Rhdf5lib installation problem
1
0
Entering edit mode
@giovanni-calice-6415
Last seen 7 months ago
Italy

Hi all,

I am having problems installing the package Rhdf5lib with the latest version 1.12.0

BiocManager::install("Rhdf5lib")

and also with the previous version 1.10.1 directly by .tar.gz file

install.packages("/usr/local/Rhdf5lib_1.10.1.tar.gz", repos = NULL, type = "source", lib="/usr/local/lib/R/site-library")

always with the same error:

cp: cannot stat 'hdf5/src/.libs/libhdf5.a': No such file or directory
make: *** [Makevars:39: copying] Error 1
ERROR: compilation failed for package ‘Rhdf5lib’
* removing ‘/usr/local/lib64/R/library_Bioc_3_12/Rhdf5lib’

The downloaded source packages are in
    ‘/tmp/RtmpW0eoX8/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘Rhdf5lib’ had non-zero exit status

I would appreciate any suggestions.

Thanks in advance, Giovanni

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=it_IT.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=it_IT.UTF-8    
 [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=it_IT.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.3      tools_4.0.3
minfi Rhdf5lib • 3.4k views
ADD COMMENT •
0
Entering edit mode

That error is almost certainly not the real problem. There it's trying to copy the compiled HDF5 library, and failing because it doesn't exist. We need to understand we the compilation is failing.

Can you update your post to include all the output that's printed during installation?

ADD REPLY •
0
Entering edit mode

Hi Mike,

OK this is the output during the latest version installation:

BiocManager::install("Rhdf5lib")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'Rhdf5lib'
provo con l'URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/Rhdf5lib_1.12.0.tar.gz'
Content type 'application/x-gzip' length 14440702 bytes (13.8 MB)
==================================================
downloaded 13.8 MB

* installing *source* package ‘Rhdf5lib’ ...
** using staged installation
checking for gcc... gcc
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 accepts -g... yes
checking for gcc 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... /usr/bin/grep
checking for egrep... /usr/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... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/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' is GNU gcc-9.3.0
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -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... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/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 /usr/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 /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt 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 supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) 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... no
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/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/src'
make  all-am
make[2]: Entering directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/src'
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -O2 -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 -DHAVE_CONFIG_H -I. -O2 -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -O2 -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 -DHAVE_CONFIG_H -I. -O2 -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -O2 -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 -DHAVE_CONFIG_H -I. -O2 -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/bash ../libtool  --tag=CC   --mode=link gcc  -O2 -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  -o libsz.la -rpath /tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/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
ar: `u' modifier ignored since `D' is the default (see `U')
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/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/src'
make[1]: Leaving directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/src'
make[1]: Entering directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip'
Making install in src
make[1]: Entering directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/src'
make[2]: Entering directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/src'
 /usr/bin/mkdir -p '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/szip/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libsz.la '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/szip/lib'
libtool: install: /usr/bin/install -c .libs/libsz.lai /tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.la
libtool: install: /usr/bin/install -c .libs/libsz.a /tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: chmod 644 /tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: ranlib /tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-11-openjdk-amd64/bin:/usr/lib/rstudio/bin/postback:/sbin" ldconfig -n /tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/szip/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/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'
ADD REPLY •
0
Entering edit mode
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /usr/bin/mkdir -p '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/szip/include'
 /usr/bin/install -c -m 644 ricehdf.h szip_adpt.h szlib.h '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/szip/include'
make[2]: Leaving directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/src'
make[1]: Leaving directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/src'
make[1]: Entering directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip'
make[2]: Entering directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/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/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip'
make[1]: Leaving directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip'
building the hdf5 library...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/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' is GNU gcc-9.3.0
compiler 'gfortran' is GNU gfortran-9.3.0
compiler 'g++ -std=gnu++11' is GNU g++-9.3.0
checking for config ./config/site-specific/host-illumina-lin... no
checking build mode... production
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking if unsupported combinations of configure options are allowed... no
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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
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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
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checking for fgrep... /usr/bin/grep -F
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checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/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 /usr/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 /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
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checking if gcc supports -fno-rtti -fno-exceptions... yes
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checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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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... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++11 linker (/usr/bin/ld -m elf_x86_64) 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... yes
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checking whether the g++ -std=gnu++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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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
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checking for sys/types.h... (cached) yes
checking sys/file.h usability... yes
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checking for sys/file.h... yes
checking stddef.h usability... yes
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checking for stddef.h... yes
checking setjmp.h usability... yes
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checking features.h usability... yes
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checking for features.h... yes
checking dirent.h usability... yes
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checking for stdint.h... (cached) yes
checking stdbool.h usability... yes
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checking for stdbool.h... yes
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checking for _FILE_OFFSET_BITS value needed for large files... no
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checking size of uint_least8_t... 1
checking size of int_fast8_t... 1
checking size of uint_fast8_t... 1
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checking size of uint_least16_t... 2
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checking size of bool... 1
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checking if dev_t is scalar... yes
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checking for SZ_BufftoBuffCompress in -lsz... yes
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checking for thread safe support... no
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checking for tm_gmtoff in struct tm... yes
checking for global timezone variable... yes
checking for st_blocks in struct stat... no
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checking for GetConsoleScreenBufferInfo... no
checking for getpwuid... yes
checking for _scrsize... no
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checking for struct videoconfig... no
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checking for TIOCGWINSZ... yes
checking for TIOCGETD... yes
checking for library containing clock_gettime... none required
checking for alarm... yes
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checking for difftime... yes
checking for fcntl... yes
checking for flock... yes
checking for fork... yes
checking for frexpf... yes
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checking for random... yes
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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
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checking for EVP_sha256 in -lcrypto... yes
checking if the Read-Only S3 virtual file driver (VFD) is enabled... yes
ADD REPLY •
0
Entering edit mode
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
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checking which version of public symbols to use by default... v110
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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: Fri Jan 15 10:29:11 CET 2021
                  Configured by: root@illumina-lin
                    Host system: x86_64-unknown-linux-gnu
              Uname information: Linux illumina-lin 5.8.0-38-generic #43~20.04.1-Ubuntu SMP Tue Jan 12 16:39:47 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/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/usr/local/lib -L-L/usr/lib/ -ltcl8.6 -L/usr/lib/ -ltk8.6 -ldl
                     H5_LDFLAGS: 
                     AM_LDFLAGS:  -L/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/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: /usr/bin/gcc
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/szip/szip/include
                        C Flags: -g -O2 -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 -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 -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wnull-dereference -Wunused-const-variable -Wduplicated-cond -Whsa -Wnormalized -Walloc-zero -Walloca -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=2 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -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 -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3
                     AM C Flags: 
               Shared C Library: no
               Static C Library: yes


                        Fortran: no

                            C++: yes
                   C++ Compiler: /usr/bin/g++ -std=gnu++11
                      C++ Flags: -g -O2 -w -fpic
                   H5 C++ Flags:   -pedantic -Wall -W -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 -finline-functions -s -O
                   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/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/src'
make[2]: Entering directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/src'
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  CC       H5Goh.lo
  CC       H5Groot.lo
  CC       H5Gstab.lo
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  CC       H5Itest.lo
  CC       H5L.lo
  CC       H5Lexternal.lo
  CC       H5make_libsettings.o
  CCLD     H5make_libsettings
../libtool: line 7486: cd: -/: invalid option
cd: usage: cd [-L|[-P [-e]] [-@]] [dir]
libtool:   error: cannot determine absolute directory name of '-L/usr/lib/'
make[2]: *** [Makefile:1122: H5make_libsettings] Error 1
make[2]: Leaving directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/src'
make[1]: *** [Makefile:1989: lib] Error 1
make[1]: Leaving directory '/tmp/RtmpgW7GyF/R.INSTALL816e6abf2d29/Rhdf5lib/src/hdf5/src'
make: *** [Makefile:1088: lib] Error 1
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 "/usr/local/lib64/R/library_Bioc_3_12/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"*.h "/usr/local/lib64/R/library_Bioc_3_12/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src/"*.h "/usr/local/lib64/R/library_Bioc_3_12/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src/"*.h "/usr/local/lib64/R/library_Bioc_3_12/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src/"*.h "/usr/local/lib64/R/library_Bioc_3_12/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"libhdf5.settings "/usr/local/lib64/R/library_Bioc_3_12/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/usr/local/lib64/R/library_Bioc_3_12/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/usr/local/lib64/R/library_Bioc_3_12/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp: impossibile eseguire stat di 'hdf5/src/.libs/libhdf5.a': File o directory non esistente
make: *** [Makevars:39: copying] Errore 1
ERROR: compilation failed for package ‘Rhdf5lib’
* removing ‘/usr/local/lib64/R/library_Bioc_3_12/Rhdf5lib’

The downloaded source packages are in
    ‘/tmp/RtmpxeF2tV/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘Rhdf5lib’ had non-zero exit status
ADD REPLY •
0
Entering edit mode
###
###
and this one is during the previous version 1.10.1 installation, directly by .tar.gz file: 
###
###
ADD REPLY •
0
Entering edit mode
install.packages("/usr/local/Rhdf5lib_1.10.1.tar.gz", repos = NULL, type = "source", lib="/usr/local/lib/R/site-library")
* installing *source* package ‘Rhdf5lib’ ...
** using staged installation
checking for gcc... gcc
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 accepts -g... yes
checking for gcc 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... /usr/bin/grep
checking for egrep... /usr/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
untarring hdf5small_cxx_hl_1.10.6.tar.gz ...
building the szip library...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/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' is GNU gcc-9.3.0
checking for gcc... gcc
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 accepts -g... yes
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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/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/src'
make  all-am
make[2]: Entering directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/src'
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -O2 -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 -DHAVE_CONFIG_H -I. -O2 -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -O2 -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 -DHAVE_CONFIG_H -I. -O2 -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -O2 -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 -DHAVE_CONFIG_H -I. -O2 -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/bash ../libtool  --tag=CC   --mode=link gcc  -O2 -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  -o libsz.la -rpath /tmp/RtmpzNRrF8/R.INSTALLb6684e381363/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
ar: `u' modifier ignored since `D' is the default (see `U')
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/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/src'
make[1]: Leaving directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/src'
make[1]: Entering directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip'
Making install in src
make[1]: Entering directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/src'
make[2]: Entering directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/src'
 /usr/bin/mkdir -p '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/szip/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libsz.la '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/szip/lib'
libtool: install: /usr/bin/install -c .libs/libsz.lai /tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.la
libtool: install: /usr/bin/install -c .libs/libsz.a /tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: chmod 644 /tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: ranlib /tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-11-openjdk-amd64/bin:/usr/lib/rstudio/bin/postback:/sbin" ldconfig -n /tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/szip/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /tmp/RtmpzNRrF8/R.INSTALLb6684e381363/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.
----------------------------------------------------------------------
ADD REPLY •
0
Entering edit mode
/usr/bin/mkdir -p '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/szip/include'
 /usr/bin/install -c -m 644 ricehdf.h szip_adpt.h szlib.h '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/szip/include'
make[2]: Leaving directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/src'
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make[1]: Entering directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip'
make[2]: Entering directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/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/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip'
make[1]: Leaving directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip'
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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
ADD REPLY •
0
Entering edit mode
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: Fri Jan 15 10:33:13 CET 2021
                  Configured by: root@illumina-lin
                    Host system: x86_64-unknown-linux-gnu
              Uname information: Linux illumina-lin 5.8.0-38-generic #43~20.04.1-Ubuntu SMP Tue Jan 12 16:39:47 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /tmp/RtmpzNRrF8/R.INSTALLb6684e381363/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/usr/local/lib -L-L/usr/lib/ -ltcl8.6 -L/usr/lib/ -ltk8.6 -ldl
                     H5_LDFLAGS: 
                     AM_LDFLAGS:  -L/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/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: /usr/bin/gcc
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/szip/szip/include
                        C Flags: -g -O2 -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 -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 -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wnull-dereference -Wunused-const-variable -Wduplicated-cond -Whsa -Wnormalized -Walloc-zero -Walloca -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=2 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -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 -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3
                     AM C Flags: 
               Shared C Library: no
               Static C Library: yes


                        Fortran: no

                            C++: yes
                   C++ Compiler: /usr/bin/g++ -std=gnu++11
                      C++ Flags: -g -O2 -w -fpic
                   H5 C++ Flags:   -pedantic -Wall -W -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 -finline-functions -s -O
                   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/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/src'
make[2]: Entering directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/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
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  CC       H5ACproxy_entry.lo
  CC       H5B.lo
  CC       H5Bcache.lo
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  CC       H5B2.lo
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  CC       H5C.lo
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  CC       H5Cprefetched.lo
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  CC       H5Dlayout.lo
  CC       H5Dnone.lo
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  CC       H5EAdbg.lo
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  CC       H5EAiblock.lo
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  CC       H5F.lo
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  CC       H5Fdbg.lo
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  CC       H5Fmount.lo
  CC       H5Fquery.lo
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  CC       H5Fspace.lo
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  CC       H5Ftest.lo
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  CC       H5FD.lo
  CC       H5FDcore.lo
  CC       H5FDfamily.lo
  CC       H5FDhdfs.lo
  CC       H5FDint.lo
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  CC       H5FDsec2.lo
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  CC       H5FDtest.lo
  CC       H5FL.lo
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  CC       H5FS.lo
  CC       H5FScache.lo
  CC       H5FSdbg.lo
  CC       H5FSint.lo
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  CC       H5FSstat.lo
  CC       H5FStest.lo
  CC       H5G.lo
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  CC       H5Gdeprec.lo
  CC       H5Gent.lo
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  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
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  CC       H5HFdblock.lo
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  CC       H5HFhuge.lo
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  CC       H5HLdblk.lo
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  CC       H5Itest.lo
  CC       H5L.lo
  CC       H5Lexternal.lo
  CC       H5make_libsettings.o
  CCLD     H5make_libsettings
../libtool: line 7486: cd: -/: invalid option
cd: usage: cd [-L|[-P [-e]] [-@]] [dir]
libtool:   error: cannot determine absolute directory name of '-L/usr/lib/'
make[2]: *** [Makefile:1122: H5make_libsettings] Error 1
make[2]: Leaving directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/src'
make[1]: *** [Makefile:1989: lib] Error 1
make[1]: Leaving directory '/tmp/RtmpzNRrF8/R.INSTALLb6684e381363/Rhdf5lib/src/hdf5/src'
make: *** [Makefile:1088: lib] Error 1
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 "/usr/local/lib/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"*.h "/usr/local/lib/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src/"*.h "/usr/local/lib/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src/"*.h "/usr/local/lib/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src/"*.h "/usr/local/lib/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/usr/local/lib/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/usr/local/lib/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp: impossibile eseguire stat di 'hdf5/src/.libs/libhdf5.a': File o directory non esistente
make: *** [Makevars:38: copying] Errore 1
ERROR: compilation failed for package ‘Rhdf5lib’
* removing ‘/usr/local/lib/R/site-library/Rhdf5lib’
Warning in install.packages :
  installation of package ‘/usr/local/Rhdf5lib_1.10.1.tar.gz’ had non-zero exit status

Thanks for the reply

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Entering edit mode
Mike Smith ★ 6.6k
@mike-smith
Last seen 6 hours ago
EMBL Heidelberg

Thanks for the details. The error occurs at the following step:

../libtool: line 7486: cd: -/: invalid option

and I think the root cause is shown on this line:

LDFLAGS: -L/usr/local/lib -L-L/usr/lib/ -ltcl8.6 -L/usr/lib/ -ltk8.6 -ldl

A link flag of -L-L/usr/lib is invalid. Rhdf5lib should get these flags from the R configuration itself, so I don't know how you've ended up with a broken one there.. Do you see the same thing if you run the following at the command line?

R CMD config LDFLAGS
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