* Package: sci-libs/netcdf-4.6.1-r1  * Repository: gentoo  * Maintainer: sci@gentoo.org  * USE: abi_x86_64 amd64 dap elibc_glibc hdf hdf5 kernel_linux mpi szip tools userland_GNU  * FEATURES: compressdebug fakeroot installsources network-sandbox preserve-libs sandbox splitdebug usersandbox Auto packing the repository in background for optimum performance. See "git help gc" for manual housekeeping. [master a9bf82b] saving uncommitted changes in /etc prior to emerge run Author: Alessandro-Barbieri 2 files changed, 486 insertions(+) create mode 100644 bash_completion.d/hwloc-completion.bash >>> -sandbox(setup) * /etc/portage/package.cflags/cflags -> */*: NOFFLAGS=1 * /etc/portage/package.cflags/cflags -> */*: LDFLAGS-="-Wl,-z,now -Wl,-z,relro" * /etc/portage/package.cflags/cflags -> */*: USE_NONGNU="" +fPIE +fstack-protector-all +D_FORTIFY_SOURCE=2 * FEATURES='candy clean-logs unknown-features-warn unmerge-logs xattr preserve-libs split-log installsources config-protect-if-modified cgroup parallel-fetch protect-owned network-sandbox multilib-strict sfperms split-elog news strict fakeroot binpkg-docompress sign parallel-install qa-unresolved-soname-deps binpkg-logs sandbox assume-digests binpkg-dostrip buildpkg userfetch usersandbox merge-sync usersync unmerge-orphans distlocks pid-sandbox splitdebug ipc-sandbox metadata-transfer fixlafiles compressdebug strict-keepdir ebuild-locks' * CFLAGS='-Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Wformat -Wformat-security -Warray-bounds -Wclobbered -Wvolatile-register-var -Wdate-time -Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Wformat -Wformat-security -Warray-bounds -Wclobbered -Wvolatile-register-var -Wdate-time -floop-interchange -ftree-loop-distribute-patterns -fpredictive-commoning -ftree-loop-distribution -fsplit-paths -ftree-vectorize -ftree-partial-pre -fgcse-after-reload -fivopts -Wimplicit-function-declaration -Wno-error=implicit-function-declaration -Wl,-O1 -Wl,--as-needed -Wl,-fuse-ld=gold -lpthread -lgomp' * CXXFLAGS='-Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Wformat -Wformat-security -Warray-bounds -Wclobbered -Wvolatile-register-var -Wdate-time -Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Wformat -Wformat-security -Warray-bounds -Wclobbered -Wvolatile-register-var -Wdate-time -floop-interchange -ftree-loop-distribute-patterns -fpredictive-commoning -ftree-loop-distribution -fsplit-paths -ftree-vectorize -ftree-partial-pre -fgcse-after-reload -fivopts -Wl,-O1 -Wl,--as-needed -Wl,-fuse-ld=gold -lpthread -lgomp' * FFLAGS='-Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Warray-bounds -Wdate-time' * FCFLAGS='-Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Warray-bounds -Wdate-time' * F77FLAGS='-Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Wformat -Wformat-security -Warray-bounds -Wclobbered -Wvolatile-register-var -Wdate-time' * LDFLAGS='-Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--as-needed -Wl,-fuse-ld=gold -lpthread -lgomp' * MAKEOPTS='-j4 -l8' * gcc (Gentoo Hardened 9.2.0-r3 p4) 9.2.0 * Linux server-NAS 4.19.0-8-amd64 #1 SMP Debian 4.19.98-1 (2020-01-26) x86_64 Intel(R) Core(TM) i5-2300 CPU @ 2.80GHz GenuineIntel GNU/Linux ]0;emerge 00:09:33 2|169 netcdf (root@server-NAS)kemerge 00:09:33 2|169 netcdf (root@server-NAS)\>>> Unpacking source... >>> Unpacking netcdf-4.6.1.tar.gz to /var/tmp/portage/sci-libs/netcdf-4.6.1-r1/work >>> Source unpacked in /var/tmp/portage/sci-libs/netcdf-4.6.1-r1/work >>> Preparing source in /var/tmp/portage/sci-libs/netcdf-4.6.1-r1/work/netcdf-c-4.6.1 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/netcdf-4.6.1-r1/work/netcdf-c-4.6.1 ... * econf: updating netcdf-c-4.6.1/config.guess with /usr/share/gnuconfig/config.guess * econf: updating netcdf-c-4.6.1/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/netcdf-4.6.1-r1 --htmldir=/usr/share/doc/netcdf-4.6.1-r1/html --libdir=/usr/lib64 --disable-examples --disable-dap-remote-tests --enable-dap --enable-hdf4 --enable-netcdf-4 --disable-static --enable-utilities configure: WARNING: you should use --build, --host, --target configure: netCDF 4.6.1 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no configure: checking user options checking whether a NCIO_MINBLOCKSIZE was specified... 256 checking if fsync support is enabled... no checking if jna bug workaround is enabledd... no checking whether we should build netCDF-4... yes checking do we require hdf5 dynamic-loading support... yes checking whether reading of HDF4 SD files is to be enabled... yes checking whether to fetch some sample HDF4 files from Unidata ftp site to test HDF4 reading (requires wget)... no checking whether we should attempt to install netcdf-fortran (EXPERIMENTAL)... no checking whether extra example tests should be run... no checking whether parallel IO tests should be run... no checking whether a default chunk size in bytes was specified... 4194304 checking whether a maximum per-variable cache size for HDF5 was specified... 67108864 checking whether a number of chunks for the default per-variable cache was specified... 10 checking whether a default file cache size for HDF5 was specified... 4194304 checking whether a default file cache maximum number of elements for HDF5 was specified... 1009 checking whether a default cache preemption for HDF5 was specified... 0.75 checking whether netCDF-4 logging is enabled... no checking whether DAP client(s) are to be built... yes checking whether make supports the include directive... yes (GNU style) checking for x86_64-pc-linux-gnu-gcc... mpicc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether mpicc accepts -g... yes checking for mpicc option to accept ISO C89... none needed checking whether mpicc understands -c and -o together... yes checking dependency style of mpicc... none checking for curl_easy_setopt in -lcurl... yes checking for library containing curl_easy_setopt... -lcurl checking whether dap remote testing should be enabled (default on)... no checking whether dap remote authorization testing should be enabled (default off)... no checking whether netcdf4 group names for DAP2 hould be enabled (default on)... yes checking which remote test server(s) to use... remotetest.unidata.ucar.edu,jetstream.unidata.ucar.edu (defaults) checking whether the time-consuming dap tests should be enabled (default off)... no checking whether to enable strict null-byte header padding when reading (default off)... no checking whether FFIO will be used... no checking whether STDIO will be used... no checking whether examples should be built... no checking whether v2 netCDF API should be built... yes checking whether the ncgen/ncdump/nccopy should be built... yes checking whether test should be built and run... yes checking whether large file (> 2GB) tests should be run... no checking whether benchmarks should be run (experimental)... no checking whether extreme numbers should be used in tests... yes checking where to put large temp files if large file tests are run... . configure: finding C compiler checking for x86_64-pc-linux-gnu-gcc... (cached) mpicc checking whether we are using the GNU C compiler... (cached) yes checking whether mpicc accepts -g... (cached) yes checking for mpicc option to accept ISO C89... (cached) none needed checking whether mpicc understands -c and -o together... (cached) yes checking dependency style of mpicc... (cached) none checking for an ANSI C-conforming const... yes checking whether CURLOPT_USERNAME is defined... yes checking whether CURLOPT_PASSWORD is defined... yes checking whether CURLOPT_KEYPASSWD is defined... yes checking whether CURLINFO_RESPONSE_CODE is defined... yes configure: setting up libtool checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by mpicc... /usr/x86_64-pc-linux-gnu/bin/ld checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... nm checking the name lister (nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-pc-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-pc-linux-gnu-ar... ar checking for archiver @FILE support... @ checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip checking for x86_64-pc-linux-gnu-ranlib... ranlib checking command to parse nm output from mpicc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for x86_64-pc-linux-gnu-mt... no checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... mpicc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC -DPIC checking if mpicc PIC flag -fPIC -DPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking if mpicc supports -c -o file.o... (cached) yes checking whether the mpicc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no configure: finding other utilities checking for m4... m4 checking for doxygen... no configure: WARNING: Doxygen not found - documentation will not be built checking for dot... dot checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no configure: displaying some results checking CPPFLAGS... checking CC CFLAGS... mpicc -Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Wformat -Wformat-security -Warray-bounds -Wclobbered -Wvolatile-register-var -Wdate-time -Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Wformat -Wformat-security -Warray-bounds -Wclobbered -Wvolatile-register-var -Wdate-time -floop-interchange -ftree-loop-distribute-patterns -fpredictive-commoning -ftree-loop-distribution -fsplit-paths -ftree-vectorize -ftree-partial-pre -fgcse-after-reload -fivopts -Wimplicit-function-declaration -Wno-error=implicit-function-declaration -Wl,-O1 -Wl,--as-needed -Wl,-fuse-ld=gold -lpthread -lgomp checking type mpicc... mpicc is /usr/bin/mpicc checking CXX... g++ checking CXXFLAGS... -Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Wformat -Wformat-security -Warray-bounds -Wclobbered -Wvolatile-register-var -Wdate-time -Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Wformat -Wformat-security -Warray-bounds -Wclobbered -Wvolatile-register-var -Wdate-time -floop-interchange -ftree-loop-distribute-patterns -fpredictive-commoning -ftree-loop-distribution -fsplit-paths -ftree-vectorize -ftree-partial-pre -fgcse-after-reload -fivopts -Wl,-O1 -Wl,--as-needed -Wl,-fuse-ld=gold -lpthread -lgomp checking type g++... g++ is /usr/bin/g++ checking FC... unset checking F90... unset checking AR... ar checking AR_FLAGS... cru checking type ar... ar is /usr/bin/ar checking NM... nm checking NMFLAGS... configure: checking types, headers, and functions checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking libgen.h usability... yes checking libgen.h presence... yes checking for libgen.h... yes checking for ANSI C header files... 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(cached) yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking ftw.h usability... yes checking ftw.h presence... yes checking for ftw.h... yes checking for strlcat... no checking for snprintf... yes checking for strdup... yes checking for strtoll... yes checking for strtoull... yes checking for mkstemp... yes checking for mktemp... yes checking for random... yes checking for getrlimit... yes checking for gettimeofday... yes checking for fsync... yes checking for MPI_Comm_f2c... yes checking whether in-memory files are enabled... yes checking for memmove... yes checking for getpagesize... yes checking for sysconf... yes checking whether mmap is enabled for in-memory files... no checking for mremap... yes mmap function or mremap function is not available: disabling mmap checking for size_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether isnan is declared... yes checking whether isinf is declared... yes checking whether isfinite is declared... yes checking for struct stat.st_blksize... yes checking for IEEE floating point format... yes checking for size_t... 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(cached) 4 checking size of ssize_t... 8 checking size of void*... 8 checking for library containing deflate... -lz checking for floor in -lm... yes checking for library containing H5Fflush... -lhdf5 checking for library containing H5DSis_scale... -lhdf5_hl checking hdf5.h usability... yes checking hdf5.h presence... yes checking for hdf5.h... yes checking for H5Z_SZIP... yes checking for H5Pget_fapl_mpiposix... no checking for H5Pget_fapl_mpio... yes checking for H5Pset_deflate... yes checking for H5Z_SZIP... (cached) yes checking for H5free_memory... yes checking for H5Pset_libver_bounds... yes checking for H5Pset_all_coll_metadata_ops... yes checking whether parallel io is enabled in hdf5... yes checking for library containing SZ_Compress... -lsz checking mfhdf.h usability... yes checking mfhdf.h presence... yes checking for mfhdf.h... yes checking for Hclose in -ldf... yes checking for SDcreate in -lmfhdf... yes checking for jpeg_set_quality in -ljpeg... no configure: error: Can't find or link to the jpeg library (required by hdf4). See config.log for errors. !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-libs/netcdf-4.6.1-r1/work/netcdf-c-4.6.1/config.log * ERROR: sci-libs/netcdf-4.6.1-r1::gentoo failed (configure phase): * econf failed * * Call stack: * ebuild.sh, line 125: Called src_configure * environment, line 3274: Called econf '' '--disable-examples' '--disable-dap-remote-tests' '--enable-dap' '--enable-hdf4' '--enable-netcdf-4' '--disable-static' '--enable-utilities' * phase-helpers.sh, line 681: Called __helpers_die 'econf failed' * isolated-functions.sh, line 112: Called die * The specific snippet of code: * die "$@" * * If you need support, post the output of `emerge --info '=sci-libs/netcdf-4.6.1-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/netcdf-4.6.1-r1::gentoo'`. * The complete build log is located at '/var/log/portage/build/sci-libs/netcdf-4.6.1-r1:20200303-230911.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/netcdf-4.6.1-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/netcdf-4.6.1-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/netcdf-4.6.1-r1/work/netcdf-c-4.6.1' * S: '/var/tmp/portage/sci-libs/netcdf-4.6.1-r1/work/netcdf-c-4.6.1'