[Debian-med-packaging] Please test sra-toolkit (Was: sra-sdk git repository totally screwed up - I start from scratch and leave sra-sdk_.git for some time if somebody really cares about the history)

[Charles Plessy]

Le Wed, Aug 14, 2013 at 11:06:33PM +0200, Andreas Tille a écrit :
> 
> On Wed, Aug 14, 2013 at 01:34:47PM +0900, Charles Plessy wrote:
> > I tested it with the following commands:
> > 
> >     wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP010%2FSRP010815/SRR407172/SRR407172.sra
> >     fastq-dump SRR407172.sra 
> > 
> > fastq-dump crashed quickly, while with the current version in Debian, it outputs
> > FASTQ reads in a file called SRR407172.fastq.
> 
> Thanks for the test - I might try downloading the file and test it.
>  
> > Sorry that this test is very inconvenient as the file is 4 Gb, but that was the
> > only example I could find quickly.  There must be other SRA files that are smaller,
> > but SRR407172.fastq is the one for which I was sure that I succeeded before.
> 
> OK, good to know - may be I might get it fixed.  At least it seems that
> I should not upload the new version before it is fixed.

Hi Adreas,

I tried the new upstream release (2.3.3-4) and now it fails to build from source...

gcc -c  -DNDEBUG      -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -D_ARCH_BITS=64 -DLIBPREFIX=lib -DSHLIBEXT=so -I/«PKGBUILDDIR»/libs/sra/linux -I/«PKGBUILDDIR»/libs/sra/unix -I/«PKGBUILDDIR»/libs/sra -I/«PKGBUILDDIR»/interfaces -I/«PKGBUILDDIR»/interfaces/cc/gcc/x86_64 -I/«PKGBUILDDIR»/interfaces/cc/gcc -I/«PKGBUILDDIR»/interfaces/os/linux -I/«PKGBUILDDIR»/interfaces/os/unix -I/«PKGBUILDDIR»/interfaces/ext -I. -MD -o reader-abi.pic.o -fPIC -O3 -Wall -Wno-variadic-macros -fno-strict-aliasing -D_LIBRARY /«PKGBUILDDIR»/libs/sra/reader-abi.c
ar -rc /«PKGBUILDDIR»/debian/tmp/linux/gcc/dyn/x86_64/rel/ilib/libsrareader.a reader-cmn.pic.o reader-fastq.pic.o reader-sff.pic.o reader-illumina.pic.o reader-abi.pic.o
make[5]: Leaving directory `/«PKGBUILDDIR»/debian/tmp/linux/gcc/dyn/x86_64/rel/obj/libs/sra'
make[4]: Leaving directory `/«PKGBUILDDIR»/libs/sra'
make[4]: Entering directory `/«PKGBUILDDIR»/libs/ncbi-vdb'
make[5]: *** No rule to make target `/«PKGBUILDDIR»/debian/tmp/linux/gcc/dyn/x86_64/rel/ilib/libbz2.a', needed by `/«PKGBUILDDIR»/debian/tmp/linux/gcc/dyn/x86_64/rel/lib/libncbi-vdb.a'.  Stop.

I did not have time to investigate further.

Chers,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan