Re: Help needed for discosnp
On Wed, Jan 23, 2019 at 09:05:47AM +0100, Olivier Sallou wrote: > > On 1/22/19 10:37 PM, Andreas Tille wrote: > > ... > > cd /build/discosnp-2.3.0/obj-x86_64-linux-gnu/tools/kissnp2 && > > /usr/bin/cmake -E cmake_link_script CMakeFiles/kissnp2.dir/link.txt > > --verbose=1 > > /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-2.3.0=. > > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > > -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic > > CMakeFiles/kissnp2.dir/src/Bubble.cpp.o > > CMakeFiles/kissnp2.dir/src/Filter.cpp.o > > CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o > > CMakeFiles/kissnp2.dir/src/main.cpp.o -o ../../bin/kissnp2 -lgatbcore > > -lhdf5 > > /usr/bin/ld: cannot find -lhdf5 > > collect2: error: ld returned 1 exit status > > well, looks like hdf5 lib is not found at link time. > > I gonna have a try I've found a possibly helpful hint here https://stackoverflow.com/questions/31438916/cmake-cannot-find-library-using-link-directories and I think I found a solution now. The position of LINK_LIBRARIES is relevant. Now it seems to work - so please save your time. Kind regards Andreas. -- http://fam-tille.de
Re: Help needed for discosnp
On 1/22/19 10:37 PM, Andreas Tille wrote: > Hi Olivier, > > I've thought I'm so close to get at least discosnp[1] linked > against gatb-core but there is a final thing missing: > > > ... > cd /build/discosnp-2.3.0/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/cmake > -E cmake_link_script CMakeFiles/kissnp2.dir/link.txt --verbose=1 > /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-2.3.0=. > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic > CMakeFiles/kissnp2.dir/src/Bubble.cpp.o > CMakeFiles/kissnp2.dir/src/Filter.cpp.o > CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o > CMakeFiles/kissnp2.dir/src/main.cpp.o -o ../../bin/kissnp2 -lgatbcore -lhdf5 > /usr/bin/ld: cannot find -lhdf5 > collect2: error: ld returned 1 exit status well, looks like hdf5 lib is not found at link time. I gonna have a try There is nobody in my lab anymore maintaining discosnp (don't know where it is managed now). Olivier > > > > My attempt[2] to sneak in some > >-L/usr/lib/x86_64-linux-gnu/hdf5/serial/ > > which is obviously missing (if I add it to the '/usr/bin/c++ ' line it > works) just failed. Any last tiny hint to get this done? > > Kind regards > > Andreas. > > > [1] https://salsa.debian.org/med-team/discosnp > [2] > https://salsa.debian.org/med-team/discosnp/commit/6b87aec1e8d587e750fd1dd25d419269fc66ed7c > -- Olivier Sallou Univ Rennes, Inria, CNRS, IRISA Irisa, Campus de Beaulieu F-35042 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Help needed for discosnp
Hi Olivier, I've thought I'm so close to get at least discosnp[1] linked against gatb-core but there is a final thing missing: ... cd /build/discosnp-2.3.0/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissnp2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/kissnp2.dir/src/Bubble.cpp.o CMakeFiles/kissnp2.dir/src/Filter.cpp.o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o CMakeFiles/kissnp2.dir/src/main.cpp.o -o ../../bin/kissnp2 -lgatbcore -lhdf5 /usr/bin/ld: cannot find -lhdf5 collect2: error: ld returned 1 exit status My attempt[2] to sneak in some -L/usr/lib/x86_64-linux-gnu/hdf5/serial/ which is obviously missing (if I add it to the '/usr/bin/c++ ' line it works) just failed. Any last tiny hint to get this done? Kind regards Andreas. [1] https://salsa.debian.org/med-team/discosnp [2] https://salsa.debian.org/med-team/discosnp/commit/6b87aec1e8d587e750fd1dd25d419269fc66ed7c -- http://fam-tille.de
