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-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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