[Debian-med-packaging] Bug#753485: Bug#753485: Status of samtools

[Charles Plessy]

Le Thu, Sep 18, 2014 at 09:22:45AM +0200, Andreas Tille a écrit :
> 
> I usually try to track down these things with a simple "debuild" but I
> guess the versioned Build-Depends are not properly set, since the build
> fails with:
> 
> ...
> make[2]: Entering directory '/home/andreas/debian-maintain/alioth/debian-med_git/samtools'
> gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
> bam_index.c: In function ‘bam_idxstats’:
> bam_index.c:92:9: warning: assignment makes pointer from integer without a cast
>      idx = sam_index_load(fp, argv[1]);
>          ^
> bam_index.c:105:5: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘int’ [-Wformat=]
>      printf("*\t0\t0\t%" PRIu64 "\n", hts_idx_get_n_no_coor(idx));
>      ^
> make[2]: *** No rule to make target '/usr/include/htslib/khash_str2int.h', needed by 'bam_plcmd.o'.  Schluss.
> make[2]: Leaving directory '/home/andreas/debian-maintain/alioth/debian-med_git/samtools'
> dh_auto_build: make -j1 HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=$(DFLAGS) $(INCLUDES) -D_FORTIFY_SOURCE=2 LDFLAGS=-Wl,-z,relro LDLIBS=-lhts returned exit code 2
> 

Hi again,

if upgrading to htslib-dev >= 1.0 solves the failure, then let's add a version
constraint in the Build-Depends field.

Cheers,

-- 
Charles