univcoor
+@@ -912,7 +912,7 @@
parserange.c parserange.h iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
samflags.h samheader.c samheader.h samread.c samread.h \
bzip2.c bzip2.h getline.c getline.h datadir.c datadir.h \
@@ -157,7 +157,7 @@ Description: getline belongs to libc - no need to have a copy here
sam_sort_CC = $(PTHREAD_CC)
sam_sort_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
-@@ -934,7 +934,7 @@ dist_sam_sort_SOURCES = $(SAM_SORT_FILES
+@@ -936,7 +936,7 @@
# chrnum.c chrnum.h \
# maxent.c maxent.h maxent_hr.c maxent_hr.h \
# branchpoint.c branchpoint.h \
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
only-do-cpuid-on-amd64-i386.patch
install-data-local
remove_getopt_code_copy.patch
+fix-gcc10-build.patch
View it on GitLab: https://salsa.debian.org/med-team/gmap/-/compare/93742d41ae5c87e378a0ce63e72516be4221532d...f587bea9e91c88b3b8b61981d1bd12466730f839
--
View it on GitLab: https://salsa.debian.org/med-team/gmap/-/compare/93742d41ae5c87e378a0ce63e72516be4221532d...f587bea9e91c88b3b8b61981d1bd12466730f839
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