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kamimrcht / REINDEER

REINDEER REad Index for abuNDancE quERy
GNU Affero General Public License v3.0
56 stars 6 forks source link

Installation issue #22

Open Mathiascode3 opened 7 months ago

Mathiascode3 commented 7 months ago

Hello, I have a problem during installation.

These are my version of gcc and cmake : image

I used git clone --recursive https://github.com/kamimrcht/REINDEER.git cd REINDEER sh install.sh

I have this error message : image

Maybe the problem is from make : image

I have already tried to replace all three -msse4 by -march=native -mtune=native

If someone can help me ? Thanks for your time and help

kamimrcht commented 7 months ago

Hi,

Can I ask for the full log please ?

Best

Mathiascode3 commented 7 months ago

Do you mean the full installation messages ? Or is there a specific log file ?

Thanks a lot

kamimrcht commented 7 months ago

Yes, the whole message.

Le mer. 27 mars 2024 à 13:58, MathiasCar @.***> a écrit :

Do you mean the full installation messages ? Or is there a specific log file ?

Thanks a lot

— Reply to this email directly, view it on GitHub https://github.com/kamimrcht/REINDEER/issues/22#issuecomment-2022705162, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB7M3ZBL6BYBKWGVCWF42V3Y2KX45AVCNFSM6AAAAABFKYKKIOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRSG4YDKMJWGI . You are receiving this because you commented.Message ID: @.***>

-- Camille Marchet Picy

Mathiascode3 commented 7 months ago

There it is :

(base) [m_caron@flamingo-lg-01 REINDEER]$ sh install.sh CMake Warning (dev) at CMakeLists.txt:1 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it.

-- The C compiler identification is GNU 4.8.5 -- The CXX compiler identification is GNU 4.8.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

CMake Warning (dev) at CMakeLists.txt:22 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it.

-- gatb-core is here '/mnt/nfs01/home/m_caron@intra.igr.fr/REINDEER/bcalm2/gatb-core/gatb-core' -- 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 CMake Warning (dev) at gatb-core/gatb-core/CMakeLists.txt:133 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it.

-- SSE 4.2 detected -- Options: -std=c++11 -Wno-invalid-offsetof -- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 96 128 <-- max supported kmer size without recompilation -- SOVERSION: 103.1.0 -- SOVERSION_TOOLS: 100.1.2 -- SOVERSION_CXX: 103.1.0 -- SOVERSION_F: 102.0.0 -- SOVERSION_HL: 100.1.2 -- SOVERSION_HL_CXX: 100.1.3 -- SOVERSION_HL_F: 100.0.4 -- SOVERSION_JAVA: 100.4.0 -- Looking for include file sys/file.h -- Looking for include file sys/file.h - found -- Looking for include files sys/file.h, sys/ioctl.h -- Looking for include files sys/file.h, sys/ioctl.h - found -- Looking for 3 include files sys/file.h, ..., sys/resource.h -- Looking for 3 include files sys/file.h, ..., sys/resource.h - found -- Looking for 4 include files sys/file.h, ..., sys/socket.h -- Looking for 4 include files sys/file.h, ..., sys/socket.h - found -- Looking for 5 include files sys/file.h, ..., sys/stat.h -- Looking for 5 include files sys/file.h, ..., sys/stat.h - found -- Looking for 6 include files sys/file.h, ..., sys/time.h -- Looking for 6 include files sys/file.h, ..., sys/time.h - found -- Looking for 7 include files sys/file.h, ..., sys/types.h -- Looking for 7 include files sys/file.h, ..., sys/types.h - found -- Looking for 8 include files sys/file.h, ..., features.h -- Looking for 8 include files sys/file.h, ..., features.h - found -- Looking for 9 include files sys/file.h, ..., dirent.h -- Looking for 9 include files sys/file.h, ..., dirent.h - found -- Looking for 10 include files sys/file.h, ..., setjmp.h -- Looking for 10 include files sys/file.h, ..., setjmp.h - found -- Looking for 11 include files sys/file.h, ..., stddef.h -- Looking for 11 include files sys/file.h, ..., stddef.h - found -- Looking for 12 include files sys/file.h, ..., stdint.h -- Looking for 12 include files sys/file.h, ..., stdint.h - found -- Looking for 13 include files sys/file.h, ..., unistd.h -- Looking for 13 include files sys/file.h, ..., unistd.h - found -- Looking for 14 include files sys/file.h, ..., mach/mach_time.h -- Looking for 14 include files sys/file.h, ..., mach/mach_time.h - not found -- Looking for 14 include files sys/file.h, ..., io.h -- Looking for 14 include files sys/file.h, ..., io.h - not found -- Looking for 14 include files sys/file.h, ..., winsock2.h -- Looking for 14 include files sys/file.h, ..., winsock2.h - not found -- Looking for 14 include files sys/file.h, ..., sys/timeb.h -- Looking for 14 include files sys/file.h, ..., sys/timeb.h - found -- Looking for 15 include files sys/file.h, ..., globus/common.h -- Looking for 15 include files sys/file.h, ..., globus/common.h - not found -- Looking for 15 include files sys/file.h, ..., pdb.h -- Looking for 15 include files sys/file.h, ..., pdb.h - not found -- Looking for 15 include files sys/file.h, ..., pthread.h -- Looking for 15 include files sys/file.h, ..., pthread.h - found -- Looking for 16 include files sys/file.h, ..., srbclient.h -- Looking for 16 include files sys/file.h, ..., srbclient.h - not found -- Looking for 16 include files sys/file.h, ..., string.h -- Looking for 16 include files sys/file.h, ..., string.h - found -- Looking for 17 include files sys/file.h, ..., strings.h -- Looking for 17 include files sys/file.h, ..., strings.h - found -- Looking for 18 include files sys/file.h, ..., stdlib.h -- Looking for 18 include files sys/file.h, ..., stdlib.h - found -- Looking for 19 include files sys/file.h, ..., memory.h -- Looking for 19 include files sys/file.h, ..., memory.h - found -- Looking for 20 include files sys/file.h, ..., dlfcn.h -- Looking for 20 include files sys/file.h, ..., dlfcn.h - found -- Looking for 21 include files sys/file.h, ..., inttypes.h -- Looking for 21 include files sys/file.h, ..., inttypes.h - found -- Looking for 22 include files sys/file.h, ..., netinet/in.h -- Looking for 22 include files sys/file.h, ..., netinet/in.h - found -- Looking for 23 include files sys/file.h, ..., stdbool.h -- Looking for 23 include files sys/file.h, ..., stdbool.h - found -- Looking for include file quadmath.h -- Looking for include file quadmath.h - 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 -- Performing Other Test STDC_HEADERS - Success -- Performing TEST_LFS_WORKS... yes -- Performing Other Test HAVE_OFF64_T - Success -- Looking for lseek64 -- Looking for lseek64 - found -- Looking for fseeko -- Looking for fseeko - found -- Performing Other Test HAVE_STAT64_STRUCT - Success -- 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 -- Check size of time_t -- Check size of time_t - done -- 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 fcntl -- Looking for fcntl - found -- Looking for flock -- Looking for flock - 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 llround -- Looking for llround - not found -- Looking for llroundf -- Looking for llroundf - not found -- Looking for lround -- Looking for lround - not found -- Looking for lroundf -- Looking for lroundf - not found -- Looking for lstat -- Looking for lstat - found -- Looking for pread -- Looking for pread - found -- Looking for pwrite -- Looking for pwrite - found -- Looking for rand_r -- Looking for rand_r - found -- Looking for random -- Looking for random - found -- Looking for round -- Looking for round - not found -- Looking for roundf -- Looking for roundf - not 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 strtoll -- Looking for strtoll - found -- Looking for strtoull -- Looking for strtoull - 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 HAVEINLINE - Success -- Performing Other Test HAVEINLINE__ - 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 - 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 -- Check size of float128 -- Check size of __float128 - done -- Check size of _Quad -- Check size of _Quad - failed -- 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 the cpu is power9 and cannot correctly converting long double values... no -- Checking IF alignment restrictions are strictly enforced... yes -- Warnings Configuration: -- Could NOT find ZLIB (missing: ZLIB_DIR) -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7") -- Filter ZLIB is ON -- Found Perl: /home/m_caron@intra.igr.fr/miniconda3/bin/perl (found version "5.22.2") -- Generating 'H5Epubgen.h' Generating 'H5Einit.h' Generating 'H5Eterm.h' Generating 'H5Edefin.h'

-- Generating '/home/m_caron@intra.igr.fr/REINDEER/bcalm2/gatb-core/gatb-core/thirdparty/hdf5/src/H5version.h'

-- Generating 'H5overflow.h'

CMake Warning (dev) at gatb-core/gatb-core/thirdparty/hdf5/CMakeLists.txt:748 (set): implicitly converting 'INTEGER' to 'STRING' type. This warning is for project developers. Use -Wno-dev to suppress it.

-- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found components: doxygen dot -- Configuring done (41.6s) -- Generating done (1.0s) -- Build files have been written to: /home/m_caron@intra.igr.fr/REINDEER/bcalm2/build [ 0%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5detect.dir/H5detect.c.o [ 0%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o [ 0%] Built target thirdparty_copy [ 0%] Linking C executable ../../../bin/H5make_libsettings [ 0%] Built target H5make_libsettings [ 0%] Linking C executable ../../../bin/H5detect [ 0%] Built target H5detect [ 0%] Generating ../H5lib_settings.c, ../gen_SRCS.stamp2 [ 0%] Generating ../H5Tinit.c, ../gen_SRCS.stamp1 [ 0%] Built target gen_hdf5-static [ 0%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5checksum.c.o [ 0%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5dbg.c.o [ 0%] Building 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Linking CXX static library ../lib/libgatbcore.a [ 99%] Built target gatbcore-static [ 99%] Building CXX object CMakeFiles/bcalm.dir/src/main.cpp.o [100%] Building CXX object CMakeFiles/bcalm.dir/src/bcalm_1.cpp.o [100%] Linking CXX executable bcalm [100%] Built target bcalm echo "#define VERSION \"1.4.6\"" > version.h g++ -o blight.o -c blight/blight.cpp -DNDEBUG -Ofast -flto -msse4 -fstrict-aliasing -g -g -std=c++17 -pipe -lz -fopenmp -Iblight/lz4 g++ -o utils_b.o -c blight/utils.cpp -DNDEBUG -Ofast -flto -msse4 -fstrict-aliasing -g -g -std=c++17 -pipe -lz -fopenmp -Iblight/lz4 gcc -o trlec.o -c trle/trlec.c -DNDEBUG -Ofast -flto -msse4 -fstrict-aliasing -g -w -Wall -std=gnu99 -DUSE_THREADS -fstrict-aliasing -Iext make: [blight.o] Error 1 make: Waiting for unfinished jobs.... g++ -o main.o -c main.cpp -DNDEBUG -Ofast -flto -msse4 -fstrict-aliasing -g -g -std=c++17 -pipe -lz -fopenmp -Iblight/lz4 (base) [m_caron@flamingo-lg-01 REINDEER]$