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Compilation fails when the folder containing the renv has a space in its name #128

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albert180 opened this issue May 16, 2023 · 5 comments
Closed

Compilation fails when the folder containing the renv has a space in its name #128

albert180 opened this issue May 16, 2023 · 5 comments

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@albert180
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The compilation of the rhdf5-package fails when the folder containing the renv has a space in it's name. If you replace the space with underscores it compiles without errors.
@grimbough
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I'm afraid I don't use renv. Can you give am example of your setup? It'd also be great if you could include the installation log and error you see here.

@albert180
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albert180 commented May 16, 2023 •
edited

Sure.
Here it is:
`R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

  • Project '~/Dokumente/Test Ordner' loaded. [renv 0.17.3]

install.packages("rhdf5")
Retrieving 'https://bioconductor.org/packages/3.17/bioc/src/contrib/rhdf5_2.44.0.tar.gz' ...
OK [downloaded 1.2 Mb in 0.37 seconds]
Retrieving 'https://bioconductor.org/packages/3.17/bioc/src/contrib/Rhdf5lib_1.22.0.tar.gz' ...
OK [downloaded 11.5 Mb in 1.2 seconds]
Retrieving 'https://bioconductor.org/packages/3.17/bioc/src/contrib/rhdf5filters_1.12.1.tar.gz' ...
OK [downloaded 1.1 Mb in 0.39 seconds]
Installing Rhdf5lib [1.22.0] ...
FAILED
Error installing package 'Rhdf5lib':
====================================

  • 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 the compiler supports GNU C... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to enable C11 features... none needed
    checking whether the compiler supports GNU C++... yes
    checking whether g++ -std=gnu++17 accepts -g... yes
    checking for g++ -std=gnu++17 option to enable C++11 features... none needed
    COMPILER = gcc
    checking whether C compiler accepts -w... yes
    checking whether to use -Wl,-rpath setting... yes
    checking for stdio.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for strings.h... yes
    checking for sys/stat.h... yes
    checking for sys/types.h... yes
    checking for unistd.h... yes
    checking for zlib.h... yes
    checking for szlib.h... yes
    checking for libaec.h... yes
    checking for SZ_BufftoBuffCompress in -lsz... yes
    checking for aec_buffer_encode in -lsz... yes
    checking for curl/curl.h... yes
    checking for openssl/evp.h... yes
    checking for openssl/hmac.h... 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
    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    using C compiler: ‘gcc (GCC) 13.1.1 20230511 (Red Hat 13.1.1-2)’
    gunzip -dc hdf5small_cxx_hl_1.10.7.tar.gz | tar xf -;
    cd hdf5;
    ./configure --with-pic --enable-shared=no --enable-cxx --enable-hl
    --enable-tests=no --enable-tools=no
    --with-szlib=yes --with-zlib=yes
    --enable-ros3-vfd
    --enable-sharedlib-rpath
    CC='gcc' CXX='g++ -std=gnu++17'
    CPPFLAGS='-I/usr/local/include'
    CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto -w -fpic'
    CXXFLAGS='-w -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto -fpic'
    LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1';
    make lib
    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-13.1.1
    compiler 'gfortran' is GNU gfortran-13.1.1
    compiler 'g++ -std=gnu++17' is GNU g++-13.1.1
    checking for config ./config/site-specific/host-fedora... no
    checking for clang sanitizer checks... 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 whether make supports the include directive... yes (GNU style)
    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
    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++17 accepts -g... yes
    checking dependency style of g++ -std=gnu++17... gcc3
    checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
    checking if c++ interface enabled... yes
    checking if g++ -std=gnu++17 needs old style header files in includes... no
    checking if g++ -std=gnu++17 can handle namespaces... yes
    checking if g++ -std=gnu++17 can handle static cast... yes
    checking if g++ -std=gnu++17 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... /usr/bin/tr
    checking if srcdir= and time commands work together... yes
    checking if Java JNI interface enabled... no
    checking if building tests is disabled... Building HDF5 tests is disabled
    checking if building tools is disabled... Building HDF5 tools is disabled
    checking how to print strings... printf
    checking for a sed that does not truncate output... /usr/bin/sed
    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... no
    checking if : is a manifest tool... no
    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... no
    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... 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++17 -E
    checking for ld used by g++ -std=gnu++17... /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++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
    checking for g++ -std=gnu++17 option to produce PIC... -fPIC -DPIC
    checking if g++ -std=gnu++17 PIC flag -fPIC -DPIC works... yes
    checking if g++ -std=gnu++17 static flag -static works... no
    checking if g++ -std=gnu++17 supports -c -o file.o... yes
    checking if g++ -std=gnu++17 supports -c -o file.o... (cached) yes
    checking whether the g++ -std=gnu++17 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
    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... 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 netdb.h usability... yes
    checking netdb.h presence... yes
    checking for netdb.h... yes
    checking netinet/in.h usability... yes
    checking netinet/in.h presence... yes
    checking for netinet/in.h... yes
    checking arpa/inet.h usability... yes
    checking arpa/inet.h presence... yes
    checking for arpa/inet.h... yes
    checking io.h usability... no
    checking io.h presence... no
    checking for io.h... no
    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 libaec.h usability... yes
    checking libaec.h presence... yes
    checking for libaec.h... yes
    checking for aec_encode in -laec... 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 enable file locking... best-effort
    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 if the Mirror 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 examples path definition... ${prefix}/share/hdf5_examples
    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 utils/Makefile
    config.status: creating utils/mirror_vfd/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: 1.10.7
              Configured on: Tue May 16 20:26:03 CEST 2023
              Configured by: pius@fedora
                Host system: x86_64-unknown-linux-gnu
          Uname information: Linux fedora 6.2.14-300.fc38.x86_64 #1 SMP PREEMPT_DYNAMIC Mon May  1 00:55:28 UTC 2023 x86_64 GNU/Linux
                   Byte sex: little-endian
         Installation point: /tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/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: -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lcrypto -lcurl -lsz -laec -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: ranlib

Languages:

                          C: yes
                 C Compiler: /usr/bin/gcc ( gcc (GCC) 13.1.1 20230511 )
                   CPPFLAGS: -I/usr/local/include
                H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                AM_CPPFLAGS: 
                    C Flags: -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto -w -fpic
                 H5 C Flags:  -std=c99  -Wno-c++-compat -Wno-format-nonliteral -Wshadow -Wundef -Wwrite-strings -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3  -Werror=bad-function-cast -Werror=declaration-after-statement -Werror=implicit-function-declaration -Werror=missing-declarations -Werror=missing-prototypes -Werror=nested-externs -Werror=old-style-definition -Werror=packed -Werror=pointer-sign -Werror=pointer-to-int-cast -Werror=redundant-decls -Werror=strict-prototypes -Werror=switch -Wunused-function -Wformat -Werror=incompatible-pointer-types -Werror=shadow -Wcast-function-type -Wmaybe-uninitialized
                 AM C Flags: 
           Shared C Library: no
           Static C Library: yes


                    Fortran: no

                        C++: yes
               C++ Compiler: /usr/bin/g++ -std=gnu++17 ( g++ (GCC) 13.1.1 20230511 )
                  C++ Flags: -w -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto -fpic
               H5 C++ Flags:   -Wall -Wconversion -Wctor-dtor-privacy -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-format-nonliteral -Wnon-virtual-dtor -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -O3  -Wcast-align -Wmissing-declarations -Werror=packed -Werror=redundant-decls -Werror=switch -Wunused-but-set-variable -Werror=unused-function -Werror=unused-variable -Wunused-parameter -Werror=shadow
               AM C++ Flags: 
         Shared C++ Library: 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: no
Build HDF5 Tools: no
Threadsafety: no
Default API mapping: v110
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
MPE: no
Direct VFD: no
Mirror 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
Use file locking: best-effort
Strict file format checks: no
Optimization instrumentation: no
make[1]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5'
for d in src . c++ hl; do
if test $d != .; then
(cd $d && make lib) || exit 1;
fi;
done
make[2]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/src'
make[3]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/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 H5FDsplitter.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_PATHecho -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 | \ 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_PATHecho -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 | \ 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[3]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/src'
make[2]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/src'
make[2]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/c++'
make[3]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/c++'
make[3]: Nothing to be done for 'build-lib'.
make[3]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/c++'

  • cd src
  • make lib
    make[3]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/c++/src'
    make[4]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/c++/src'
    CXX H5Exception.lo
    CXX H5IdComponent.lo
    CXX H5DataSpace.lo
    CXX H5PropList.lo
    CXX H5Library.lo
    CXX H5FaccProp.lo
    CXX H5FcreatProp.lo
    CXX H5LcreatProp.lo
    CXX H5LaccProp.lo
    CXX H5DaccProp.lo
    CXX H5DxferProp.lo
    CXX H5DcreatProp.lo
    CXX H5Location.lo
    CXX H5AbstractDs.lo
    CXX H5Attribute.lo
    CXX H5Object.lo
    CXX H5OcreatProp.lo
    CXX H5DataType.lo
    CXX H5AtomType.lo
    CXX H5PredType.lo
    CXX H5EnumType.lo
    CXX H5IntType.lo
    CXX H5FloatType.lo
    CXX H5StrType.lo
    CXX H5ArrayType.lo
    CXX H5VarLenType.lo
    CXX H5CompType.lo
    CXX H5DataSet.lo
    CXX H5CommonFG.lo
    CXX H5Group.lo
    CXX H5File.lo
    CXXLD libhdf5_cpp.la
    make[4]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/c++/src'
    make[3]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/c++/src'
    make[2]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/c++'
    make[2]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl'
    make[3]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl'
    make[3]: Nothing to be done for 'build-lib'.
    make[3]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl'
  • cd src
  • make lib
    make[3]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/src'
    make[4]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/src'
    CC H5DO.lo
    CC H5DS.lo
    CC H5IM.lo
    CC H5LT.lo
    CC H5LTanalyze.lo
    CC H5LTparse.lo
    CC H5PT.lo
    CC H5TB.lo
    CC H5LD.lo
    CCLD libhdf5_hl.la
    make[4]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/src'
    make[3]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/src'
  • cd c++
  • make lib
    make[3]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/c++'
    make[4]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/c++'
    make[4]: Nothing to be done for 'build-lib'.
    make[4]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/c++'
  • cd src
  • make lib
    make[4]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/c++/src'
    make[5]: Entering directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/c++/src'
    CXX H5PacketTable.lo
    CXXLD libhdf5_hl_cpp.la
    make[5]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/c++/src'
    make[4]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/c++/src'
    make[3]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl/c++'
    make[2]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5/hl'
    make[1]: Leaving directory '/tmp/RtmpFGs5uc/R.INSTALL8419c4179a44e/Rhdf5lib/src/hdf5'
    mkdir -p "/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
    cp "hdf5/src"/.h "/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
    cp "hdf5/c++/src"/    .h "/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
    cp "hdf5/hl/src"/.h "/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
    cp "hdf5/hl/c++/src"/    .h "/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
    cp "hdf5/src"/libhdf5.settings "/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
    mkdir -p "/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
    cp "hdf5/src/.libs/libhdf5.a" "/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
    cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
    cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
    cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
    gcc -I"/usr/include/R" -DNDEBUG -I/home/pius/Dokumente/Test Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto -c Rhdf5lib.c -o Rhdf5lib.o
    gcc: warning: Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include: linker input file unused because linking not done
    gcc: error: Ordner/renv/staging/1/00LOCK-Rhdf5lib/00new/Rhdf5lib/include: linker input file not found: No such file or directory
    make: *** [/usr/lib64/R/etc/Makeconf:191: Rhdf5lib.o] Error 1
    ERROR: compilation failed for package ‘Rhdf5lib’
  • removing ‘/home/pius/Dokumente/Test Ordner/renv/staging/1/Rhdf5lib’
    Error: install of package 'Rhdf5lib' failed [error code 1]

It compiles without issues, if you remove the space from the folder name

@grimbough
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Thanks for the extra information. I think there's a path that I need to enclose in quotes to stop the path breaking around the space.

Can you try installing the latest version of Rhdf5lib via renv::install("grimbough/Rhdf5lib") and let me know if it works any better for you.

@albert180
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albert180 commented May 25, 2023 via email

@grimbough
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I'm closing this and assuming it worked. Please reopen if that's not the case

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@grimbough @albert180