MBXBB
commented
3 years ago Closed MBXBB closed 2 years ago
MBXBB
commented
3 years ago 
grimbough
commented
3 years ago I'm wondering if this is related to #34 Does it work any better if you install the version from here on Github? You can do that via:
BiocManager::install('grimbough/Rhdf5lib')Looks like the same error.
> BiocManager::install('grimbough/Rhdf5lib')
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing github package(s) 'grimbough/Rhdf5lib'
Downloading GitHub repo grimbough/Rhdf5lib@HEAD
checking for file ‘/tmp/RtmpLgjqu1/remotes4c3a00b0ad/grimbough-Rhdf5lib-f86b0✔ checking for file ‘/tmp/RtmpLgjqu1/remotes4c3a00b0ad/grimbough-Rhdf5lib-f86b022/DESCRIPTION’ (404ms)
─ preparing ‘Rhdf5lib’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘Rhdf5lib_1.13.3.tar.gz’
* installing *source* package ‘Rhdf5lib’ ...
** using staged installation
checking for gcc... gcc -std=gnu99
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 gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking whether C++ compiler accepts -w... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -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 zlib.h... yes
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking openssl/evp.h usability... yes
checking openssl/evp.h presence... yes
checking for openssl/evp.h... yes
checking openssl/hmac.h usability... yes
checking openssl/hmac.h presence... yes
checking for openssl/hmac.h... yes
checking openssl/sha.h usability... yes
checking openssl/sha.h presence... yes
checking for openssl/sha.h... yes
checking for curl_global_init in -lcurl... yes
checking for EVP_sha256 in -lcrypto... yes
S3_VFD=--enable-ros3-vfd
untarring hdf5small_cxx_hl_1.10.6.tar.gz ...
building the szip library...
checking for a BSD-compatible install... /bin/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
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'gcc -std=gnu99' is GNU gcc-4.8.5
checking for gcc... gcc -std=gnu99
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 gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking whether gcc -std=gnu99 understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc -std=gnu99... gcc3
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for ar... ar
checking whether make sets $(MAKE)... (cached) yes
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 gcc -std=gnu99... /bin/ld
checking if the linker (/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B
checking the name lister (/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /bin/nm -B output from gcc -std=gnu99 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
./configure: line 6829: /usr/bin/file: No such file or directory
checking for mt... no
checking if : is a manifest tool... no
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 gcc -std=gnu99 supports -fno-rtti -fno-exceptions... yes
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu99 static flag -static works... no
checking if gcc -std=gnu99 supports -c -o file.o... yes
checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker (/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for build mode... production
checking for math library support... no
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for error_at_line... yes
checking for working memcmp... yes
checking for vprintf... yes
checking for _doprnt... no
checking for memset... yes
checking if encoding enabled... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/SZconfig.h
config.status: executing depfiles commands
config.status: executing libtool commands
Making all in src
make[1]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/src'
make all-am
make[2]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/src'
/bin/sh ../libtool --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I/usr/local/include -I/n/apps/CentOS7/include -I/usr/include -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c -o rice.lo rice.c
libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I/usr/local/include -I/n/apps/CentOS7/include -I/usr/include -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c rice.c -fPIC -DPIC -o rice.o
mv -f .deps/rice.Tpo .deps/rice.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I/usr/local/include -I/n/apps/CentOS7/include -I/usr/include -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c -o sz_api.lo sz_api.c
libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I/usr/local/include -I/n/apps/CentOS7/include -I/usr/include -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c sz_api.c -fPIC -DPIC -o sz_api.o
mv -f .deps/sz_api.Tpo .deps/sz_api.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I/usr/local/include -I/n/apps/CentOS7/include -I/usr/include -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c -o encoding.lo encoding.c
libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I/usr/local/include -I/n/apps/CentOS7/include -I/usr/include -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c encoding.c -fPIC -DPIC -o encoding.o
mv -f .deps/encoding.Tpo .deps/encoding.Plo
/bin/sh ../libtool --tag=CC --mode=link gcc -std=gnu99 -I/n/apps/CentOS7/include -I/usr/include -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -version-info 2:0:0 -L/n/apps/CentOS7/lib64 -L/n/apps/CentOS7/lib -L/usr/lib64 -L/usr/lib -o libsz.la -rpath /tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib rice.lo sz_api.lo encoding.lo -lm
libtool: link: ar cru .libs/libsz.a rice.o sz_api.o encoding.o
libtool: link: ranlib .libs/libsz.a
libtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" )
make[2]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/src'
make[1]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/src'
make[1]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip'
Making install in src
make[1]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/src'
make[2]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/src'
/bin/mkdir -p '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib'
/bin/sh ../libtool --mode=install /bin/install -c libsz.la '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib'
libtool: install: /bin/install -c .libs/libsz.lai /tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.la
libtool: install: /bin/install -c .libs/libsz.a /tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: chmod 644 /tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: ranlib /tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: finish: PATH="/n/apps/CentOS7/install/r-4.0.3/bin:/n/apps/CentOS7/bin:/n/apps/CentOS7/install/r-4.0.3/bin:/usr/lib/jvm/jre-1.8.0/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/biouser/.local/bin:/home/biouser/bin:/sbin" ldconfig -n /tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib
----------------------------------------------------------------------
Libraries have been installed in:
/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the 'LD_RUN_PATH' environment variable
during linking
- use the '-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to '/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
/bin/mkdir -p '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/include'
/bin/install -c -m 644 ricehdf.h szip_adpt.h szlib.h '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/include'
make[2]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/src'
make[1]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/src'
make[1]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip'
make[2]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip'
make[1]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip'
building the hdf5 library...
checking for a BSD-compatible install... /bin/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 make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'gcc -std=gnu99' is GNU gcc-4.8.5
compiler 'gfortran' is GNU gfortran-4.8.5
compiler 'g++ -std=gnu++11' is GNU g++-4.8.5
checking for config ./config/site-specific/host-a158d665935e... no
checking build mode... production
checking for gcc... gcc -std=gnu99
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 gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking whether gcc -std=gnu99 understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc -std=gnu99... gcc3
checking if unsupported combinations of configure options are allowed... no
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -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 off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking whether byte ordering is bigendian... no
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of unsigned... 4
checking size of long... 8
checking size of long long... 8
checking size of __int64... 0
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of __float128... 16
checking size of _Quad... 0
checking quadmath.h usability... yes
checking quadmath.h presence... yes
checking for quadmath.h... yes
checking maximum decimal precision for C... 33
checking if Fortran interface enabled... no
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking dependency style of g++ -std=gnu++11... gcc3
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking if c++ interface enabled... yes
checking if g++ -std=gnu++11 needs old style header files in includes... no
checking if g++ -std=gnu++11 can handle namespaces... yes
checking if g++ -std=gnu++11 can handle static cast... yes
checking if g++ -std=gnu++11 has offsetof extension... yes
checking if the high-level library is enabled... yes
checking for ar... ar
checking whether make sets $(MAKE)... (cached) yes
checking for tr... /bin/tr
checking if srcdir= and time commands work together... no
checking if Java JNI interface enabled... no
checking if building tests is disabled... checking if building tools is disabled... checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc -std=gnu99... /bin/ld
checking if the linker (/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B
checking the name lister (/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /bin/nm -B output from gcc -std=gnu99 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
./configure: line 12860: /usr/bin/file: No such file or directory
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... yes
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu99 static flag -static works... no
checking if gcc -std=gnu99 supports -c -o file.o... yes
checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker (/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking for ld used by g++ -std=gnu++11... /bin/ld
checking if the linker (/bin/ld) is GNU ld... yes
checking whether the g++ -std=gnu++11 linker (/bin/ld) supports shared libraries... yes
checking for g++ -std=gnu++11 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++11 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++11 static flag -static works... no
checking if g++ -std=gnu++11 supports -c -o file.o... yes
checking if g++ -std=gnu++11 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++11 linker (/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if we should install only statically linked executables... no
checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes
checking for ceil in -lm... yes
checking for dlopen in -ldl... (cached) yes
checking for ANSI C header files... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking for sys/stat.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/types.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking setjmp.h usability... yes
checking setjmp.h presence... yes
checking for setjmp.h... yes
checking features.h usability... yes
checking features.h presence... yes
checking for features.h... yes
checking dirent.h usability... yes
checking dirent.h presence... yes
checking for dirent.h... yes
checking for stdint.h... (cached) yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking mach/mach_time.h usability... no
checking mach/mach_time.h presence... no
checking for mach/mach_time.h... no
checking io.h usability... yes
checking io.h presence... no
configure: WARNING: io.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: io.h: proceeding with the compiler's result
checking for io.h... yes
checking winsock2.h usability... no
checking winsock2.h presence... no
checking for winsock2.h... no
checking sys/timeb.h usability... yes
checking sys/timeb.h presence... yes
checking for sys/timeb.h... yes
checking for _FILE_OFFSET_BITS value needed for large files... no
checking size of int8_t... 1
checking size of uint8_t... 1
checking size of int_least8_t... 1
checking size of uint_least8_t... 1
checking size of int_fast8_t... 1
checking size of uint_fast8_t... 1
checking size of int16_t... 2
checking size of uint16_t... 2
checking size of int_least16_t... 2
checking size of uint_least16_t... 2
checking size of int_fast16_t... 8
checking size of uint_fast16_t... 8
checking size of int32_t... 4
checking size of uint32_t... 4
checking size of int_least32_t... 4
checking size of uint_least32_t... 4
checking size of int_fast32_t... 8
checking size of uint_fast32_t... 8
checking size of int64_t... 8
checking size of uint64_t... 8
checking size of int_least64_t... 8
checking size of uint_least64_t... 8
checking size of int_fast64_t... 8
checking size of uint_fast64_t... 8
checking size of size_t... 8
checking size of ssize_t... 8
checking size of ptrdiff_t... 8
checking size of off_t... 8
checking size of bool... 1
checking size of time_t... 8
checking if dev_t is scalar... yes
checking for dmalloc library... suppressed
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for compress2 in -lz... yes
checking for compress2... yes
checking szlib.h usability... yes
checking szlib.h presence... yes
checking for szlib.h... yes
checking for SZ_BufftoBuffCompress in -lsz... yes
checking for szlib encoder... yes
checking for thread safe support... no
checking whether CLOCK_MONOTONIC is declared... yes
checking for tm_gmtoff in struct tm... yes
checking for global timezone variable... yes
checking for st_blocks in struct stat... no
checking for _getvideoconfig... no
checking for gettextinfo... no
checking for GetConsoleScreenBufferInfo... no
checking for getpwuid... yes
checking for _scrsize... no
checking for ioctl... yes
checking for struct videoconfig... no
checking for struct text_info... no
checking for TIOCGWINSZ... yes
checking for TIOCGETD... yes
checking for library containing clock_gettime... none required
checking for alarm... yes
checking for clock_gettime... yes
checking for difftime... yes
checking for fcntl... yes
checking for flock... yes
checking for fork... yes
checking for frexpf... yes
checking for frexpl... yes
checking for gethostname... yes
checking for getrusage... yes
checking for gettimeofday... yes
checking for lstat... yes
checking for rand_r... yes
checking for random... yes
checking for setsysinfo... no
checking for signal... yes
checking for longjmp... yes
checking for setjmp... yes
checking for siglongjmp... yes
checking for sigsetjmp... no
checking for sigprocmask... yes
checking for snprintf... yes
checking for srandom... yes
checking for strdup... yes
checking for symlink... yes
checking for system... yes
checking for strtoll... yes
checking for strtoull... yes
checking for tmpfile... yes
checking for asprintf... yes
checking for vasprintf... yes
checking for vsnprintf... yes
checking for waitpid... yes
checking for roundf... yes
checking for lroundf... yes
checking for llroundf... yes
checking for round... yes
checking for lround... yes
checking for llround... yes
checking for an ANSI C-conforming const... yes
checking if the compiler understands __inline__... yes
checking if the compiler understands __inline... yes
checking if the compiler understands inline... yes
checking for __attribute__ extension... yes
checking for __func__ extension... yes
checking for __FUNCTION__ extension... yes
checking for C99 designated initialization support... yes
checking how to print long long... %ld and %lu
checking enable debugging symbols... no
checking enable asserts... no
checking enable developer warnings... no
checking profiling... no
checking optimization level... high
checking for internal debug output... none
checking whether function stack tracking is enabled... no
checking for API tracing... no
checking whether a memory checking tool will be used... no
checking whether internal memory allocation sanity checking is used... no
checking for parallel support files... skipped
checking whether O_DIRECT is declared... yes
checking for posix_memalign... yes
checking if the direct I/O virtual file driver (VFD) is enabled... no
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking openssl/evp.h usability... yes
checking openssl/evp.h presence... yes
checking for openssl/evp.h... yes
checking openssl/hmac.h usability... yes
checking openssl/hmac.h presence... yes
checking for openssl/hmac.h... yes
checking openssl/sha.h usability... yes
checking openssl/sha.h presence... yes
checking for openssl/sha.h... yes
checking for curl_global_init in -lcurl... yes
checking for EVP_sha256 in -lcrypto... yes
checking if the Read-Only S3 virtual file driver (VFD) is enabled... yes
checking for libhdfs... suppressed
checking for custom plugin default path definition... /usr/local/hdf5/lib/plugin
checking whether exception handling functions is checked during data conversions... yes
checking whether data accuracy is guaranteed during data conversions... yes
checking if the machine has window style path name... no
checking if using special algorithm to convert long double to (unsigned) long values... no
checking if using special algorithm to convert (unsigned) long to long double values... 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 system is IBM ppc64le and cannot correctly convert some long double values... no
checking additional programs should be built... no
checking if deprecated public symbols are available... yes
checking which version of public symbols to use by default... v110
checking whether to perform strict file format checks... no
checking for pread... yes
checking for pwrite... yes
checking whether to use pread/pwrite instead of read/write in certain VFDs... yes
checking whether to have library information embedded in the executables... yes
checking if alignment restrictions are strictly enforced... no
configure: creating ./config.lt
config.lt: creating libtool
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating src/libhdf5.settings
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating bin/h5cc
config.status: creating bin/Makefile
config.status: creating c++/Makefile
config.status: creating c++/src/Makefile
config.status: creating c++/src/h5c++
config.status: creating hl/Makefile
config.status: creating hl/src/Makefile
config.status: creating hl/c++/Makefile
config.status: creating hl/c++/src/Makefile
config.status: creating src/H5config.h
config.status: executing pubconf commands
creating src/H5pubconf.h
Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing .classes commands
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.10.6
Configured on: Thu Dec 24 00:15:40 UTC 2020
Configured by: biouser@a158d665935e
Host system: x86_64-unknown-linux-gnu
Uname information: Linux a158d665935e 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 01:06:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/hdf5
Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Linking Options:
----------------
Libraries: static
Statically Linked Executables:
LDFLAGS: -L/n/apps/CentOS7/lib64 -L/n/apps/CentOS7/lib -L/usr/lib64 -L/usr/lib
H5_LDFLAGS:
AM_LDFLAGS: -L/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib
Extra libraries: -lcrypto -lcurl -lsz -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: ranlib
Languages:
----------
C: yes
C Compiler: /bin/gcc -std=gnu99 ( gcc (GCC) 4.8.5 20150623 )
CPPFLAGS: -I/usr/local/include
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/include
C Flags: -I/n/apps/CentOS7/include -I/usr/include -w -fpic
H5 C Flags: -std=c99 -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Wno-format-nonliteral -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-enum -Wswitch-default -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -Wno-long-long -Wvolatile-register-var -Wstrict-aliasing -Wvla -Wlogical-op -Wlarger-than=2560 -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-suggest-attribute=const -Wno-suggest-attribute=pure -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=format -O3
AM C Flags:
Shared C Library: no
Static C Library: yes
Fortran: no
C++: yes
C++ Compiler: /bin/g++ -std=gnu++11 ( g++ (GCC) 4.8.5 20150623 )
C++ Flags: -g -O2 -w -fpic
H5 C++ Flags: -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wendif-labels -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -s -O3
AM C++ Flags:
Shared C++ Library: no
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),szip(encoder)
MPE: no
Direct VFD: no
(Read-Only) S3 VFD: yes
(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
Strict file format checks: no
Optimization instrumentation: no
for d in src . c++ hl; do \
if test $d != .; then \
(cd $d && make lib) || exit 1; \
fi; \
done
make[1]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/src'
make[2]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/src'
CC H5.lo
CC H5checksum.lo
CC H5dbg.lo
CC H5system.lo
CC H5timer.lo
CC H5trace.lo
CC H5A.lo
CC H5Abtree2.lo
CC H5Adense.lo
CC H5Adeprec.lo
CC H5Aint.lo
CC H5Atest.lo
CC H5AC.lo
CC H5ACdbg.lo
CC H5ACproxy_entry.lo
CC H5B.lo
CC H5Bcache.lo
CC H5Bdbg.lo
CC H5B2.lo
CC H5B2cache.lo
CC H5B2dbg.lo
CC H5B2hdr.lo
CC H5B2int.lo
CC H5B2internal.lo
CC H5B2leaf.lo
CC H5B2stat.lo
CC H5B2test.lo
CC H5C.lo
CC H5Cdbg.lo
CC H5Cepoch.lo
CC H5Cimage.lo
CC H5Clog.lo
CC H5Clog_json.lo
CC H5Clog_trace.lo
CC H5Cprefetched.lo
CC H5Cquery.lo
CC H5Ctag.lo
CC H5Ctest.lo
CC H5CS.lo
CC H5CX.lo
CC H5D.lo
CC H5Dbtree.lo
CC H5Dbtree2.lo
CC H5Dchunk.lo
CC H5Dcompact.lo
CC H5Dcontig.lo
CC H5Ddbg.lo
CC H5Ddeprec.lo
CC H5Dearray.lo
CC H5Defl.lo
CC H5Dfarray.lo
CC H5Dfill.lo
CC H5Dint.lo
CC H5Dio.lo
CC H5Dlayout.lo
CC H5Dnone.lo
CC H5Doh.lo
CC H5Dscatgath.lo
CC H5Dselect.lo
CC H5Dsingle.lo
CC H5Dtest.lo
CC H5Dvirtual.lo
CC H5E.lo
CC H5Edeprec.lo
CC H5Eint.lo
CC H5EA.lo
CC H5EAcache.lo
CC H5EAdbg.lo
CC H5EAdblkpage.lo
CC H5EAdblock.lo
CC H5EAhdr.lo
CC H5EAiblock.lo
CC H5EAint.lo
CC H5EAsblock.lo
CC H5EAstat.lo
CC H5EAtest.lo
CC H5F.lo
CC H5Faccum.lo
CC H5Fcwfs.lo
CC H5Fdbg.lo
CC H5Fdeprec.lo
CC H5Fefc.lo
CC H5Ffake.lo
CC H5Fint.lo
CC H5Fio.lo
CC H5Fmount.lo
CC H5Fquery.lo
CC H5Fsfile.lo
CC H5Fspace.lo
CC H5Fsuper.lo
CC H5Fsuper_cache.lo
CC H5Ftest.lo
CC H5FA.lo
CC H5FAcache.lo
CC H5FAdbg.lo
CC H5FAdblock.lo
CC H5FAdblkpage.lo
CC H5FAhdr.lo
CC H5FAint.lo
CC H5FAstat.lo
CC H5FAtest.lo
CC H5FD.lo
CC H5FDcore.lo
CC H5FDfamily.lo
CC H5FDhdfs.lo
CC H5FDint.lo
CC H5FDlog.lo
CC H5FDmulti.lo
CC H5FDsec2.lo
CC H5FDspace.lo
CC H5FDstdio.lo
CC H5FDtest.lo
CC H5FL.lo
CC H5FO.lo
CC H5FS.lo
CC H5FScache.lo
CC H5FSdbg.lo
CC H5FSint.lo
CC H5FSsection.lo
CC H5FSstat.lo
CC H5FStest.lo
CC H5G.lo
CC H5Gbtree2.lo
CC H5Gcache.lo
CC H5Gcompact.lo
CC H5Gdense.lo
CC H5Gdeprec.lo
CC H5Gent.lo
CC H5Gint.lo
CC H5Glink.lo
CC H5Gloc.lo
CC H5Gname.lo
CC H5Gnode.lo
CC H5Gobj.lo
CC H5Goh.lo
CC H5Groot.lo
CC H5Gstab.lo
CC H5Gtest.lo
CC H5Gtraverse.lo
CC H5HF.lo
CC H5HFbtree2.lo
CC H5HFcache.lo
CC H5HFdbg.lo
CC H5HFdblock.lo
CC H5HFdtable.lo
CC H5HFhdr.lo
CC H5HFhuge.lo
CC H5HFiblock.lo
CC H5HFiter.lo
CC H5HFman.lo
CC H5HFsection.lo
CC H5HFspace.lo
CC H5HFstat.lo
CC H5HFtest.lo
CC H5HFtiny.lo
CC H5HG.lo
CC H5HGcache.lo
CC H5HGdbg.lo
CC H5HGquery.lo
CC H5HL.lo
CC H5HLcache.lo
CC H5HLdbg.lo
CC H5HLint.lo
CC H5HLprfx.lo
CC H5HLdblk.lo
CC H5HP.lo
CC H5I.lo
CC H5Itest.lo
CC H5L.lo
CC H5Lexternal.lo
CC H5make_libsettings.o
CCLD H5make_libsettings
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/n/apps/CentOS7/lib64 -L/n/apps/CentOS7/lib -L/usr/lib64 -L/usr/lib | \
sed -e 's/-L/:/g' -e 's/ //g'`" \
./H5make_libsettings > H5lib_settings.c || \
(test $HDF5_Make_Ignore && echo "*** Error ignored") || \
(rm -f H5lib_settings.c ; exit 1)
CC H5lib_settings.lo
CC H5MF.lo
CC H5MFaggr.lo
CC H5MFdbg.lo
CC H5MFsection.lo
CC H5MM.lo
CC H5MP.lo
CC H5MPtest.lo
CC H5O.lo
CC H5Odeprec.lo
CC H5Oainfo.lo
CC H5Oalloc.lo
CC H5Oattr.lo
CC H5Oattribute.lo
CC H5Obogus.lo
CC H5Obtreek.lo
CC H5Ocache.lo
CC H5Ocache_image.lo
CC H5Ochunk.lo
CC H5Ocont.lo
CC H5Ocopy.lo
CC H5Odbg.lo
CC H5Odrvinfo.lo
CC H5Odtype.lo
CC H5Oefl.lo
CC H5Ofill.lo
CC H5Oflush.lo
CC H5Ofsinfo.lo
CC H5Oginfo.lo
CC H5Oint.lo
CC H5Olayout.lo
CC H5Olinfo.lo
CC H5Olink.lo
CC H5Omessage.lo
CC H5Omtime.lo
CC H5Oname.lo
CC H5Onull.lo
CC H5Opline.lo
CC H5Orefcount.lo
CC H5Osdspace.lo
CC H5Oshared.lo
CC H5Oshmesg.lo
CC H5Ostab.lo
CC H5Otest.lo
CC H5Ounknown.lo
CC H5P.lo
CC H5Pacpl.lo
CC H5Pdapl.lo
CC H5Pdcpl.lo
CC H5Pdeprec.lo
CC H5Pdxpl.lo
CC H5Pencdec.lo
CC H5Pfapl.lo
CC H5Pfcpl.lo
CC H5Pfmpl.lo
CC H5Pgcpl.lo
CC H5Pint.lo
CC H5Plapl.lo
CC H5Plcpl.lo
CC H5Pocpl.lo
CC H5Pocpypl.lo
CC H5Pstrcpl.lo
CC H5Ptest.lo
CC H5PB.lo
CC H5PL.lo
CC H5PLint.lo
CC H5PLpath.lo
CC H5PLplugin_cache.lo
CC H5R.lo
CC H5Rint.lo
CC H5Rdeprec.lo
CC H5UC.lo
CC H5RS.lo
CC H5S.lo
CC H5Sall.lo
CC H5Sdbg.lo
CC H5Shyper.lo
CC H5Snone.lo
CC H5Spoint.lo
CC H5Sselect.lo
CC H5Stest.lo
CC H5SL.lo
CC H5SM.lo
CC H5SMbtree2.lo
CC H5SMcache.lo
CC H5SMmessage.lo
CC H5SMtest.lo
CC H5ST.lo
CC H5T.lo
CC H5Tarray.lo
CC H5Tbit.lo
CC H5Tcommit.lo
CC H5Tcompound.lo
CC H5Tconv.lo
CC H5Tcset.lo
CC H5Tdbg.lo
CC H5Tdeprec.lo
CC H5Tenum.lo
CC H5Tfields.lo
CC H5Tfixed.lo
CC H5Tfloat.lo
CC H5detect.o
CCLD H5detect
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/n/apps/CentOS7/lib64 -L/n/apps/CentOS7/lib -L/usr/lib64 -L/usr/lib | \
sed -e 's/-L/:/g' -e 's/ //g'`" \
./H5detect > H5Tinit.c || \
(test $HDF5_Make_Ignore && echo "*** Error ignored") || \
(rm -f H5Tinit.c ; exit 1)
CC H5Tinit.lo
CC H5Tnative.lo
CC H5Toffset.lo
CC H5Toh.lo
CC H5Topaque.lo
CC H5Torder.lo
CC H5Tpad.lo
CC H5Tprecis.lo
CC H5Tstrpad.lo
CC H5Tvisit.lo
CC H5Tvlen.lo
CC H5TS.lo
CC H5VM.lo
CC H5WB.lo
CC H5Z.lo
CC H5Zdeflate.lo
CC H5Zfletcher32.lo
CC H5Znbit.lo
CC H5Zshuffle.lo
CC H5Zscaleoffset.lo
CC H5Zszip.lo
CC H5Ztrans.lo
CC H5FDros3.lo
CC H5FDs3comms.lo
CCLD libhdf5.la
make[2]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/src'
make[1]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/src'
make[1]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/c++'
make[2]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/c++'
make[2]: Nothing to be done for 'build-lib'.
make[2]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/c++'
+ cd src
+ make lib
make[2]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/c++/src'
make[3]: Entering directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/c++/src'
CXX H5Exception.lo
CXX H5IdComponent.lo
In file included from H5IdComponent.cpp:16:0:
../../src/H5private.h:153:19: fatal error: io.h: No such file or directory
# include <io.h>
^
compilation terminated.
make[3]: *** [Makefile:1004: H5IdComponent.lo] Error 1
make[3]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/c++/src'
make[2]: *** [Makefile:1431: lib] Error 1
make[2]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/c++/src'
make[1]: *** [Makefile:1249: lib] Error 1
make[1]: Leaving directory '/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/c++'
make: *** [Makefile:1088: lib] Error 1
./configure: line 3888: 2: command not found
configure: HDF5_INCLUDE=hdf5/src
configure: HDF5_CXX_INCLUDE=hdf5/c++/src
configure: HDF5_HL_INCLUDE=hdf5/hl/src
configure: HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src
configure: HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure: HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure: HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a
configure: HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a
configure: SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/n/apps/CentOS7/install/r-4.0.3/lib64/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"*.h "/n/apps/CentOS7/install/r-4.0.3/lib64/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src/"*.h "/n/apps/CentOS7/install/r-4.0.3/lib64/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src/"*.h "/n/apps/CentOS7/install/r-4.0.3/lib64/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src/"*.h "/n/apps/CentOS7/install/r-4.0.3/lib64/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"libhdf5.settings "/n/apps/CentOS7/install/r-4.0.3/lib64/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/n/apps/CentOS7/install/r-4.0.3/lib64/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/n/apps/CentOS7/install/r-4.0.3/lib64/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/n/apps/CentOS7/install/r-4.0.3/lib64/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp: cannot stat ‘hdf5/c++/src/.libs/libhdf5_cpp.a’: No such file or directory
make: *** [Makevars:40: copying] Error 1
ERROR: compilation failed for package ‘Rhdf5lib’
* removing ‘/n/apps/CentOS7/install/r-4.0.3/lib64/R/library/Rhdf5lib’
* restoring previous ‘/n/apps/CentOS7/install/r-4.0.3/lib64/R/library/Rhdf5lib’
Error: Failed to install 'Rhdf5lib' from GitHub:
(converted from warning) installation of package ‘/tmp/RtmpLgjqu1/file4cadb1495/Rhdf5lib_1.13.3.tar.gz’ had non-zero exit status
Execution haltedIs there a fix for this yet by any chance?
grimbough
commented
3 years ago Sorry, this slipped off the radar over the Christmas break.
I guess we need to inderstand where io.h is and why the C++ compiler can't find it (but I think the C compiler probably can).
Do you get any output if you run locate /io.h in a terminal?
MBXBB
commented
3 years ago [biouser@7c72eefd7201 ~]$ locate -b '\io.h' /usr/include/geos/io.h /usr/include/sys/io.h /usr/src/kernels/3.10.0-1160.6.1.el7.x86_64/arch/x86/include/asm/io.h /usr/src/kernels/3.10.0-1160.6.1.el7.x86_64/include/asm-generic/io.h /usr/src/kernels/3.10.0-1160.6.1.el7.x86_64/include/config/fb/deferred/io.h /usr/src/kernels/3.10.0-1160.6.1.el7.x86_64/include/config/generic/io.h /usr/src/kernels/3.10.0-1160.6.1.el7.x86_64/include/linux/io.h [biouser@7c72eefd7201 ~]$
On Mon, Feb 1, 2021 at 5:02 PM Mike Smith notifications@github.com wrote:
Sorry, this slipped off the radar over the Christmas break.
I guess we need to inderstand where io.h is and why the C++ compiler can find it (but I think the C compiler probably can).
Do you get any output if you run locate io.h in a terminal?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/grimbough/Rhdf5lib/issues/37#issuecomment-771221850, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANWNPTPDMK7V26LCUA2BICTS44XJ3ANCNFSM4VHLADMQ .
grimbough
commented
3 years ago I'm just posting the relevant settings determined by the configure script here so I don't have to keep scrolling back up through the compiler log.
LDFLAGS: -L/n/apps/CentOS7/lib64 -L/n/apps/CentOS7/lib -L/usr/lib64 -L/usr/lib
AM_LDFLAGS: -L/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib
Extra libraries: -lcrypto -lcurl -lsz -lz -ldl -lm
C Compiler: /bin/gcc -std=gnu99 ( gcc (GCC) 4.8.5 20150623 )
CPPFLAGS: -I/usr/local/include
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/include
C Flags: -I/n/apps/CentOS7/include -I/usr/include -w -fpic
H5 C Flags: -std=c99 -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Wno-format-nonliteral -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-enum -Wswitch-default -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -Wno-long-long -Wvolatile-register-var -Wstrict-aliasing -Wvla -Wlogical-op -Wlarger-than=2560 -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-suggest-attribute=const -Wno-suggest-attribute=pure -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=format -O3
C++ Compiler: /bin/g++ -std=gnu++11 ( g++ (GCC) 4.8.5 20150623 )
C++ Flags: -g -O2 -w -fpic
H5 C++ Flags: -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wendif-labels -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -s -O3I'm currently unable to replicate the issue on a CentOS 7 VM.
MBXBB
commented
3 years ago Do the settings look the same for you when you try to replicate?
On Thu, Feb 4, 2021 at 8:50 AM Mike Smith notifications@github.com wrote:
I'm just posting the relevant settings determined by the configure script here so I don't have to keep scrolling back up through the compiler log.
LDFLAGS: -L/n/apps/CentOS7/lib64 -L/n/apps/CentOS7/lib -L/usr/lib64 -L/usr/lib AM_LDFLAGS: -L/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/lib Extra libraries: -lcrypto -lcurl -lsz -lz -ldl -lm C Compiler: /bin/gcc -std=gnu99 ( gcc (GCC) 4.8.5 20150623 ) CPPFLAGS: -I/usr/local/include H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: -I/tmp/RtmpN6ArG2/R.INSTALL8f60f94621/Rhdf5lib/src/hdf5/szip/szip/include C Flags: -I/n/apps/CentOS7/include -I/usr/include -w -fpic H5 C Flags: -std=c99 -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Wno-format-nonliteral -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-enum -Wswitch-default -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -Wno-long-long -Wvolatile-register-var -Wstrict-aliasing -Wvla -Wlogical-op -Wlarger-than=2560 -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-suggest-attribute=const -Wno-suggest-attribute=pure -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=format -O3 C++ Compiler: /bin/g++ -std=gnu++11 ( g++ (GCC) 4.8.5 20150623 ) C++ Flags: -g -O2 -w -fpic H5 C++ Flags: -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wendif-labels -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -s -O3I'm currently unable to replicate the issue on a CentOS 7 VM.
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MBXBB
commented
3 years ago I have no issues with R version 3.6. The only time this fails is when I use R 4.0.0 or R 4.0.3
grimbough
commented
3 years ago Do you see anything obviously different in the out printed to screen during compilation? The important part is the structured table of configuration options that's found between the following headings.
Linking Options:
----------------
...
Features:
---------That details all the compilation options it determines, most of which are actually obtained from R CMD config. It's definitely possible that the output from those call will be different for various R versions on your system.
grimbough
commented
2 years ago The compilation process for the package has changed significantly since this was first reported. If it reoccurs as an issue please re-open.