I just tried to compile bcalm today (as part of bwise) and I get this error message:
-- The C compiler identification is GNU 4.9.2
-- The CXX compiler identification is GNU 4.9.2
-- Check for working C compiler: /opt/rh/devtoolset-3/root/usr/bin/cc
-- Check for working C compiler: /opt/rh/devtoolset-3/root/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /opt/rh/devtoolset-3/root/usr/bin/c++
-- Check for working CXX compiler: /opt/rh/devtoolset-3/root/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- gatb-core is here '/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core'
-- CppUnit: found headers (in CPPUNIT_INCLUDE_DIR-NOTFOUND) but not the static library (CPPUNIT_INCLUDE_DIR-NOTFOUND/../lib/libcppunit.a)
-- CppUnit NOT FOUND
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of __uint128
-- Check size of __uint128 - failed
-- Check size of __uint128_t
-- Check size of __uint128_t - done
-- SSE 4.2 detected
-- Options: -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-format -Wno-unknown-pragmas -Wno-invalid-offsetof
-- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 128 256 512 1024 <-- max supported kmer size without recompilation
-- SOVERSION: 10.2.1
-- SOVERSION_TOOLS: 10.0.4
-- SOVERSION_CXX: 13.0.0
-- SOVERSION_F: 10.0.4
-- SOVERSION_HL: 10.1.1
-- SOVERSION_HL_CXX: 11.1.0
-- SOVERSION_HL_F: 10.0.3
-- Check for STD namespace
-- Check for STD namespace - found
-- Looking for ceil in m;
-- Looking for ceil in m; - found
-- Looking for dlopen in dl;m
-- Looking for dlopen in dl;m - found
-- Looking for WSAStartup in ws2_32;m;dl
-- Looking for WSAStartup in ws2_32;m;dl - not found
-- Looking for gethostbyname in wsock32;m;dl
-- Looking for gethostbyname in wsock32;m;dl - not found
-- Looking for gethostname in ucb;m;dl
-- Looking for gethostname in ucb;m;dl - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Performing Other Test STDC_HEADERS - Success
-- Looking for include file sys/resource.h
-- Looking for include file sys/resource.h - found
-- Looking for include files sys/resource.h, sys/time.h
-- Looking for include files sys/resource.h, sys/time.h - found
-- Looking for 3 include files sys/resource.h, ..., unistd.h
-- Looking for 3 include files sys/resource.h, ..., unistd.h - found
-- Looking for 4 include files sys/resource.h, ..., sys/ioctl.h
-- Looking for 4 include files sys/resource.h, ..., sys/ioctl.h - found
-- Looking for 5 include files sys/resource.h, ..., sys/stat.h
-- Looking for 5 include files sys/resource.h, ..., sys/stat.h - found
-- Looking for 6 include files sys/resource.h, ..., sys/socket.h
-- Looking for 6 include files sys/resource.h, ..., sys/socket.h - found
-- Looking for 7 include files sys/resource.h, ..., sys/types.h
-- Looking for 7 include files sys/resource.h, ..., sys/types.h - found
-- Looking for 8 include files sys/resource.h, ..., stddef.h
-- Looking for 8 include files sys/resource.h, ..., stddef.h - found
-- Looking for 9 include files sys/resource.h, ..., setjmp.h
-- Looking for 9 include files sys/resource.h, ..., setjmp.h - found
-- Looking for 10 include files sys/resource.h, ..., features.h
-- Looking for 10 include files sys/resource.h, ..., features.h - found
-- Looking for 11 include files sys/resource.h, ..., dirent.h
-- Looking for 11 include files sys/resource.h, ..., dirent.h - found
-- Looking for 12 include files sys/resource.h, ..., stdint.h
-- Looking for 12 include files sys/resource.h, ..., stdint.h - found
-- Looking for C++ include stdint.h
-- Looking for C++ include stdint.h - found
-- Looking for 13 include files sys/resource.h, ..., mach/mach_time.h
-- Looking for 13 include files sys/resource.h, ..., mach/mach_time.h - not found
-- Looking for 13 include files sys/resource.h, ..., io.h
-- Looking for 13 include files sys/resource.h, ..., io.h - not found
-- Looking for 13 include files sys/resource.h, ..., winsock2.h
-- Looking for 13 include files sys/resource.h, ..., winsock2.h - not found
-- Looking for 13 include files sys/resource.h, ..., sys/timeb.h
-- Looking for 13 include files sys/resource.h, ..., sys/timeb.h - found
-- Looking for 14 include files sys/resource.h, ..., globus/common.h
-- Looking for 14 include files sys/resource.h, ..., globus/common.h - not found
-- Looking for 14 include files sys/resource.h, ..., pdb.h
-- Looking for 14 include files sys/resource.h, ..., pdb.h - not found
-- Looking for 14 include files sys/resource.h, ..., pthread.h
-- Looking for 14 include files sys/resource.h, ..., pthread.h - found
-- Looking for 15 include files sys/resource.h, ..., srbclient.h
-- Looking for 15 include files sys/resource.h, ..., srbclient.h - not found
-- Looking for 15 include files sys/resource.h, ..., string.h
-- Looking for 15 include files sys/resource.h, ..., string.h - found
-- Looking for 16 include files sys/resource.h, ..., strings.h
-- Looking for 16 include files sys/resource.h, ..., strings.h - found
-- Looking for 17 include files sys/resource.h, ..., stdlib.h
-- Looking for 17 include files sys/resource.h, ..., stdlib.h - found
-- Looking for 18 include files sys/resource.h, ..., memory.h
-- Looking for 18 include files sys/resource.h, ..., memory.h - found
-- Looking for 19 include files sys/resource.h, ..., dlfcn.h
-- Looking for 19 include files sys/resource.h, ..., dlfcn.h - found
-- Looking for 20 include files sys/resource.h, ..., inttypes.h
-- Looking for 20 include files sys/resource.h, ..., inttypes.h - found
-- Looking for 21 include files sys/resource.h, ..., netinet/in.h
-- Looking for 21 include files sys/resource.h, ..., netinet/in.h - found
-- Performing TEST_LFS_WORKS... yes
-- Performing Other Test HAVE_OFF64_T - Success
-- Looking for lseek64
-- Looking for lseek64 - found
-- Looking for fseeko64
-- Looking for fseeko64 - found
-- Looking for ftello64
-- Looking for ftello64 - found
-- Looking for ftruncate64
-- Looking for ftruncate64 - found
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for ftello
-- Looking for ftello - found
-- Performing Other Test HAVE_STAT64_STRUCT - Success
-- Looking for fstat64
-- Looking for fstat64 - found
-- Looking for stat64
-- Looking for stat64 - found
-- Check size of char
-- Check size of char - done
-- Check size of short
-- Check size of short - done
-- Check size of int
-- Check size of int - done
-- Check size of unsigned
-- Check size of unsigned - done
-- Check size of long
-- Check size of long - done
-- Check size of long long
-- Check size of long long - done
-- Check size of __int64
-- Check size of __int64 - failed
-- Check size of float
-- Check size of float - done
-- Check size of double
-- Check size of double - done
-- Check size of long double
-- Check size of long double - done
-- Check size of int8_t
-- Check size of int8_t - done
-- Check size of uint8_t
-- Check size of uint8_t - done
-- Check size of int_least8_t
-- Check size of int_least8_t - done
-- Check size of uint_least8_t
-- Check size of uint_least8_t - done
-- Check size of int_fast8_t
-- Check size of int_fast8_t - done
-- Check size of uint_fast8_t
-- Check size of uint_fast8_t - done
-- Check size of int16_t
-- Check size of int16_t - done
-- Check size of uint16_t
-- Check size of uint16_t - done
-- Check size of int_least16_t
-- Check size of int_least16_t - done
-- Check size of uint_least16_t
-- Check size of uint_least16_t - done
-- Check size of int_fast16_t
-- Check size of int_fast16_t - done
-- Check size of uint_fast16_t
-- Check size of uint_fast16_t - done
-- Check size of int32_t
-- Check size of int32_t - done
-- Check size of uint32_t
-- Check size of uint32_t - done
-- Check size of int_least32_t
-- Check size of int_least32_t - done
-- Check size of uint_least32_t
-- Check size of uint_least32_t - done
-- Check size of int_fast32_t
-- Check size of int_fast32_t - done
-- Check size of uint_fast32_t
-- Check size of uint_fast32_t - done
-- Check size of int64_t
-- Check size of int64_t - done
-- Check size of uint64_t
-- Check size of uint64_t - done
-- Check size of int_least64_t
-- Check size of int_least64_t - done
-- Check size of uint_least64_t
-- Check size of uint_least64_t - done
-- Check size of int_fast64_t
-- Check size of int_fast64_t - done
-- Check size of uint_fast64_t
-- Check size of uint_fast64_t - done
-- Check size of size_t
-- Check size of size_t - done
-- Check size of ssize_t
-- Check size of ssize_t - done
-- Check size of ptrdiff_t
-- Check size of ptrdiff_t - done
-- Check size of off_t
-- Check size of off_t - done
-- Check size of off64_t
-- Check size of off64_t - done
-- Looking for 22 include files sys/resource.h, ..., stdbool.h
-- Looking for 22 include files sys/resource.h, ..., stdbool.h - found
-- Check size of _Bool
-- Check size of _Bool - done
-- Performing Other Test DEV_T_IS_SCALAR - Success
-- Looking for CLOCK_MONOTONIC
-- Looking for CLOCK_MONOTONIC - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Performing Other Test HAVE_TM_GMTOFF - Success
-- Performing Other Test HAVE___TM_GMTOFF - Failed
-- Performing Other Test HAVE_STRUCT_TIMEZONE - Success
-- Performing Other Test GETTIMEOFDAY_GIVES_TZ - Success
-- Performing Other Test TIME_WITH_SYS_TIME - Success
-- Performing Other Test HAVE_TM_ZONE - Failed
-- Performing Other Test HAVE_STRUCT_TM_TM_ZONE - Failed
-- Performing Other Test HAVE_TIMEZONE - Success
-- Performing Other Test HAVE_STAT_ST_BLOCKS - Success
-- Looking for ioctl
-- Looking for ioctl - found
-- Performing Other Test HAVE_STRUCT_VIDEOCONFIG - Failed
-- Performing Other Test HAVE_STRUCT_TEXT_INFO - Failed
-- Looking for _getvideoconfig
-- Looking for _getvideoconfig - not found
-- Looking for gettextinfo
-- Looking for gettextinfo - not found
-- Looking for scrsize
-- Looking for scrsize - not found
-- Looking for GetConsoleScreenBufferInfo
-- Looking for GetConsoleScreenBufferInfo - not found
-- Looking for TIOCGWINSZ
-- Looking for TIOCGWINSZ - found
-- Looking for TIOCGETD
-- Looking for TIOCGETD - found
-- Looking for getpwuid
-- Looking for getpwuid - found
-- Looking for alarm
-- Looking for alarm - found
-- Looking for fork
-- Looking for fork - found
-- Looking for frexpf
-- Looking for frexpf - found
-- Looking for frexpl
-- Looking for frexpl - found
-- Looking for gethostname
-- Looking for gethostname - found
-- Looking for getrusage
-- Looking for getrusage - found
-- Looking for lstat
-- Looking for lstat - found
-- Looking for rand_r
-- Looking for rand_r - found
-- Looking for random
-- Looking for random - found
-- Looking for setsysinfo
-- Looking for setsysinfo - not found
-- Looking for signal
-- Looking for signal - found
-- Looking for longjmp
-- Looking for longjmp - found
-- Looking for setjmp
-- Looking for setjmp - found
-- Looking for siglongjmp
-- Looking for siglongjmp - found
-- Looking for sigsetjmp
-- Looking for sigsetjmp - not found
-- Looking for sigprocmask
-- Looking for sigprocmask - found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for srandom
-- Looking for srandom - found
-- Looking for strdup
-- Looking for strdup - found
-- Looking for symlink
-- Looking for symlink - found
-- Looking for system
-- Looking for system - found
-- Looking for tmpfile
-- Looking for tmpfile - found
-- Looking for asprintf
-- Looking for asprintf - found
-- Looking for vasprintf
-- Looking for vasprintf - found
-- Looking for waitpid
-- Looking for waitpid - found
-- Looking for vsnprintf
-- Looking for vsnprintf - found
-- Performing Other Test VSNPRINTF_WORKS - Success
-- Looking for sigsetjmp
-- Looking for sigsetjmp - found
-- Performing Other Test HAVE_ATTRIBUTE - Success
-- Performing Other Test HAVE_C99_FUNC - Success
-- Performing Other Test HAVE_FUNCTION - Success
-- Performing Other Test HAVE_C99_DESIGNATED_INITIALIZER - Success
-- Performing Other Test SYSTEM_SCOPE_THREADS - Success
-- Performing Other Test HAVE_SOCKLEN_T - Success
-- Performing Other Test CXX_HAVE_OFFSETOF - Success
-- Performing CXX Test OLD_HEADER_FILENAME - Failed
-- Performing CXX Test H5_NO_NAMESPACE - Failed
-- Performing CXX Test H5_NO_STD - Failed
-- Performing CXX Test BOOL_NOTDEFINED - Failed
-- Performing CXX Test NO_STATIC_CAST - Failed
-- Performing Other Test HAVE_INLINE - Success
-- Performing Other Test HAVE___INLINE - Success
-- Performing Other Test HAVE___INLINE - Success
-- Checking for appropriate format for 64 bit long:
-- Checking for appropriate format for 64 bit long: found "l"
-- Looking for difftime
-- Looking for difftime - found
-- Looking for clock_gettime
-- Looking for clock_gettime - not found
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for clock_gettime in posix4
-- Looking for clock_gettime in posix4 - not found
-- Performing Other Test HAVE_DIRECT - Success
-- Checking IF your system converts long double to (unsigned) long values with special algorithm... no
-- Checking IF your system can convert (unsigned) long to long double values with special algorithm... no
-- Checking IF correctly converting long double to (unsigned) long long values... yes
-- Checking IF correctly converting (unsigned) long long to long double values... yes
-- Checking IF alignment restrictions are strictly enforced... yes
CMake Warning at gatb-core/gatb-core/thirdparty/hdf5/CMakeFilters.cmake:36 (find_package):
Could not find a package configuration file provided by "ZLIB" with any of
the following names:
ZLIBConfig.cmake
zlib-config.cmake
Add the installation prefix of "ZLIB" to CMAKE_PREFIX_PATH or set
"ZLIB_DIR" to a directory containing one of the above files. If "ZLIB"
provides a separate development package or SDK, be sure it has been
installed.
Call Stack (most recent call first):
gatb-core/gatb-core/thirdparty/hdf5/CMakeLists.txt:574 (include)
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Filter ZLIB is ON
DYNAMIC BINARIES for gatb-h5dump
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Configuring done
-- Generating done
-- Build files have been written to: /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build
Scanning dependencies of target thirdparty_copy
Scanning dependencies of target hdf5_postbuild
Scanning dependencies of target H5make_libsettings
Scanning dependencies of target H5detect
[ 0%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o
[ 0%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5detect.dir/H5detect.c.o
[ 0%] Built target thirdparty_copy
[ 1%] Linking C executable ../../../bin/H5make_libsettings
[ 1%] Built target H5make_libsettings
[ 1%] Linking C executable ../../../bin/H5detect
[ 1%] Built target H5detect
[ 1%] Generating ../H5lib_settings.c
[ 1%] Generating ../H5Tinit.c
Scanning dependencies of target hdf5
[ 1%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5.dir/H5.c.o
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[ 67%] Built target hdf5_tools
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[ 68%] Building C object ext/gatb-core/thirdparty/hdf5/tools/h5dump/CMakeFiles/gatb-h5dump.dir/h5dump.c.o
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[ 73%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o
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[ 74%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o
[ 74%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o
[ 74%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o
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[ 75%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o
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[ 75%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o
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[ 76%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o
[ 76%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o
[ 76%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o
[ 76%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o
[ 77%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o
[ 77%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o
[ 77%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o
[ 78%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o
[ 78%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o
[ 78%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o
[ 78%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemMacos.cpp.o
[ 79%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/System.cpp.o
[ 79%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/SystemInfoCommon.cpp.o
[ 79%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadLinux.cpp.o
[ 79%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadMacos.cpp.o
[ 80%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o
[ 80%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor 'gatb::core::system::impl::ThreadLinux::ThreadLinux(void* ()(void), void*)':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:51:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret = pthread_attr_init ( &tattr ) ;
^
[ 80%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o
[ 80%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o
[ 81%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o
[ 81%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o
[ 81%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o
[ 81%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o
[ 82%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o
[ 82%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o
[ 82%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o
[ 82%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o
[ 83%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o
[ 83%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o
[ 83%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o
[ 83%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o
[ 84%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o
[ 84%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o
[ 84%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_1024.cpp.o
[ 84%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o
[ 85%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_256.cpp.o
[ 85%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o
[ 85%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_512.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_1024.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 1024ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_1024.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_256.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 256ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_256.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_512.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 512ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_512.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
[ 85%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o
[ 86%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_1024.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
[ 86%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o
[ 86%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_256.cpp.o
[ 86%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o
[ 87%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_512.cpp.o
[ 87%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o
[ 87%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 1024ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 1024ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 1024ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 1024ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 1024ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<1024ul>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
[ 87%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o
[ 88%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_256.cpp.o
[ 88%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o
[ 88%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_512.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 128ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_256.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 256ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_256.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 128ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<128ul>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 256ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 256ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_256.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
[ 89%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o
[ 89%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_1024.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 32ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_256.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 256ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 256ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<256ul>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_256.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_512.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 512ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_512.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 512ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 512ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_512.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
[ 89%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o
[ 89%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_256.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 32ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_512.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 512ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 512ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<512ul>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_512.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 64ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 64ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<64ul>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
[ 90%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o
[ 90%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_512.cpp.o
[ 90%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o
[ 90%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_1024.cpp.o
[ 91%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o
[ 91%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_256.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_1024.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 1024ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_1024.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 128ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
[ 91%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_256.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 256ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_256.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 32ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
[ 91%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_512.cpp.o
[ 92%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o
[ 92%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_1024.cpp.o
[ 92%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_512.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 512ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_512.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 64ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
[ 92%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_256.cpp.o
[ 93%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o
[ 93%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_512.cpp.o
[ 93%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o
[ 93%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_1024.cpp.o
[ 94%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o
[ 94%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_256.cpp.o
[ 94%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o
[ 95%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_512.cpp.o
[ 95%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o
[ 95%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_1024.cpp.o
[ 95%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o
c++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See http://bugzilla.redhat.com/bugzilla for instructions.
make[2]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_1024.cpp.o] Error 4
make[2]: *** Waiting for unfinished jobs....
c++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See http://bugzilla.redhat.com/bugzilla for instructions.
make[2]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o] Error 4
make[1]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/all] Error 2
make: *** [all] Error 2