D: [iurt_root_command] chroot Installing /home/iurt/rpmbuild/SRPMS/gmt-6.1.0-2.mga8.src.rpm Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.ItAy8s + umask 022 + cd /home/iurt/rpmbuild/BUILD + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + cd /home/iurt/rpmbuild/BUILD + rm -rf gmt-6.1.0 + /usr/bin/xz -dc /home/iurt/rpmbuild/SOURCES/gmt-6.1.0-src.tar.xz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd gmt-6.1.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.iLFb5r + umask 022 + cd /home/iurt/rpmbuild/BUILD + cd gmt-6.1.0 + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + export 'CFLAGS=-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fstrict-aliasing' + CFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fstrict-aliasing' + CFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fstrict-aliasing' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables ' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables ' + export FCFLAGS + LDFLAGS=' -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags' + export LDFLAGS + /usr/bin/cmake -Wno-dev -S . -B build -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_LIBDIR:PATH=/usr/lib64 -DCMAKE_INSTALL_LIBEXECDIR:PATH=/usr/libexec -DCMAKE_INSTALL_RUNSTATEDIR:PATH=/run -DCMAKE_INSTALL_SYSCONFDIR:PATH=/etc -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-DNDEBUG -DCMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-DNDEBUG -DLIB_SUFFIX=64 -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON '-DCMAKE_MODULE_LINKER_FLAGS=-Wl,--as-needed -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags' -DBUILD_SHARED_LIBS:BOOL=ON -DBUILD_STATIC_LIBS:BOOL=OFF -DGMT_MANDIR=share/man -DBASH_COMPLETION_DIR=/usr/share/bash-completion/completions -DDCW_PATH=/usr/share/gmt/dcw -DGSHHG_PATH=/usr/share/gmt/gshhg -DGMT_INSTALL_MODULE_LINKS=OFF -DGMT_INSTALL_TRADITIONAL_FOLDERNAMES=OFF -DGMT_ENABLE_OPENMP=BOOL:ON -DGMT_USE_THREADS=BOOL:ON -DLICENSE_RESTRICTED=LGPL CMake version: 3.18.4 -- The C compiler identification is GNU 10.2.0 -- 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 -- Found UnixCommands: /usr/bin/bash -- Could NOT find Git (missing: GIT_EXECUTABLE) -- Searching dependent libraries. This may take a few minutes... -- Looking for nc_def_var_deflate -- Looking for nc_def_var_deflate - found -- Found NETCDF: /usr/lib64/libnetcdf.so -- Found CURL: /usr/lib64/libcurl.so (found version "7.72.0") -- Found GDAL: /usr/lib64/libgdal.so -- Found GEOS: /usr/lib64/libgeos_c.so (3.8.1) -- Found PCRE: /usr/lib64/libpcre.so -- Looking for fftwf_plan_with_nthreads in /usr/lib64/libfftw3f.so -- Looking for fftwf_plan_with_nthreads in /usr/lib64/libfftw3f.so - not found -- Looking for fftwf_import_wisdom_from_filename -- Looking for fftwf_import_wisdom_from_filename - found -- Found FFTW3: /usr/lib64/libfftw3f.so -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib64/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "1.7.3") -- Found GLIB: /usr/include/glib-2.0;/usr/lib64/glib-2.0/include (found version "2.66.1") CMake Error at cmake/modules/FindGSHHG.cmake:69 (message): Cannot determine GSHHG version: Change Dir: /home/iurt/rpmbuild/BUILD/gmt-6.1.0/build/CMakeTmp/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/gmake cmTC_c9699/fast && /usr/bin/gmake -f CMakeFiles/cmTC_c9699.dir/build.make CMakeFiles/cmTC_c9699.dir/build gmake[1]: Entering directory '/home/iurt/rpmbuild/BUILD/gmt-6.1.0/build/CMakeTmp/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_c9699.dir/gshhg_version.c.o /usr/bin/cc -DSTANDALONE -std=gnu99 -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fstrict-aliasing -fopenmp -o CMakeFiles/cmTC_c9699.dir/gshhg_version.c.o -c /home/iurt/rpmbuild/BUILD/gmt-6.1.0/src/gshhg_version.c Linking C executable cmTC_c9699 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_c9699.dir/link.txt --verbose=1 /usr/bin/cc -std=gnu99 -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -fstrict-aliasing -fopenmp -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags -rdynamic CMakeFiles/cmTC_c9699.dir/gshhg_version.c.o -o cmTC_c9699 /usr/lib64/libnetcdf.so gmake[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/gmt-6.1.0/build/CMakeTmp/CMakeFiles/CMakeTmp' Warning! ***HDF5 library version mismatched error*** The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.10.6, library is 1.10.7 SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.10.7 Configured on: Tue Oct 13 14:37:45 UTC 2020 Configured by: iurt@ec2x2.mageia.org Host system: x86_64-mageia-linux-gnu Uname information: Linux ec2x2.mageia.org 5.6.8-server-1.mga7 #1 SMP Thu Apr 30 06:46:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Byte sex: little-endian Installation point: /usr Compiling Options: ------------------ Build Mode: production Debugging Symbols: no Asserts: no Profiling: no Optimization Level: high Linking Options: ---------------- Libraries: static, shared Statically Linked Executables: LDFLAGS: -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-O1 -Wl,--build-id -Wl,--enable-new-dtags H5_LDFLAGS: AM_LDFLAGS: Extra libraries: -lz -ldl -lm Archiver: ar AR_FLAGS: cr Ranlib: x86_64-mageia-linux-gnu-ranlib Languages: ---------- C: yes C Compiler: /usr/bin/gcc CPPFLAGS: H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: C Flags: -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables H5 C Flags: -std=c99 -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-c++-compat -Wno-format-nonliteral -Wshadow -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3 -Werror=bad-function-cast -Werror=declaration-after-statement -Werror=implicit-function-declaration -Werror=missing-declarations -Werror=missing-prototypes -Werror=nested-externs -Werror=old-style-definition -Werror=packed -Werror=pointer-sign -Werror=pointer-to-int-cast -Werror=redundant-decls -Werror=strict-prototypes -Werror=switch -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wunused-but-set-variable -Wformat -Werror=incompatible-pointer-types -Werror=shadow -Wcast-function-type -Wmaybe-uninitialized AM C Flags: Shared C Library: yes Static C Library: yes Fortran: yes Fortran Compiler: /usr/bin/gfortran Fortran Flags: -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables H5 Fortran Flags: -std=f2008 -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -Warray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Wuse-without-only -Winteger-division -Wfrontend-loop-interchange -s -O3 AM Fortran Flags: Shared Fortran Library: yes Static Fortran Library: yes C++: yes C++ Compiler: /usr/bin/g++ C++ Flags: -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables H5 C++ Flags: -Wall -Wcast-qual -Wconversion -Wctor-dtor-privacy -Weffc++ -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-format-nonliteral -Wnon-virtual-dtor -Wold-style-cast -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -O3 -Wcast-align -Wmissing-declarations -Werror=packed -Werror=redundant-decls -Werror=switch -Wunused-but-set-variable -Werror=unused-function -Werror=unused-variable -Wunused-parameter -Werror=shadow AM C++ Flags: Shared C++ Library: yes Static C++ Library: yes Java: no Features: --------- Parallel HDF5: no Parallel Filtered Dataset Writes: no Large Parallel I/O: no High-level library: yes Build HDF5 Tests: yes Build HDF5 Tools: yes Threadsafety: no Default API mapping: v110 With deprecated public symbols: yes I/O filters (external): deflate(zlib) MPE: no Direct VFD: no Mirror VFD: no (Read-Only) S3 VFD: no (Read-Only) HDFS VFD: no dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: no Memory allocation sanity checks: no Function stack tracing: no Use file locking: best-effort Strict file format checks: no Optimization instrumentation: no Bye... Child aborted Call Stack (most recent call first): src/CMakeLists.txt:307 (find_package) -- Configuring incomplete, errors occurred! See also "/home/iurt/rpmbuild/BUILD/gmt-6.1.0/build/CMakeFiles/CMakeOutput.log". See also "/home/iurt/rpmbuild/BUILD/gmt-6.1.0/build/CMakeFiles/CMakeError.log". error: Bad exit status from /home/iurt/rpmbuild/tmp/rpm-tmp.iLFb5r (%build) RPM build errors: Bad exit status from /home/iurt/rpmbuild/tmp/rpm-tmp.iLFb5r (%build) I: [iurt_root_command] ERROR: chroot