Hi Gert,
On Tue, Oct 22, 2013 at 11:40:54AM +0200, Gert Wollny wrote:
> Hello Andreas,
>
> well, for me in the Debian-unstable VM I use for package preparation the
> error stays the same like I reported yesterday, i.e. the build
> terminates in the dh_install phase and not unexpected, because there
> are o directories "mod??/*" (see below)
I can confirm that if I build manually in an unstable chroot with your
patch I get the same result. Strange. I need to check this out.
Thanks for your help in any case
Andreas.
> gcc
> -o
> /var/cache/pbuilder/workspace/test/sra-sdk/debian/tmp/linux/gcc/dyn/x86_64/rel/bin/cache-mgr.2.3.3
> -m64 cache-mgr.o
> -L/var/cache/pbuilder/workspace/test/sra-sdk/debian/tmp/linux/gcc/dyn/x86_64/rel/lib
>
> -L/var/cache/pbuilder/workspace/test/sra-sdk/debian/tmp/linux/gcc/dyn/x86_64/rel/ilib
> -Wl,-Bstatic -lkapp -lsraschema -lvdb -lkdb -lvfs -lkurl -lkrypto -lkfg
> -lkfs -lksrch -lkproc -lklib -Wl,-Bdynamic -lz -lbz2 -ldl -lpthread -lm
> ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
> preloaded: ignored.
> ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
> preloaded: ignored.
> ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
> preloaded: ignored.
> ln -s cache-mgr.2.3.3 cache-mgr.2
> ln -s cache-mgr.2 cache-mgr
> make[5]: Leaving directory
> `/var/cache/pbuilder/workspace/test/sra-sdk/debian/tmp/linux/gcc/dyn/x86_64/rel/obj/tools/cache-mgr'
> make[4]: Leaving directory
> `/var/cache/pbuilder/workspace/test/sra-sdk/tools/cache-mgr'
> make[3]: Leaving directory
> `/var/cache/pbuilder/workspace/test/sra-sdk/tools'
> make[2]: Leaving directory `/var/cache/pbuilder/workspace/test/sra-sdk'
> make[1]: Leaving directory `/var/cache/pbuilder/workspace/test/sra-sdk'
> dh_testroot
> debian/rules override_dh_prep
> make[1]: Entering directory `/var/cache/pbuilder/workspace/test/sra-sdk'
> dh_prep -X debian/tmp
> make[1]: Leaving directory `/var/cache/pbuilder/workspace/test/sra-sdk'
> dh_auto_install
> dh_install
> dh_install: sra-toolkit missing files (mod??/*), aborting
> make: *** [binary] Fehler 255
>
>
> On Tue, 2013-10-22 at 07:58 +0200, Andreas Tille wrote:
> > 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-packag...@plessy.org> -----
> > > >
> > > > Date: Mon, 21 Oct 2013 18:48:37 +0900
> > > > From: Charles Plessy <charles-listes-med-packag...@plessy.org>
> > > > To: debian-med-packag...@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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