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

albert180 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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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... 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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 commented 1 year ago

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 commented 1 year ago

Yes I will do it tomorrow

Am Mi., 17. Mai 2023 um 15:58 Uhr schrieb Mike Smith < @.***>:

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.

— Reply to this email directly, view it on GitHub https://github.com/grimbough/rhdf5/issues/128#issuecomment-1551450559, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC4ODFUF7W754X3GYWRCHTDXGTKRJANCNFSM6AAAAAAYDZ7SCA . You are receiving this because you authored the thread.Message ID: @.***>

grimbough commented 10 months ago

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

grimbough / rhdf5