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) best regards, Gert 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-packaging@plessy.org> ----- > > > > > > Date: Mon, 21 Oct 2013 18:48:37 +0900 > > > From: Charles Plessy <charles-listes-med-packaging@plessy.org> > > > To: debian-med-packaging@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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