Install on Fedora 23

[HerefordGuy]

I was able to install ZipHMM on Fedora 23, but I had to make several changes.

First, I had to compile ATLAS from source, and make sure all of the appropriate directories were added to my path.
In the zipHMM/CMakeList.txt, I had to add "-std=c++0x" to line 22.
I had to add "#include " to MapReduceJobControl.hpp and Stage2JobControl.hpp.
I moved "#include <Python.h>" to the first line of pyZipHMM.cpp.
In lines 348 and 439 of forwarder.cpp, I had to initialize *sequences = 0.

rZipHMM still fails during make test.

[Haify]

Hello,

im using CentOS and i'm stuck at exactly the same point you are. Did you made any progress ?

[mailund]

Let me have a look at it tomorrow when I am at our cluster where we have linux machines... It is quite possible that there are some issues that I haven't looked at since Andreas left the group. I will see if I can replicate the problems and then do what I can to fix them.

[Haify]

Thank you for looking into it.
I followed this one:
#2 (comment)

I'm using zipHMM-1.1.0:

the interesting line in my zipHMM/CMakeLists.txt is:
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}-std=c++11 -Wall -Wconversion -O3 ${CMAKE_THREAD_LIBS_INIT} -fPIC")

This works without R!

But when i try to install zipHMM-1.1.0 with R then I'm running into issues:

cmake -DCMAKE_INSTALL_PREFIX=/software/hmm/1.1.0
-- CXX_FLAGS: -std=c++11 -Wall -Wconversion -O3 -lpthread -fPIC
-- Python bindings will be compiled.
-- Found LibR: /software/R/3.2.4-atlas/lib64/R
-- Found R: /software/R/3.2.4-atlas/lib64/R
-- R bindings will be compiled.
-- R include: /software/R/3.2.4-atlas/lib64/R/include
-- R library: /software/R/3.2.4-atlas/lib64/R/lib/libR.so;/software/R/3.2.4-atlas/lib64/R/lib/libRlapack.so;gfortran
-- Configuring done
-- Generating done
-- Build files have been written to: /software/sources/ziphmm/versions/zipHMM-1.1.0
✓ BWozny@bioinf-blc-15:/software/sources/ziphmm/versions/zipHMM-1.1.0$ make
Scanning dependencies of target zipHMM
[ 4%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/forwarder.cpp.o
[ 8%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/matrix.cpp.o
[ 12%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/seq_io.cpp.o
[ 16%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/hmm_io.cpp.o
[ 20%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/io_utils.cpp.o
[ 24%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/prob_spaces.cpp.o
[ 28%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/hmm_utils.cpp.o
[ 32%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/PThreadProcessingDevice.cpp.o
[ 36%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/performance_description.cpp.o
[ 40%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/posterior_decoding.cpp.o
[ 44%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/viterbi.cpp.o
[ 48%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/test_utils.cpp.o
[ 52%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/calibrate.cpp.o
[ 56%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/debug.cpp.o
Linking CXX shared library libzipHMM.so
[ 56%] Built target zipHMM
Scanning dependencies of target build_forwarder
[ 60%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/build_forwarder.cpp.o
Linking CXX executable ../bin/build_forwarder
[ 60%] Built target build_forwarder
Scanning dependencies of target calibrate
[ 64%] Building CXX object zipHMM/CMakeFiles/calibrate.dir/calibrate_main.cpp.o
Linking CXX executable ../bin/calibrate
[ 64%] Built target calibrate
Scanning dependencies of target cpp_example
[ 68%] Building CXX object zipHMM/CMakeFiles/cpp_example.dir/cpp_example.cpp.o
Linking CXX executable ../bin/cpp_example
[ 68%] Built target cpp_example
Scanning dependencies of target forward
[ 72%] Building CXX object zipHMM/CMakeFiles/forward.dir/forward.cpp.o
Linking CXX executable ../bin/forward
[ 72%] Built target forward
Scanning dependencies of target generate_01_seq
[ 76%] Building CXX object zipHMM/CMakeFiles/generate_01_seq.dir/generate_01_seq.cpp.o
Linking CXX executable ../bin/generate_01_seq
[ 76%] Built target generate_01_seq
Scanning dependencies of target generate_biased_hmm
[ 80%] Building CXX object zipHMM/CMakeFiles/generate_biased_hmm.dir/generate_biased_hmm.cpp.o
Linking CXX executable ../bin/generate_biased_hmm
[ 80%] Built target generate_biased_hmm
Scanning dependencies of target generate_hmm
[ 84%] Building CXX object zipHMM/CMakeFiles/generate_hmm.dir/generate_hmm.cpp.o
Linking CXX executable ../bin/generate_hmm
[ 84%] Built target generate_hmm
Scanning dependencies of target generate_seq
[ 88%] Building CXX object zipHMM/CMakeFiles/generate_seq.dir/generate_seq.cpp.o
Linking CXX executable ../bin/generate_seq
[ 88%] Built target generate_seq
Scanning dependencies of target pyZipHMM
[ 92%] Building CXX object zipHMM/CMakeFiles/pyZipHMM.dir/pyZipHMM.cpp.o
In file included from /usr/include/python2.7/pyconfig.h:6:0,
from /usr/include/python2.7/Python.h:8,
from /software/sources/ziphmm/versions/zipHMM-1.1.0/zipHMM/pyZipHMM.cpp:14:
/usr/include/python2.7/pyconfig-64.h:1182:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
#define _POSIX_C_SOURCE 200112L
^
In file included from /usr/include/c++/4.8.2/x86_64-redhat-linux/bits/os_defines.h:39:0,
from /usr/include/c++/4.8.2/x86_64-redhat-linux/bits/c++config.h:2097,
from /usr/include/c++/4.8.2/cmath:41,
from /software/sources/ziphmm/versions/zipHMM-1.1.0/zipHMM/prob_spaces.hpp:4,
from /software/sources/ziphmm/versions/zipHMM-1.1.0/zipHMM/matrix.hpp:4,
from /software/sources/ziphmm/versions/zipHMM-1.1.0/zipHMM/forwarder.hpp:4,
from /software/sources/ziphmm/versions/zipHMM-1.1.0/zipHMM/pyZipHMM.cpp:1:
/usr/include/features.h:168:0: note: this is the location of the previous definition

define _POSIX_C_SOURCE 200809L

^
In file included from /usr/include/python2.7/pyconfig.h:6:0,
from /usr/include/python2.7/Python.h:8,
from /software/sources/ziphmm/versions/zipHMM-1.1.0/zipHMM/pyZipHMM.cpp:14:
/usr/include/python2.7/pyconfig-64.h:1204:0: warning: "_XOPEN_SOURCE" redefined [enabled by default]
#define _XOPEN_SOURCE 600
^
In file included from /usr/include/c++/4.8.2/x86_64-redhat-linux/bits/os_defines.h:39:0,
from /usr/include/c++/4.8.2/x86_64-redhat-linux/bits/c++config.h:2097,
from /usr/include/c++/4.8.2/cmath:41,
from /software/sources/ziphmm/versions/zipHMM-1.1.0/zipHMM/prob_spaces.hpp:4,
from /software/sources/ziphmm/versions/zipHMM-1.1.0/zipHMM/matrix.hpp:4,
from /software/sources/ziphmm/versions/zipHMM-1.1.0/zipHMM/forwarder.hpp:4,
from /software/sources/ziphmm/versions/zipHMM-1.1.0/zipHMM/pyZipHMM.cpp:1:
/usr/include/features.h:170:0: note: this is the location of the previous definition

define _XOPEN_SOURCE 700

^
Linking CXX shared library libpyZipHMM.so
[ 92%] Built target pyZipHMM
Scanning dependencies of target rZipHMM
In file included from ProcessingDevice.hpp:6:0,
from PThreadProcessingDevice.hpp:4,
from forwarder.hpp:5,
from rZipHMM.cpp:3:
Stage2JobControl.hpp: In member function ‘size_t zipHMM::Stage2JobControl::getBlockBegin(size_t) const’:
Stage2JobControl.hpp:35:46: error: expected type-specifier before ‘uint_least64_t’
return static_cast<size_t>(static_cast<uint_least64_t>(block) * (seqLength-1) / nBlocks + 1);
^
Stage2JobControl.hpp:35:46: error: expected ‘>’ before ‘uint_least64_t’
Stage2JobControl.hpp:35:46: error: expected ‘(’ before ‘uint_least64_t’
Stage2JobControl.hpp:35:46: error: ‘uint_least64_t’ was not declared in this scope
Stage2JobControl.hpp:35:99: error: expected ‘)’ before ‘;’ token
return static_cast<size_t>(static_cast<uint_least64_t>(block) * (seqLength-1) / nBlocks + 1);
^
In file included from ProcessingDevice.hpp:7:0,
from PThreadProcessingDevice.hpp:4,
from forwarder.hpp:5,
from rZipHMM.cpp:3:
MapReduceJobControl.hpp: In member function ‘size_t zipHMM::MapReduceJobControl::getBlockBegin(size_t) const’:
MapReduceJobControl.hpp:29:46: error: expected type-specifier before ‘uint_least64_t’
return static_cast<size_t>(static_cast<uint_least64_t>(block) * vectorLength / nBlocks);
^
MapReduceJobControl.hpp:29:46: error: expected ‘>’ before ‘uint_least64_t’
MapReduceJobControl.hpp:29:46: error: expected ‘(’ before ‘uint_least64_t’
MapReduceJobControl.hpp:29:46: error: ‘uint_least64_t’ was not declared in this scope
MapReduceJobControl.hpp:29:94: error: expected ‘)’ before ‘;’ token
return static_cast<size_t>(static_cast<uint_least64_t>(block) * vectorLength / nBlocks);
^
make[3]: *** [rZipHMM.o] Error 1
make[2]: *** [zipHMM/CMakeFiles/rZipHMM] Error 1
make[1]: *** [zipHMM/CMakeFiles/rZipHMM.dir/all] Error 2
make: *** [all] Error 2

[mailund]

Could I get you to pull the current version and try again? I have fixed the makefile with --std=c++0x a couple of places and included and now I can compile the library, including python and R extensions, without errors or warnings on our cluster which runs CentOS.

LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: CentOS
Description: CentOS release 6.8 (Final)
Release: 6.8
Codename: Final

That is currently the only Linux system I have easy access to, but if you still have problems let me know what they are and I might be able to suggest solutions.

[Haify]

Hi Thomas,
unfortunately there is still an error. Below is the history:

cmake -DCMAKE_INSTALL_PREFIX=/software/hmm/1.1.0
-- The CXX compiler identification is GNU 4.8.5
-- The C compiler identification is GNU 4.8.5
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- CXX_FLAGS: -std=c++0x -Wall -Wconversion -O3 -lpthread
-- Found PythonLibs: /usr/lib64/libpython2.7.so (found version "2.7.5")
-- Found PythonInterp: /usr/bin/python (found version "2.7.5")
-- Python bindings will be compiled.
-- Found LibR: /software/R/3.2.4-atlas/lib64/R
-- Found R: /software/R/3.2.4-atlas/lib64/R
-- R bindings will be compiled.
-- R include: /software/R/3.2.4-atlas/lib64/R/include
-- R library: /software/R/3.2.4-atlas/lib64/R/lib/libR.so;/software/R/3.2.4-atlas/lib64/R/lib/libRlapack.so;gfortran
-- Configuring done
-- Generating done
-- Build files have been written to: /software/sources/ziphmm
✓ BWozny@bioinf-blc-15:/software/sources/ziphmm$ make
Scanning dependencies of target zipHMM
[ 4%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/forwarder.cpp.o
[ 8%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/matrix.cpp.o
[ 12%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/seq_io.cpp.o
[ 16%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/hmm_io.cpp.o
[ 20%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/io_utils.cpp.o
[ 24%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/prob_spaces.cpp.o
[ 28%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/hmm_utils.cpp.o
[ 32%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/PThreadProcessingDevice.cpp.o
[ 36%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/performance_description.cpp.o
[ 40%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/posterior_decoding.cpp.o
[ 44%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/viterbi.cpp.o
[ 48%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/test_utils.cpp.o
[ 52%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/calibrate.cpp.o
[ 56%] Building CXX object zipHMM/CMakeFiles/zipHMM.dir/debug.cpp.o
Linking CXX shared library libzipHMM.so
[ 56%] Built target zipHMM
Scanning dependencies of target build_forwarder
[ 60%] Building CXX object zipHMM/CMakeFiles/build_forwarder.dir/build_forwarder.cpp.o
Linking CXX executable ../bin/build_forwarder
[ 60%] Built target build_forwarder
Scanning dependencies of target calibrate
[ 64%] Building CXX object zipHMM/CMakeFiles/calibrate.dir/calibrate_main.cpp.o
Linking CXX executable ../bin/calibrate
[ 64%] Built target calibrate
Scanning dependencies of target cpp_example
[ 68%] Building CXX object zipHMM/CMakeFiles/cpp_example.dir/cpp_example.cpp.o
Linking CXX executable ../bin/cpp_example
[ 68%] Built target cpp_example
Scanning dependencies of target forward
[ 72%] Building CXX object zipHMM/CMakeFiles/forward.dir/forward.cpp.o
Linking CXX executable ../bin/forward
[ 72%] Built target forward
Scanning dependencies of target generate_01_seq
[ 76%] Building CXX object zipHMM/CMakeFiles/generate_01_seq.dir/generate_01_seq.cpp.o
Linking CXX executable ../bin/generate_01_seq
[ 76%] Built target generate_01_seq
Scanning dependencies of target generate_biased_hmm
[ 80%] Building CXX object zipHMM/CMakeFiles/generate_biased_hmm.dir/generate_biased_hmm.cpp.o
Linking CXX executable ../bin/generate_biased_hmm
[ 80%] Built target generate_biased_hmm
Scanning dependencies of target generate_hmm
[ 84%] Building CXX object zipHMM/CMakeFiles/generate_hmm.dir/generate_hmm.cpp.o
Linking CXX executable ../bin/generate_hmm
[ 84%] Built target generate_hmm
Scanning dependencies of target generate_seq
[ 88%] Building CXX object zipHMM/CMakeFiles/generate_seq.dir/generate_seq.cpp.o
Linking CXX executable ../bin/generate_seq
[ 88%] Built target generate_seq
Scanning dependencies of target pyZipHMM
[ 92%] Building CXX object zipHMM/CMakeFiles/pyZipHMM.dir/pyZipHMM.cpp.o
Linking CXX shared library libpyZipHMM.so
[ 92%] Built target pyZipHMM
Scanning dependencies of target rZipHMM
In file included from /usr/include/c++/4.8.2/cstdint:35:0,
from Stage2JobControl.hpp:7,
from ProcessingDevice.hpp:6,
from PThreadProcessingDevice.hpp:4,
from forwarder.hpp:5,
from rZipHMM.cpp:3:
/usr/include/c++/4.8.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
#error This file requires compiler and library support for the
^
In file included from ProcessingDevice.hpp:6:0,
from PThreadProcessingDevice.hpp:4,
from forwarder.hpp:5,
from rZipHMM.cpp:3:
Stage2JobControl.hpp: In member function ‘size_t zipHMM::Stage2JobControl::getBlockBegin(size_t) const’:
Stage2JobControl.hpp:36:46: error: expected type-specifier before ‘uint_least64_t’
return static_cast<size_t>(static_cast<uint_least64_t>(block) * (seqLength-1) / nBlocks + 1);
^
Stage2JobControl.hpp:36:46: error: expected ‘>’ before ‘uint_least64_t’
Stage2JobControl.hpp:36:46: error: expected ‘(’ before ‘uint_least64_t’
Stage2JobControl.hpp:36:46: error: ‘uint_least64_t’ was not declared in this scope
Stage2JobControl.hpp:36:99: error: expected ‘)’ before ‘;’ token
return static_cast<size_t>(static_cast<uint_least64_t>(block) * (seqLength-1) / nBlocks + 1);
^
In file included from ProcessingDevice.hpp:7:0,
from PThreadProcessingDevice.hpp:4,
from forwarder.hpp:5,
from rZipHMM.cpp:3:
MapReduceJobControl.hpp: In member function ‘size_t zipHMM::MapReduceJobControl::getBlockBegin(size_t) const’:
MapReduceJobControl.hpp:29:46: error: expected type-specifier before ‘uint_least64_t’
return static_cast<size_t>(static_cast<uint_least64_t>(block) * vectorLength / nBlocks);
^
MapReduceJobControl.hpp:29:46: error: expected ‘>’ before ‘uint_least64_t’
MapReduceJobControl.hpp:29:46: error: expected ‘(’ before ‘uint_least64_t’
MapReduceJobControl.hpp:29:46: error: ‘uint_least64_t’ was not declared in this scope
MapReduceJobControl.hpp:29:94: error: expected ‘)’ before ‘;’ token
return static_cast<size_t>(static_cast<uint_least64_t>(block) * vectorLength / nBlocks);
^
make[3]: *** [rZipHMM.o] Error 1
make[2]: *** [zipHMM/CMakeFiles/rZipHMM] Error 1
make[1]: *** [zipHMM/CMakeFiles/rZipHMM.dir/all] Error 2
make: *** [all] Error 2

[mailund]

This looks like the exact errors I just fixed. Can you check if there is an

#include

in Stage2JobControl.hpp? That is where the uint_least64_t type is defined.

[Haify]

The include is in there.

more Stage2JobControl.hpp
include "debug.hpp"

#include
#include

.....

[mailund]

Ok, I will have a look at it again tomorrow.

[mailund]

Since I cannot replicate this, it is hard to test, but I suspect it is the -std=c++0x/c++11 flag that is the problem and that is compiler version dependent. I have tried setting it in the CMakeList.txt file and tested it on both an older and a newer version of gcc. Please let me know if this fixes the problem.

[Haify]

The errors are still the same.

I agree that the -std=c++0x/c++11 is most likely the problem. my question about the order of -std=c++0x/c++11 and -fPIC might help me to solve this:

for me it looks like the linking process could somehow not work

Below is the version number of my c-compiler: and after it a grep for the -fPIC

Do you have similar Options ( -fPIC and -std=c++11 in different order?? )

gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
----------------------------------------------------grep--------------------------------------------------------
✓ BWozny@bioinf-blc-15:/software/sources/ziphmm$ grep -i -r "-fPIC" *
zipHMM/CMakeFiles/pyZipHMM.dir/link.txt:/usr/bin/c++ -fPIC -std=c++11 -Wall -Wconversion -O3 -lpthread -shared -Wl,-soname,libpyZipHMM.so -o libpyZipHMM.so CMakeFiles/pyZipHMM.dir/pyZipHMM.cpp.o -L/software/atlas/3.10.3-shared/lib -lpython2.7 libzipHMM.so -lpython2.7 -lrt -lcblas -latlas -Wl,-rpath,/software/atlas/3.10.3-shared/lib:/software/sources/ziphmm/zipHMM
zipHMM/CMakeFiles/pyZipHMM.dir/flags.make:CXX_FLAGS = -std=c++11 -Wall -Wconversion -O3 -lpthread -fPIC -I/software/sources/ziphmm -I/software/atlas/3.10.3-shared/include -I/usr/include/python2.7 -I/software/R/3.2.4-atlas/lib64/R/include
zipHMM/CMakeFiles/zipHMM.dir/flags.make:CXX_FLAGS = -std=c++11 -Wall -Wconversion -O3 -lpthread -fPIC -I/software/sources/ziphmm -I/software/atlas/3.10.3-shared/include -I/usr/include/python2.7 -I/software/R/3.2.4-atlas/lib64/R/include
zipHMM/CMakeFiles/zipHMM.dir/link.txt:/usr/bin/c++ -fPIC -std=c++11 -Wall -Wconversion -O3 -lpthread -shared -Wl,-soname,libzipHMM.so -o libzipHMM.so CMakeFiles/zipHMM.dir/forwarder.cpp.o CMakeFiles/zipHMM.dir/matrix.cpp.o CMakeFiles/zipHMM.dir/seq_io.cpp.o CMakeFiles/zipHMM.dir/hmm_io.cpp.o CMakeFiles/zipHMM.dir/io_utils.cpp.o CMakeFiles/zipHMM.dir/prob_spaces.cpp.o CMakeFiles/zipHMM.dir/hmm_utils.cpp.o CMakeFiles/zipHMM.dir/PThreadProcessingDevice.cpp.o CMakeFiles/zipHMM.dir/performance_description.cpp.o CMakeFiles/zipHMM.dir/posterior_decoding.cpp.o CMakeFiles/zipHMM.dir/viterbi.cpp.o CMakeFiles/zipHMM.dir/test_utils.cpp.o CMakeFiles/zipHMM.dir/calibrate.cpp.o CMakeFiles/zipHMM.dir/debug.cpp.o -L/software/atlas/3.10.3-shared/lib -lrt -lcblas -latlas -Wl,-rpath,/software/atlas/3.10.3-shared/lib:
✓ BWozny@bioinf-blc-15:/software/sources/ziphmm$ grep -i -r "-std=c++11"
zipHMM/CMakeLists.txt: # but after we need -std=c++11
zipHMM/CMakeLists.txt: set(CPP_STD_FLAG "-std=c++11")
zipHMM/CMakeFiles/pyZipHMM.dir/link.txt:/usr/bin/c++ -fPIC -std=c++11 -Wall -Wconversion -O3 -lpthread -shared -Wl,-soname,libpyZipHMM.so -o libpyZipHMM.so CMakeFiles/pyZipHMM.dir/pyZipHMM.cpp.o -L/software/atlas/3.10.3-shared/lib -lpython2.7 libzipHMM.so -lpython2.7 -lrt -lcblas -latlas -Wl,-rpath,/software/atlas/3.10.3-shared/lib:/software/sources/ziphmm/zipHMM
zipHMM/CMakeFiles/pyZipHMM.dir/flags.make:CXX_FLAGS = -std=c++11 -Wall -Wconversion -O3 -lpthread -fPIC -I/software/sources/ziphmm -I/software/atlas/3.10.3-shared/include -I/usr/include/python2.7 -I/software/R/3.2.4-atlas/lib64/R/include
zipHMM/CMakeFiles/calibrate.dir/flags.make:CXX_FLAGS = -std=c++11 -Wall -Wconversion -O3 -lpthread -I/software/sources/ziphmm -I/software/atlas/3.10.3-shared/include -I/usr/include/python2.7 -I/software/R/3.2.4-atlas/lib64/R/include
zipHMM/CMakeFiles/calibrate.dir/link.txt:/usr/bin/c++ -std=c++11 -Wall -Wconversion -O3 -lpthread CMakeFiles/calibrate.dir/calibrate_main.cpp.o -o ../bin/calibrate -L/software/atlas/3.10.3-shared/lib -rdynamic -lpython2.7 -lrt -lcblas -latlas libzipHMM.so -lrt -lcblas -latlas -Wl,-rpath,/software/atlas/3.10.3-shared/lib:/software/sources/ziphmm/zipHMM:
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