Re: [Debian-med-packaging] Please help: sra-sdk
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-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
Re: [Debian-med-packaging] Please help: sra-sdk
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
Re: [Debian-med-packaging] Please help: sra-sdk
Le Tue, Oct 22, 2013 at 08:43:05PM +0200, Andreas Tille a écrit : I have done the changes needed to build sra-sdk in an unstable chroot manually. It remains totally unclear to me why the build fails with pbuilder but works in a minimal unstable chroot anyway. Charles, if you can build the package, could you at least run your test to confirm whether the upstream code leads to the same results as our current version? Thanks Andreas, I tested the 'fastq-dump' command using the file at the URL below, and this time it worked. http://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX001/SRX001881/SRR006565/SRR006565.sra I can not upload from work, becaues I removed my GPG key from my Debian computer after I started to share administrative privileges with a colleague, so if you are faster than me, please do not hesitate to upload. Just pull the most recent changes before, as I updated the symbols file. Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131023010012.gf17...@falafel.plessy.net
Re: [Debian-med-packaging] Please help: sra-sdk
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)
