mailund
commented
8 years ago It looks like you are missing the linear algebra libraries you need for ZipHMM. clubs and atlas. I am not sure which package that would be on Fedora, sorry.
On 02 Nov 2015, at 11:50, vikaskumar1019 notifications@github.com<mailto:notifications@github.com> wrote:
Hi Thomas I am trying to install ZIPHMM, but I am getting some errors, can you help me to resolve the issues. I am using Fedora22 right now.
zipHMM-1.0.0 [fritjof@localhost zipHMM-1.0.0]$ make [ 0%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/build_forwarder.cpp.o [ 1%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/forwarder.cpp.o [ 2%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/hmm_utils.cpp.o [ 2%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/PThreadProcessingDevice.cpp.o [ 3%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/performance_description.cpp.o [ 4%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/Stage1JobControl.cpp.o [ 5%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/matrix.cpp.o [ 5%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/seq_io.cpp.o [ 6%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/hmm_io.cpp.o [ 7%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/io_utils.cpp.o [ 7%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/prob_spaces.cpp.o [ 8%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/debug.cpp.o [ 9%] Linking CXX executable ../bin/build_forwarder /usr/bin/ld: cannot find -lcblas /usr/bin/ld: cannot find -latlas collect2: error: ld returned 1 exit status zipHMM/CMakeFiles/build_forwarder.dir/build.make:380: recipe for target 'bin/build_forwarder' failed make[2]: * [bin/build_forwarder] Error 1 CMakeFiles/Makefile2:139: recipe for target 'zipHMM/CMakeFiles/build_forwarder.dir/all' failed make[1]: * [zipHMM/CMakeFiles/build_forwarder.dir/all] Error 2 Makefile:160: recipe for target 'all' failed make: *\ [all] Error 2
With ZIPHMM 1.0.1 [fritjof@localhost ziphmm]$ make [ 2%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/forwarder.cpp.o In file included from /home/fritjof/software/ziphmm/zipHMM/ProcessingDevice.hpp:6:0, from /home/fritjof/software/ziphmm/zipHMM/PThreadProcessingDevice.hpp:4, from /home/fritjof/software/ziphmm/zipHMM/forwarder.hpp:5, from /home/fritjof/software/ziphmm/zipHMM/forwarder.cpp:1: /home/fritjof/software/ziphmm/zipHMM/Stage2JobControl.hpp: In member function ‘size_t zipHMM::Stage2JobControl::getBlockBegin(size_t) const’: /home/fritjof/software/ziphmm/zipHMM/Stage2JobControl.hpp:35:46: error: ‘uint_least64_t’ does not name a type return static_cast(static_cast(block) * (seqLength-1) / nBlocks + 1); ^ In file included from /home/fritjof/software/ziphmm/zipHMM/ProcessingDevice.hpp:7:0, from /home/fritjof/software/ziphmm/zipHMM/PThreadProcessingDevice.hpp:4, from /home/fritjof/software/ziphmm/zipHMM/forwarder.hpp:5, from /home/fritjof/software/ziphmm/zipHMM/forwarder.cpp:1: /home/fritjof/software/ziphmm/zipHMM/MapReduceJobControl.hpp: In member function ‘size_t zipHMM::MapReduceJobControl::getBlockBegin(size_t) const’: /home/fritjof/software/ziphmm/zipHMM/MapReduceJobControl.hpp:29:46: error: ‘uint_least64_t’ does not name a type return static_cast(static_cast(block) * vectorLength / nBlocks); ^ zipHMM/CMakeFiles/zipHMM.dir/build.make:62: recipe for target 'zipHMM/CMakeFiles/zipHMM.dir/forwarder.cpp.o' failed make[2]: * [zipHMM/CMakeFiles/zipHMM.dir/forwarder.cpp.o] Error 1 CMakeFiles/Makefile2:640: recipe for target 'zipHMM/CMakeFiles/zipHMM.dir/all' failed make[1]: * [zipHMM/CMakeFiles/zipHMM.dir/all] Error 2 Makefile:160: recipe for target 'all' failed
— Reply to this email directly or view it on GitHubhttps://github.com/birc-aeh/coalhmm/issues/4.
HerefordGuy
Hi Thomas I am trying to install ZIPHMM, but I am getting some errors, can you help me to resolve the issues. I am using Fedora22 right now.
zipHMM-1.0.0 [fritjof@localhost zipHMM-1.0.0]$ make [ 0%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/build_forwarder.cpp.o [ 1%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/forwarder.cpp.o [ 2%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/hmm_utils.cpp.o [ 2%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/PThreadProcessingDevice.cpp.o [ 3%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/performance_description.cpp.o [ 4%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/Stage1JobControl.cpp.o [ 5%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/matrix.cpp.o [ 5%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/seq_io.cpp.o [ 6%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/hmm_io.cpp.o [ 7%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/io_utils.cpp.o [ 7%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/prob_spaces.cpp.o [ 8%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/debug.cpp.o [ 9%] Linking CXX executable ../bin/build_forwarder /usr/bin/ld: cannot find -lcblas /usr/bin/ld: cannot find -latlas collect2: error: ld returned 1 exit status zipHMM/CMakeFiles/build_forwarder.dir/build.make:380: recipe for target 'bin/build_forwarder' failed make[2]: * [bin/build_forwarder] Error 1 CMakeFiles/Makefile2:139: recipe for target 'zipHMM/CMakeFiles/build_forwarder.dir/all' failed make[1]: * [zipHMM/CMakeFiles/build_forwarder.dir/all] Error 2 Makefile:160: recipe for target 'all' failed make: *\ [all] Error 2
With ZIPHMM 1.0.1 [fritjof@localhost ziphmm]$ make [ 2%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/forwarder.cpp.o In file included from /home/fritjof/software/ziphmm/zipHMM/ProcessingDevice.hpp:6:0, from /home/fritjof/software/ziphmm/zipHMM/PThreadProcessingDevice.hpp:4, from /home/fritjof/software/ziphmm/zipHMM/forwarder.hpp:5, from /home/fritjof/software/ziphmm/zipHMM/forwarder.cpp:1: /home/fritjof/software/ziphmm/zipHMM/Stage2JobControl.hpp: In member function ‘size_t zipHMM::Stage2JobControl::getBlockBegin(size_t) const’: /home/fritjof/software/ziphmm/zipHMM/Stage2JobControl.hpp:35:46: error: ‘uint_least64_t’ does not name a type return static_cast(static_cast(block) * (seqLength-1) / nBlocks + 1);
^
In file included from /home/fritjof/software/ziphmm/zipHMM/ProcessingDevice.hpp:7:0,
from /home/fritjof/software/ziphmm/zipHMM/PThreadProcessingDevice.hpp:4,
from /home/fritjof/software/ziphmm/zipHMM/forwarder.hpp:5,
from /home/fritjof/software/ziphmm/zipHMM/forwarder.cpp:1:
/home/fritjof/software/ziphmm/zipHMM/MapReduceJobControl.hpp: In member function ‘size_t zipHMM::MapReduceJobControl::getBlockBegin(size_t) const’:
/home/fritjof/software/ziphmm/zipHMM/MapReduceJobControl.hpp:29:46: error: ‘uint_least64_t’ does not name a type
return static_cast(static_cast(block) * vectorLength / nBlocks);
^
zipHMM/CMakeFiles/zipHMM.dir/build.make:62: recipe for target 'zipHMM/CMakeFiles/zipHMM.dir/forwarder.cpp.o' failed
make[2]: * [zipHMM/CMakeFiles/zipHMM.dir/forwarder.cpp.o] Error 1
CMakeFiles/Makefile2:640: recipe for target 'zipHMM/CMakeFiles/zipHMM.dir/all' failed
make[1]: * [zipHMM/CMakeFiles/zipHMM.dir/all] Error 2
Makefile:160: recipe for target 'all' failed