netcdf-4.6.1-r1:20200303-230911.log

netcdf-4.6.1-r1:20200303-230911.log (text/plain), 19.74 KB, created by Alessandro Barbieri on 2020-03-03 23:29:06 UTC

[32;01m * [39;49;00mPackage:    sci-libs/netcdf-4.6.1-r1
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:        abi_x86_64 amd64 dap elibc_glibc hdf hdf5 kernel_linux mpi szip tools userland_GNU
[32;01m * [39;49;00mFEATURES:   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 <[e-mail]>
 2 files changed, 486 insertions(+)
 create mode 100644 bash_completion.d/hwloc-completion.bash
[1;34m>[1;36m>[1;35m>[0m  -sandbox(setup)
 [32;01m*[0m /etc/portage/package.cflags/cflags -> */*: NOFFLAGS=1
 [32;01m*[0m /etc/portage/package.cflags/cflags -> */*: LDFLAGS-="-Wl,-z,now -Wl,-z,relro"
 [32;01m*[0m /etc/portage/package.cflags/cflags -> */*: USE_NONGNU="" +fPIE +fstack-protector-all +D_FORTIFY_SOURCE=2 
 [32;01m*[0m 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'
 [32;01m*[0m 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'
 [32;01m*[0m 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'
 [32;01m*[0m FFLAGS='-Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Warray-bounds -Wdate-time'
 [32;01m*[0m FCFLAGS='-Os -pipe -mtune=native -mfpmath=sse -fopenmp -pthread -fno-unroll-all-loops -fno-unroll-loops -fno-peel-loops -Warray-bounds -Wdate-time'
 [32;01m*[0m 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'
 [32;01m*[0m LDFLAGS='-Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--as-needed -Wl,-fuse-ld=gold -lpthread -lgomp'
 [32;01m*[0m MAKEOPTS='-j4 -l8'
 [32;01m*[0m gcc (Gentoo Hardened 9.2.0-r3 p4) 9.2.0
 [32;01m*[0m 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... (cached) yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for sys/types.h... (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... (cached) yes
checking for ssize_t... yes
checking for schar... no
checking for uchar... no
checking for longlong... no
checking for ushort... yes
checking for uint... yes
checking for int64... no
checking for uint64... no
checking for off_t... yes
checking whether byte ordering is bigendian... no
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of float... 4
checking size of double... 8
checking size of off_t... 8
checking size of size_t... 8
checking size of unsigned long long... 8
checking whether CDF5 support should be enabled... yes
checking size of unsigned char... 1
checking size of ushort... 2
checking size of uint... 4
checking size of ushort... (cached) 2
checking size of uint... (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
 [31;01m*[0m ERROR: sci-libs/netcdf-4.6.1-r1::gentoo failed (configure phase):
 [31;01m*[0m   econf failed
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m               ebuild.sh, line  125:  Called src_configure
 [31;01m*[0m             environment, line 3274:  Called econf '' '--disable-examples' '--disable-dap-remote-tests' '--enable-dap' '--enable-hdf4' '--enable-netcdf-4' '--disable-static' '--enable-utilities'
 [31;01m*[0m        phase-helpers.sh, line  681:  Called __helpers_die 'econf failed'
 [31;01m*[0m   isolated-functions.sh, line  112:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   		die "$@"
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of `emerge --info '=sci-libs/netcdf-4.6.1-r1::gentoo'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-libs/netcdf-4.6.1-r1::gentoo'`.
 [31;01m*[0m The complete build log is located at '/var/log/portage/build/sci-libs/netcdf-4.6.1-r1:20200303-230911.log'.
 [31;01m*[0m For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/netcdf-4.6.1-r1/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-libs/netcdf-4.6.1-r1/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/sci-libs/netcdf-4.6.1-r1/work/netcdf-c-4.6.1'
 [31;01m*[0m S: '/var/tmp/portage/sci-libs/netcdf-4.6.1-r1/work/netcdf-c-4.6.1'