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 > <[email protected]> ----- > > Date: Mon, 21 Oct 2013 18:48:37 +0900 > From: Charles Plessy <[email protected]> > To: [email protected] > 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)
