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

[Andreas Tille]

Hi Gert,

I applied your patch but in my unstable chroot (and this is where the
problem occures) the error remains the same.  IMHO the problem is not
that the third party copy of libbz2 is built but rather that a -L
option

  -L/tmp/buildd/sra-sdk-2.3.3-4~dfsg/debian/tmp/linux/gcc/dyn/x86_64/rel/lib \
  -L/ tmp/buildd/sra-sdk-2.3.3-4~dfsg/debian/tmp/linux/gcc/dyn/x86_64/rel/ilib

is forcing ldd to seek at the wrong location.

However, I was not able to suppress this option reasonably enough that
the other internal sra-sdk libraries will remain to be found there.

Thanks for your hint anyway

       Andreas.

On Tue, Oct 22, 2013 at 12:15:19AM +0200, Gert Wollny wrote:
> Hello Andreas, 
> 
> the attached patch eliminates the downloads and building of libbz2 and
> libz and uses the system versions. 
> Building the packages now fails for different reasons (on wheezy):
> 
> debian/rules override_dh_prep
> make[1]: Entering directory `/home/gerddie/src/sra-sdk'
> dh_prep -X debian/tmp
> make[1]: Leaving directory `/home/gerddie/src/sra-sdk'
>    dh_installdirs
>    dh_auto_install
>    dh_install
> dh_install: sra-toolkit missing files (mod??/*), aborting
> make: *** [binary] Fehler 255
> dpkg-buildpackage: Fehler: Fehler-Exitstatus von fakeroot debian/rules
> binary war 2
> debuild: fatal error at line 1357:
> dpkg-buildpackage -rfakeroot -D -us -uc -i -I -b failed
> 
> 
> hope that helps, 
> Gert 
> 
> 
> On Mon, 2013-10-21 at 23:10 +0200, Andreas Tille wrote:
> > 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.
> > 
> 

> diff --git a/libs/Makefile b/libs/Makefile
> index ce40007..159c77e 100644
> --- a/libs/Makefile
> +++ b/libs/Makefile
> @@ -32,7 +32,6 @@ include $(TOP)/build/Makefile.shell
>  # default
>  #
>  SUBDIRS = \
> -	ext \
>  	klib \
>  	kproc \
>  	kfs \
> diff --git a/libs/ncbi-vdb/Makefile b/libs/ncbi-vdb/Makefile
> index 7b08def..a9c1618 100644
> --- a/libs/ncbi-vdb/Makefile
> +++ b/libs/ncbi-vdb/Makefile
> @@ -88,7 +88,6 @@ endif
>  
>  VDB_LIB_CMN = \
>  	align-access \
> -	bz2 \
>  	kfg \
>  	kfs \
>  	klib \
> @@ -98,8 +97,7 @@ VDB_LIB_CMN = \
>  	ksrch \
>  	$(LIBKXML) \
>  	kurl \
> -	vfs \
> -	z
> +	vfs
>  
>  VDB_LIB_RD = \
>  	$(VDB_LIB_CMN) \
> @@ -116,7 +114,7 @@ VDB_OBJ = \
>  	$(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RD)))
>  
>  VDB_LIB = \
> -	$(addprefix -s,$(VDB_LIB_RD))
> +	$(addprefix -s,$(VDB_LIB_RD)) -lbz2 -lz
>  
>  $(LIBDIR)/libncbi-vdb.$(SHLX): $(VDB_OBJ)
>  	$(LD) --dlib --vers $(SRCDIR) -o $@ $(VDB_LIB)


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