I tried to install GAPipeline-1.5.0 in my desktop (64-bit linux Ubuntu 9.10). I have installed all prerequisites, and still got the following errors. Basically, the first error is "‘uint64_t’ was not declared in this scope" Does someone know how to fix it? Thanks.
The command I used is:
sudo make install WITH_IO_LIB=1
====== screen message ======
CPATH=: LIBRARY_PATH=: ./validate.sh --prereqs
Checking for prerequisites
Prerequisites OK (no further validation requested)
make --directory opt cmake
make[1]: Entering directory `/share/apps/GAPipeline/opt'
PATH=/share/apps/GAPipeline/opt/bin:$PATH bootstrap/bootstrap.sh cmake
cmake version "cmake version 2.6-patch 2" is already installed
nothing to be done
make[1]: Leaving directory `/share/apps/GAPipeline/opt'
cd build && PATH=/share/apps/GAPipeline/opt/bin:$PATH LIB=: cmake ..
-- Found PTHREAD header: /usr/include/pthread.h
-- Found PTHREAD library: /usr/lib/libpthread.so
-- Found ZLIB header: /usr/include/zlib.h
-- Found ZLIB library: /usr/lib/libz.so
-- gzip compression supported
-- Found BZIP2 header: /usr/include/bzlib.h
-- Found BZIP2 library: /usr/lib/libbz2.so
-- bzip2 compression supported
-- Found FFTW3F header: /usr/include/fftw3.h
-- Found FFTW3F library: /usr/lib/libfftw3f.so
-- Using FFTW header: /usr/include/fftw3.h
-- Using FFTW library: /usr/lib/libfftw3f.so
-- mkl_emt64 library: MKL_EM64T_LIBRARY-NOTFOUND
-- guide library: GUIDE_LIBRARY-NOTFOUND
-- Found CPPUNIT header: /usr/include/cppunit/Test.h
-- Found CPPUNIT library: /usr/lib/libcppunit.so
-- using compiler: gcc version 4.4.1
-- C++ unit testing with CPPUNIT: /usr/lib/libcppunit.so
-- Adding subdirectory: unittest
-- Adding the c++ library subdirectory: common
-- Adding the cppunit subdirectory for common
-- Adding the data subdirectory for the cppunits under common
-- Adding the c++ library subdirectory: imaging
-- Adding the c++ library subdirectory: basecalling
-- Adding the cppunit subdirectory for basecalling
-- Adding the c++ library subdirectory: qcalibration
-- Adding the cppunit subdirectory for qcalibration
-- Adding the data subdirectory for the cppunits under qcalibration
-- Adding the c++ library subdirectory: statistics
-- Adding the cppunit subdirectory for statistics
-- Adding the c++ library subdirectory: alignment
-- Adding the cppunit subdirectory for alignment
-- Adding the data subdirectory for the cppunits under alignment
-- Adding the c++ library subdirectory: legacy
-- Adding the c++ program subdirectory: programs
-- Looking for doxygen...
-- Looking for doxygen... - found /usr/bin/doxygen
-- Looking for dot tool...
-- Looking for dot tool... - NOT found
-- Doxygen: /usr/bin/doxygen. Dot: DOXYGEN_DOT_EXECUTABLE-NOTFOUND.
-- Creating Doxygen config file: /share/apps/GAPipeline/build/c++/Doxyfile
-- Adding the python program subdirectory: setup
-- Adding the python program subdirectory: imaging
-- Adding the python modules subdirectory: lib
-- Adding the pyunit test subdirectory: python/pyunit/lib
-- Adding the perl program subdirectory: setup
-- Adding the perl program subdirectory: alignment
-- Adding the perl program subdirectory: statistics
-- Adding the perl program subdirectory: legacy
-- Adding the black box tests:
-- Adding the black box tests:
-- Configuring done
-- Generating done
-- Build files have been written to: /share/apps/GAPipeline/build
make --directory opt install_io_lib
make[1]: Entering directory `/share/apps/GAPipeline/opt'
make --directory io_lib
make[2]: Entering directory `/share/apps/GAPipeline/opt/io_lib'
make all-recursive
make[3]: Entering directory `/share/apps/GAPipeline/opt/io_lib'
Making all in io_lib
make[4]: Entering directory `/share/apps/GAPipeline/opt/io_lib/io_lib'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/share/apps/GAPipeline/opt/io_lib/io_lib'
Making all in progs
make[4]: Entering directory `/share/apps/GAPipeline/opt/io_lib/progs'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/share/apps/GAPipeline/opt/io_lib/progs'
Making all in tests
make[4]: Entering directory `/share/apps/GAPipeline/opt/io_lib/tests'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/share/apps/GAPipeline/opt/io_lib/tests'
make[4]: Entering directory `/share/apps/GAPipeline/opt/io_lib'
make[4]: Leaving directory `/share/apps/GAPipeline/opt/io_lib'
make[3]: Leaving directory `/share/apps/GAPipeline/opt/io_lib'
make[2]: Leaving directory `/share/apps/GAPipeline/opt/io_lib'
cp io_lib/progs/illumina2srf /share/apps/GAPipeline/bin
cp io_lib/progs/srf2illumina /share/apps/GAPipeline/bin
make[1]: Leaving directory `/share/apps/GAPipeline/opt'
make --directory build install
make[1]: Entering directory `/share/apps/GAPipeline/build'
make[2]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 0%] Built target ga_cppunit
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 11%] Built target ga_common
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 14%] Built target common_cppunitTest
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 14%] Built target common_data
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 15%] Built target common_passed
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 24%] Built target ga_imaging
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 31%] Built target ga_basecalling
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 32%] Built target basecalling_cppunitTest
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 32%] Built target basecalling_passed
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 37%] Built target ga_qcalibration
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 38%] Built target qcalibration_cppunitTest
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 38%] Built target qcalibration_data
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 39%] Built target qcalibration_passed
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
make[3]: Entering directory `/share/apps/GAPipeline/build'
[ 39%] Building CXX object c++/statistics/CMakeFiles/ga_statistics.dir/Quality_Value_Stats_Set.cpp.o
In file included from /share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:14:
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:33: error: ‘uint64_t’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:33: error: template argument 2 is invalid
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:33: error: template argument 4 is invalid
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:34: error: typedef name may not be a nested-name-specifier
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:34: error: expected ‘;’ before ‘Qual_Val_Freq_Map_CIter’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:35: error: typedef name may not be a nested-name-specifier
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:35: error: expected ‘;’ before ‘Qual_Val_Freq_Map_CRIter’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:39: error: ‘uint64_t’ does not name a type
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp: In constructor ‘Quality_Value_Stats_Set::Quality_Value_Stats_Set()’:
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:19: error: class ‘Quality_Value_Stats_Set’ does not have any field named ‘my_num_bases’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp: In member function ‘void Quality_Value_Stats_Set::add_read_align_info(const Read_Align_Info&)’:
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:59: error: ‘my_num_bases’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:62: error: invalid types ‘int[const int]’ for array subscript
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:65: error: invalid types ‘int[const int]’ for array subscript
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp: In function ‘std:stream& operator<<(std:stream&, const Quality_Value_Stats_Set&)’:
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:89: error: expected initializer before ‘&’ token
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:90: error: ‘uint64_t’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:90: error: expected ‘;’ before ‘cum_freq’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:91: error: expected ‘;’ before ‘cum_err_count’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:93: error: ‘Qual_Val_Freq_Map_CRIter’ is not a member of ‘Quality_Value_Stats_Set’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:94: error: expected ‘;’ before ‘pair_citer’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:95: error: ‘pair_citer’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:95: error: request for member ‘rend’ in ‘qual_val_freq_map’, which is of non-class type ‘const int’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:99: error: ‘uint64_t’ does not name a type
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:102: error: ‘Qual_Val_Freq_Map_CIter’ is not a member of ‘Quality_Value_Stats_Set’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:103: error: expected ‘;’ before ‘err_pair_citer’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:104: error: ‘uint64_t’ does not name a type
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:109: error: ‘cum_freq’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:109: error: ‘curr_freq’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:110: error: ‘cum_err_count’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:110: error: ‘curr_err_count’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:117: error: ‘num_bases’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:86: warning: unused variable ‘errs_by_qual_val_freq_map’
make[3]: *** [c++/statistics/CMakeFiles/ga_statistics.dir/Quality_Value_Stats_Set.cpp.o] Error 1
make[3]: Leaving directory `/share/apps/GAPipeline/build'
make[2]: *** [c++/statistics/CMakeFiles/ga_statistics.dir/all] Error 2
make[2]: Leaving directory `/share/apps/GAPipeline/build'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/share/apps/GAPipeline/build'
make: *** [install] Error 2
The command I used is:
sudo make install WITH_IO_LIB=1
====== screen message ======
CPATH=: LIBRARY_PATH=: ./validate.sh --prereqs
Checking for prerequisites
Prerequisites OK (no further validation requested)
make --directory opt cmake
make[1]: Entering directory `/share/apps/GAPipeline/opt'
PATH=/share/apps/GAPipeline/opt/bin:$PATH bootstrap/bootstrap.sh cmake
cmake version "cmake version 2.6-patch 2" is already installed
nothing to be done
make[1]: Leaving directory `/share/apps/GAPipeline/opt'
cd build && PATH=/share/apps/GAPipeline/opt/bin:$PATH LIB=: cmake ..
-- Found PTHREAD header: /usr/include/pthread.h
-- Found PTHREAD library: /usr/lib/libpthread.so
-- Found ZLIB header: /usr/include/zlib.h
-- Found ZLIB library: /usr/lib/libz.so
-- gzip compression supported
-- Found BZIP2 header: /usr/include/bzlib.h
-- Found BZIP2 library: /usr/lib/libbz2.so
-- bzip2 compression supported
-- Found FFTW3F header: /usr/include/fftw3.h
-- Found FFTW3F library: /usr/lib/libfftw3f.so
-- Using FFTW header: /usr/include/fftw3.h
-- Using FFTW library: /usr/lib/libfftw3f.so
-- mkl_emt64 library: MKL_EM64T_LIBRARY-NOTFOUND
-- guide library: GUIDE_LIBRARY-NOTFOUND
-- Found CPPUNIT header: /usr/include/cppunit/Test.h
-- Found CPPUNIT library: /usr/lib/libcppunit.so
-- using compiler: gcc version 4.4.1
-- C++ unit testing with CPPUNIT: /usr/lib/libcppunit.so
-- Adding subdirectory: unittest
-- Adding the c++ library subdirectory: common
-- Adding the cppunit subdirectory for common
-- Adding the data subdirectory for the cppunits under common
-- Adding the c++ library subdirectory: imaging
-- Adding the c++ library subdirectory: basecalling
-- Adding the cppunit subdirectory for basecalling
-- Adding the c++ library subdirectory: qcalibration
-- Adding the cppunit subdirectory for qcalibration
-- Adding the data subdirectory for the cppunits under qcalibration
-- Adding the c++ library subdirectory: statistics
-- Adding the cppunit subdirectory for statistics
-- Adding the c++ library subdirectory: alignment
-- Adding the cppunit subdirectory for alignment
-- Adding the data subdirectory for the cppunits under alignment
-- Adding the c++ library subdirectory: legacy
-- Adding the c++ program subdirectory: programs
-- Looking for doxygen...
-- Looking for doxygen... - found /usr/bin/doxygen
-- Looking for dot tool...
-- Looking for dot tool... - NOT found
-- Doxygen: /usr/bin/doxygen. Dot: DOXYGEN_DOT_EXECUTABLE-NOTFOUND.
-- Creating Doxygen config file: /share/apps/GAPipeline/build/c++/Doxyfile
-- Adding the python program subdirectory: setup
-- Adding the python program subdirectory: imaging
-- Adding the python modules subdirectory: lib
-- Adding the pyunit test subdirectory: python/pyunit/lib
-- Adding the perl program subdirectory: setup
-- Adding the perl program subdirectory: alignment
-- Adding the perl program subdirectory: statistics
-- Adding the perl program subdirectory: legacy
-- Adding the black box tests:
-- Adding the black box tests:
-- Configuring done
-- Generating done
-- Build files have been written to: /share/apps/GAPipeline/build
make --directory opt install_io_lib
make[1]: Entering directory `/share/apps/GAPipeline/opt'
make --directory io_lib
make[2]: Entering directory `/share/apps/GAPipeline/opt/io_lib'
make all-recursive
make[3]: Entering directory `/share/apps/GAPipeline/opt/io_lib'
Making all in io_lib
make[4]: Entering directory `/share/apps/GAPipeline/opt/io_lib/io_lib'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/share/apps/GAPipeline/opt/io_lib/io_lib'
Making all in progs
make[4]: Entering directory `/share/apps/GAPipeline/opt/io_lib/progs'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/share/apps/GAPipeline/opt/io_lib/progs'
Making all in tests
make[4]: Entering directory `/share/apps/GAPipeline/opt/io_lib/tests'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/share/apps/GAPipeline/opt/io_lib/tests'
make[4]: Entering directory `/share/apps/GAPipeline/opt/io_lib'
make[4]: Leaving directory `/share/apps/GAPipeline/opt/io_lib'
make[3]: Leaving directory `/share/apps/GAPipeline/opt/io_lib'
make[2]: Leaving directory `/share/apps/GAPipeline/opt/io_lib'
cp io_lib/progs/illumina2srf /share/apps/GAPipeline/bin
cp io_lib/progs/srf2illumina /share/apps/GAPipeline/bin
make[1]: Leaving directory `/share/apps/GAPipeline/opt'
make --directory build install
make[1]: Entering directory `/share/apps/GAPipeline/build'
make[2]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 0%] Built target ga_cppunit
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 11%] Built target ga_common
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 14%] Built target common_cppunitTest
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 14%] Built target common_data
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 15%] Built target common_passed
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 24%] Built target ga_imaging
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 31%] Built target ga_basecalling
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 32%] Built target basecalling_cppunitTest
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 32%] Built target basecalling_passed
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 37%] Built target ga_qcalibration
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 38%] Built target qcalibration_cppunitTest
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 38%] Built target qcalibration_data
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
[ 39%] Built target qcalibration_passed
make[3]: Entering directory `/share/apps/GAPipeline/build'
make[3]: Leaving directory `/share/apps/GAPipeline/build'
make[3]: Entering directory `/share/apps/GAPipeline/build'
[ 39%] Building CXX object c++/statistics/CMakeFiles/ga_statistics.dir/Quality_Value_Stats_Set.cpp.o
In file included from /share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:14:
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:33: error: ‘uint64_t’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:33: error: template argument 2 is invalid
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:33: error: template argument 4 is invalid
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:34: error: typedef name may not be a nested-name-specifier
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:34: error: expected ‘;’ before ‘Qual_Val_Freq_Map_CIter’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:35: error: typedef name may not be a nested-name-specifier
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:35: error: expected ‘;’ before ‘Qual_Val_Freq_Map_CRIter’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.h:39: error: ‘uint64_t’ does not name a type
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp: In constructor ‘Quality_Value_Stats_Set::Quality_Value_Stats_Set()’:
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:19: error: class ‘Quality_Value_Stats_Set’ does not have any field named ‘my_num_bases’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp: In member function ‘void Quality_Value_Stats_Set::add_read_align_info(const Read_Align_Info&)’:
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:59: error: ‘my_num_bases’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:62: error: invalid types ‘int[const int]’ for array subscript
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:65: error: invalid types ‘int[const int]’ for array subscript
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp: In function ‘std:stream& operator<<(std:stream&, const Quality_Value_Stats_Set&)’:
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:89: error: expected initializer before ‘&’ token
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:90: error: ‘uint64_t’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:90: error: expected ‘;’ before ‘cum_freq’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:91: error: expected ‘;’ before ‘cum_err_count’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:93: error: ‘Qual_Val_Freq_Map_CRIter’ is not a member of ‘Quality_Value_Stats_Set’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:94: error: expected ‘;’ before ‘pair_citer’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:95: error: ‘pair_citer’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:95: error: request for member ‘rend’ in ‘qual_val_freq_map’, which is of non-class type ‘const int’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:99: error: ‘uint64_t’ does not name a type
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:102: error: ‘Qual_Val_Freq_Map_CIter’ is not a member of ‘Quality_Value_Stats_Set’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:103: error: expected ‘;’ before ‘err_pair_citer’
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:104: error: ‘uint64_t’ does not name a type
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:109: error: ‘cum_freq’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:109: error: ‘curr_freq’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:110: error: ‘cum_err_count’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:110: error: ‘curr_err_count’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:117: error: ‘num_bases’ was not declared in this scope
/share/apps/GAPipeline/c++/statistics/Quality_Value_Stats_Set.cpp:86: warning: unused variable ‘errs_by_qual_val_freq_map’
make[3]: *** [c++/statistics/CMakeFiles/ga_statistics.dir/Quality_Value_Stats_Set.cpp.o] Error 1
make[3]: Leaving directory `/share/apps/GAPipeline/build'
make[2]: *** [c++/statistics/CMakeFiles/ga_statistics.dir/all] Error 2
make[2]: Leaving directory `/share/apps/GAPipeline/build'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/share/apps/GAPipeline/build'
make: *** [install] Error 2
Comment