[Debian-med-packaging] Please help: sra-sdk

[Andreas Tille]

Hi,

we have some trouble with the latest version of sra-sdk which is
maintained here:

   git://git.debian.org/debian-med/sra-sdk.git

----- Forwarded message from Charles Plessy <charles-listes-med-packaging at plessy.org> -----

Date: Mon, 21 Oct 2013 18:48:37 +0900
From: Charles Plessy <charles-listes-med-packaging at plessy.org>
To: debian-med-packaging at lists.alioth.debian.org
Subject: Re: 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)

> 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.

----- End forwarded message -----

I tried to fiddle around with preventing the self made build system to
try using a locally shipped bz2 library but failed.

Any help would be more than welcome.

Kind regards

        Andreas.

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