[Debian-med-packaging] Bug#906509: sra-sdk: FTBFS in buster/sid (unknown type name 'HttpProxy')
Santiago Vila
sanvila at debian.org
Fri Aug 17 20:22:45 BST 2018
Package: src:sra-sdk
Version: 2.8.2-5+dfsg-1
Severity: serious
Tags: ftbfs
Dear maintainer:
I tried to build this package in buster but it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-arch
dh build-arch --no-parallel
debian/rules override_dh_update_autotools_config
make[1]: Entering directory '/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg'
echo "do nothing"
do nothing
make[1]: Leaving directory '/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg'
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg'
# output dir will be checked so create it before
mkdir -p debian/tmp/usr/lib
ln -s /usr/lib/x86_64-linux-gnu debian/tmp/usr/lib
#
[... snipped ...]
gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/interfaces/override -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/linux -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/unix -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util -I/usr/include/ncbi-vdb/ -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/usr/include/ncbi-vdb/ext -I/usr/include -I. -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -MD -o md5cp.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/md5cp.c -D__mod_name__=tools/util -D__file_name__=md5cp -D__file_ext__=c
+++++++++++++++++++++++++ adding zlib +++++++++++++++++++++++++++++++++++++++
gcc -static-libgcc -o /<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/md5cp.2.8.2 -DNDEBUG -m64 -Wl,-z,relro -Wl,-z,now md5cp.o -L/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/lib -L/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm -lz -lbz2 -lsz -lmbedx509 -lmbedtls -lmbedcrypto
ln -s md5cp.2.8.2 md5cp.2
ln -s md5cp.2 md5cp
gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/interfaces/override -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/linux -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/unix -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util -I/usr/include/ncbi-vdb/ -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/usr/include/ncbi-vdb/ext -I/usr/include -I. -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -MD -o vdb-lock.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/vdb-lock.c -D__mod_name__=tools/util -D__file_name__=vdb-lock -D__file_ext__=c
+++++++++++++++++++++++++ adding zlib +++++++++++++++++++++++++++++++++++++++
gcc -static-libgcc -o /<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/vdb-lock.2.8.2 -DNDEBUG -m64 -Wl,-z,relro -Wl,-z,now vdb-lock.o -L/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/lib -L/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm -lz -lbz2 -lsz -lmbedx509 -lmbedtls -lmbedcrypto
ln -s vdb-lock.2.8.2 vdb-lock.2
ln -s vdb-lock.2 vdb-lock
gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/interfaces/override -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/linux -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/unix -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util -I/usr/include/ncbi-vdb/ -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/usr/include/ncbi-vdb/ext -I/usr/include -I. -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -MD -o vdb-unlock.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/vdb-unlock.c -D__mod_name__=tools/util -D__file_name__=vdb-unlock -D__file_ext__=c
+++++++++++++++++++++++++ adding zlib +++++++++++++++++++++++++++++++++++++++
gcc -static-libgcc -o /<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/vdb-unlock.2.8.2 -DNDEBUG -m64 -Wl,-z,relro -Wl,-z,now vdb-unlock.o -L/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/lib -L/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm -lz -lbz2 -lsz -lmbedx509 -lmbedtls -lmbedcrypto
ln -s vdb-unlock.2.8.2 vdb-unlock.2
ln -s vdb-unlock.2 vdb-unlock
gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/interfaces/override -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/linux -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/unix -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util -I/usr/include/ncbi-vdb/ -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/usr/include/ncbi-vdb/ext -I/usr/include -I. -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -MD -o PrintOS.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/unix/PrintOS.c -D__mod_name__=tools/util -D__file_name__=PrintOS -D__file_ext__=c
gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/interfaces/override -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/linux -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/unix -I/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util -I/usr/include/ncbi-vdb/ -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/usr/include/ncbi-vdb/ext -I/usr/include -I. -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -MD -o test-sra.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/test-sra.c -D__mod_name__=tools/util -D__file_name__=test-sra -D__file_ext__=c
/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/test-sra.c: In function 'MainNetwotk':
/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/test-sra.c:2619:19: error: unknown type name 'HttpProxy'
const HttpProxy *p = KNSManagerGetHttpProxy(self->knsMgr);
^~~~~~~~~
/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/test-sra.c:2619:34: warning: implicit declaration of function 'KNSManagerGetHttpProxy'; did you mean 'KNSManagerGetProxies'? [-Wimplicit-function-declaration]
const HttpProxy *p = KNSManagerGetHttpProxy(self->knsMgr);
^~~~~~~~~~~~~~~~~~~~~~
KNSManagerGetProxies
/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/test-sra.c:2619:34: warning: initialization of 'const int *' from 'int' makes pointer from integer without a cast [-Wint-conversion]
/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/test-sra.c:2624:17: warning: implicit declaration of function 'HttpProxyGet' [-Wimplicit-function-declaration]
HttpProxyGet(p, &http_proxy, &http_proxy_port);
^~~~~~~~~~~~
/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/test-sra.c:2644:21: warning: implicit declaration of function 'HttpProxyGetNextHttpProxy' [-Wimplicit-function-declaration]
p = HttpProxyGetNextHttpProxy ( p );
^~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util/test-sra.c:2644:19: warning: assignment to 'const int *' from 'int' makes pointer from integer without a cast [-Wint-conversion]
p = HttpProxyGetNextHttpProxy ( p );
^
make[5]: *** [/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/build/Makefile.rules:31: test-sra.o] Error 1
make[5]: Leaving directory '/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/obj/tools/util'
make[4]: *** [Makefile:63: std] Error 2
make[4]: Leaving directory '/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools/util'
make[3]: *** [Makefile:81: util] Error 2
make[3]: Leaving directory '/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg/tools'
make[2]: *** [Makefile:48: tools] Error 2
make[2]: Leaving directory '/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg'
make[1]: *** [debian/rules:36: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/sra-sdk-2.8.2-5+dfsg'
make: *** [debian/rules:9: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
The build was made with "dpkg-buildpackage -B" in my autobuilder.
Most probably, it also fails here in reproducible builds:
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/sra-sdk.html
where you can get a full build log if you need it.
If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the BTS web page for this package.
Thanks.
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