[med-svn] [Git][med-team/bcftools][master] try to fix the i386 build

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / bcftools


Commits:
02aa6cb5 by Michael R. Crusoe at 2020-01-02T13:59:00+01:00
try to fix the i386 build

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/patches/skip_new_test_failing_on_32bit.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+bcftools (1.10.2-2) unstable; urgency=medium
+
+  * Fix build on i386 by using SSE2
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com>  Thu, 02 Jan 2020 13:58:57 +0100
+
 bcftools (1.10.2-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/control
=====================================
@@ -20,7 +20,8 @@ Package: bcftools
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         ${perl:Depends}
+         ${perl:Depends},
+         sse2-support [i386]
 Suggests:
 # These are needed for plot-vcfstats
           python,


=====================================
debian/patches/skip_new_test_failing_on_32bit.patch
=====================================
@@ -11,12 +11,12 @@ Description: Skip single test causing new failures
 
 --- bcftools.orig/test/test.pl
 +++ bcftools/test/test.pl
-@@ -143,7 +143,7 @@
- test_vcf_query($opts,in=>'query.filter.3',out=>'query.51.out',args=>q[-f'[\\t%GT\\n]\\n' -i'GT~"1" && GT~"2"']);
- test_vcf_query($opts,in=>'query.filter.3',out=>'query.52.out',args=>q[-f'[\\t%GT\\n]\\n' -i'GT~"1" &  GT~"2"']);
- test_vcf_query($opts,in=>'query.filter.3',out=>'query.53.out',args=>q[-f'%POS[\\t%GT]\\n' -i'COUNT(GT="het")=1']);
--test_vcf_query($opts,in=>'filter.5',out=>'query.54.out',args=>q[-f'[%POS  %SAMPLE  %AD\\n]\\n' -i'AD[:0]+AD[:1] > 12']);
-+#test_vcf_query($opts,in=>'filter.5',out=>'query.54.out',args=>q[-f'[%POS  %SAMPLE  %AD\\n]\\n' -i'AD[:0]+AD[:1] > 12']);
- test_vcf_query($opts,in=>'query.filter.4',out=>'query.55.out',args=>q[-f'%POS\\t%REF\\t%ALT[\\t%GT]\\n' -e'TYPE!="snp" || ALT="*"']);
- test_vcf_query($opts,in=>'view',out=>'query.56.out',args=>q[-f'%ID\\n' -i 'ID=@].$$opts{path}.q[/query.56.out']);
- test_vcf_query($opts,in=>'query.filter.5',out=>'query.57.out',args=>q[-f'[%POS\\t%SAMPLE\\t%GT\\t%AD\\n]' -i'GT="het" & binom(FMT/AD)>0.01']);
+@@ -156,7 +156,7 @@
+ test_vcf_query($opts,in=>'query.negative',out=>'query.62.out',args=>q[-f'%POS\\t%TAGV2\\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)']);
+ test_vcf_query($opts,in=>'query',out=>'query.63.out',args=>q[-f'[%POS\\t%SAMPLE\\t%GQ\\n]' -i'N_PASS(GQ<20)==1']);
+ test_vcf_query($opts,in=>'query',out=>'query.64.out',args=>q[-f'%CHROM\\t%POS\\t%INFO\\t%FORMAT\\n' -s D,C]);
+-test_vcf_query($opts,in=>'query.pbinom.1',out=>'query.65.out',args=>q[-f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\\n]' -i'phred(binom(FMT/AD))>=0']);
++#test_vcf_query($opts,in=>'query.pbinom.1',out=>'query.65.out',args=>q[-f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\\n]' -i'phred(binom(FMT/AD))>=0']);
+ test_vcf_query($opts,in=>'query.filter.6',out=>'query.66.out',args=>q[-f'%POS\\n' -i'POS==16777217 || POS==33554432 || POS=118673904']);
+ test_vcf_query($opts,in=>'query.filter.7',out=>'query.68.out',args=>q[-f'%POS\\t%II[\\t%FI]\\n' -i'sum(II)==6']);
+ test_vcf_query($opts,in=>'query.filter.7',out=>'query.68.out',args=>q[-f'%POS\\t%II[\\t%FI]\\n' -i'sum(FORMAT/FI)==7']);


=====================================
debian/rules
=====================================
@@ -1,7 +1,11 @@
 #!/usr/bin/make -f
 
 #export DH_VERBOSE = 1
-#include /usr/share/dpkg/default.mk
+include /usr/share/dpkg/default.mk
+
+ifneq (,$(filter $(DEB_TARGET_ARCH),i386))
+export DEB_CFLAGS_MAINT_APPEND += -mfpmath=sse -msse2
+endif
 
 %:
 	dh $@



View it on GitLab: https://salsa.debian.org/med-team/bcftools/commit/02aa6cb5aaf785d68c8ab3df516f9a969620881b

-- 
View it on GitLab: https://salsa.debian.org/med-team/bcftools/commit/02aa6cb5aaf785d68c8ab3df516f9a969620881b
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