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grimbough / Rhdf5lib

Distribution of the HDF5 library in an R package
https://bioconductor.org/packages/Rhdf5lib/
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Rhdf5lib failed installation in R 4.2.0 and Bioconductor 3.15 #44

Closed robby81 closed 2 years ago

robby81 commented 2 years ago

with this output:

cp ""hdf5/hl/src/.libs/libhdf5_hl.a"" "/home/robby/R/x86_64-suse-linux-gnu-library/4.2/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp ""hdf5 /hl/c++/src/.libs/libhdf5_hl_cpp.a"" "/home/robby/R/x86_64-suse-linux-gnu-library/4.2/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "/home/robby/R/x86_64-suse-linux-gnu-library/4.2/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp: cannot stat 'hdf5/libaec-1.0.4/build/szip/lib/libsz.a': No such file or directory make: *** [Makevars:32: copy-szip] Error 1 ERROR: compilation failed for package ‘Rhdf5lib’

  • removing ‘/home/robby/R/x86_64-suse-linux-gnu-library/4.2/Rhdf5lib’ ERROR: dependency ‘Rhdf5lib’ is not available for package ‘cytolib’

I am using openSUSE Tumbleweed as base system.

grimbough commented 2 years ago

Thanks for the report. This part of the error message is because it tries to copy a file that doesn't exist and fails. However we want to know why that file doesn't exist; it should have been compiled in the installation process.

Is there a section much earlier in the installation output that relates to libaec ? That should have the relevant details. Feel free to attach the entire output in a file if that's the easiest approach.

robby81 commented 2 years ago

Log-File is attached

--

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On Dienstag, 26. April 2022 10:29:51 CEST Mike Smith wrote:

Thanks for the report. This part of the error message is because it tries to copy a file that doesn't exist and fails. However we want to know why that file doesn't exist; it should have been compiled in the installation process.

Is there a section much earlier in the installation output that relates to libaec ? That should have the relevant details. Feel free to attach the entire output in a file if that's the easiest approach.

BiocManager::install("flowCore") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://ftp.gwdg.de/pub/misc/cran

Bioconductor version 3.15 (BiocManager 1.30.17), R 4.2.0 (2022-04-22) Installing package(s) 'flowCore' also installing the dependencies ‘Rhdf5lib’, ‘cytolib’

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Rhdf5lib_1.17.3.tar.gz' Content type 'application/x-gzip' length 14649424 bytes (14.0 MB)

downloaded 14.0 MB

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/cytolib_2.7.4.tar.gz' Content type 'application/x-gzip' length 5474142 bytes (5.2 MB)

downloaded 5.2 MB

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/flowCore_2.7.1.tar.gz' Content type 'application/x-gzip' length 7356990 bytes (7.0 MB)

downloaded 7.0 MB

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:

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/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c aec '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin' libtool: install: /usr/bin/install -c aec /tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin/aec /usr/bin/mkdir -p '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include' /usr/bin/install -c -m 644 ../../src/libaec.h ../../src/szlib.h '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include' /usr/bin/mkdir -p '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1' /usr/bin/install -c -m 644 ../../src/aec.1 '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1' make[3]: Leaving directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' make[2]: Leaving directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' make[2]: Entering directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[3]: Entering directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[2]: Leaving directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[1]: Leaving directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build' cd hdf5; \ ./configure --with-pic --enable-shared=no --enable-cxx --enable-hl \ --enable-tests=no --enable-tools=no \ --with-szlib=/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --with-zlib=yes \ --enable-ros3-vfd \ --enable-sharedlib-rpath \ CC='gcc' CXX='g++ -std=gnu++14' \ CPPFLAGS='-I/usr/local/include' \ CFLAGS='-O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -flto=auto -w -fpic' \ CXXFLAGS='-w -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -flto=auto -fpic'; \ make lib configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu 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-11.2.1 compiler 'gfortran' is GNU gfortran-11.2.1 compiler 'g++ -std=gnu++14' is GNU g++-11.2.1 checking for config ./config/site-specific/host-linux-6mz9... 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++14 accepts -g... yes checking dependency style of g++ -std=gnu++14... gcc3 checking how to run the C++ preprocessor... g++ -std=gnu++14 -E checking if c++ interface enabled... yes checking if g++ -std=gnu++14 needs old style header files in includes... no checking if g++ -std=gnu++14 can handle namespaces... yes checking if g++ -std=gnu++14 can handle static cast... yes checking if g++ -std=gnu++14 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/x86_64-suse-linux/bin/ld checking if the linker (/usr/x86_64-suse-linux/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/x86_64-suse-linux/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 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/x86_64-suse-linux/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... 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Szip not enabled. 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 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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 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(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 Apr 26 13:36:11 CEST 2022
              Configured by: ***@***.***
                Host system: x86_64-unknown-linux-gnu
          Uname information: Linux linux-6mz9 5.17.4-1-default #1 SMP PREEMPT Wed Apr 20 07:43:03 UTC 2022 (75e9961) x86_64 x86_64 x86_64 GNU/Linux
                   Byte sex: little-endian
         Installation point: /tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/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: H5_LDFLAGS: AM_LDFLAGS: Extra libraries: -lcrypto -lcurl -lz -ldl -lm Archiver: ar AR_FLAGS: cr Ranlib: ranlib

Languages:

                          C: yes
                 C Compiler: /usr/bin/gcc
                   CPPFLAGS: -I/usr/local/include
                H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                AM_CPPFLAGS: 
                    C Flags: -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -flto=auto -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++14
                  C++ Flags: -w -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -flto=auto -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) 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/RtmpveTiuu/R.INSTALL41c3e6b8a1d/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/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/src' make[3]: Entering directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/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 | \ 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 | \ 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/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/src' make[2]: Leaving directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/src' make[2]: Entering directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/c++' make[3]: Entering directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/c++' make[3]: Nothing to be done for 'build-lib'. make[3]: Leaving directory '/tmp/RtmpveTiuu/R.INSTALL41c3e6b8a1d/Rhdf5lib/src/hdf5/c++'

The downloaded source packages are in ‘/tmp/Rtmpsx7IUV/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib64/R/library packages: MASS, RcppParallel, rJava, rstudioapi Warning messages: 1: In install.packages(...) : installation of package ‘Rhdf5lib’ had non-zero exit status 2: In install.packages(...) : installation of package ‘cytolib’ had non-zero exit status 3: In install.packages(...) : installation of package ‘flowCore’ had non-zero exit status

grimbough commented 2 years ago

Thanks for the report. It shows that the libsz.a file is being created in hdf5/libaec-1.0.4/build/szip/lib64 but the package installation script is hard coded to copy it from hdf5/libaec-1.0.4/build/szip/lib and fails when that doesn't exist.

I'll take a look at why the folder names are different and how to make this more flexible to such differences.

grimbough commented 2 years ago

This is hopefully fixed in version 1.19.1 which you can install via BiocManager::install('grimbough/Rhdf5lib').

It will propagate through the Bioconductor build system and be available in the normal way in a couple of days.

robby81 commented 2 years ago

Thanx!!:

installing to /home/robby/R/x86_64-suse-linux-gnu-library/4.2/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs R inst byte-compile and prepare package for lazy loading help installing help indices copying figures building package indices installing vignettes testing if installed package can be loaded from temporary location checking absolute paths in shared objects and dynamic libraries testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path

grimbough commented 2 years ago

Awesome, thanks for confirming that it works for you. I'll also backport the patch to the Biconductor 3.15 version of the package, and hopefully this won't crop for you again in the future.