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grimbough / Rhdf5lib

Distribution of the HDF5 library in an R package
https://bioconductor.org/packages/Rhdf5lib/
6 stars 14 forks source link

Version 1.9.1 fails on Mac OSX #26

Closed grimbough closed 4 years ago

grimbough commented 4 years ago

Reported via email from CRAN maintainers.

Compilation runs, but fails with the following errors when trying to move the shared libraries:

configure:    HDF5_INCLUDE=hdf5/src
configure:    HDF5_CXX_INCLUDE=hdf5/c++/src
configure:    HDF5_HL_INCLUDE=hdf5/hl/src
configure:    HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src
configure:    HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure:    HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure:    HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a
configure:    HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a
configure:    SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure:    ZLIB_HOME=yes
** libs
/usr/local/clang9/bin/clang -I"/Users/ripley/R/R-devel/include" -DNDEBUG
   -I/usr/local/include  -Ihdf5/src -Iyes/include -Lyes/lib -fPIC  -g
-O2 -Wall -pedantic -Wconversion -Wno-sign-conversion  -c Rhdf5lib.c -o
Rhdf5lib.o
clang-9: warning: argument unused during compilation: '-Lyes/lib'
[-Wunused-command-line-argument]
/usr/local/clang9/bin/clang -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/Users/ripley/R/R-devel/lib -L/usr/local/clang9/lib -L/usr/local/lib
-o Rhdf5lib.so Rhdf5lib.o
/Users/ripley/R/test-4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a
/Users/ripley/R/test-4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a -lz
-L/Users/ripley/R/R-devel/lib -lR -Wl,-framework -Wl,CoreFoundation
clang-9: error: no such file or directory:
'/Users/ripley/R/test-4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a'
clang-9: error: no such file or directory:
'/Users/ripley/R/test-4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a'
grimbough commented 4 years ago

Issue seems to have been introduced between 6581de4d35a7515d72049a956d54e8e2b5366e81 (works) and 283de8c40c9224059143bfb493cbf19fed77c861 (doesn't work)

annebozack commented 4 years ago

I'm getting a similar error installing on an Linux-based HPC. Any suggestions?

configure:    HDF5_INCLUDE=hdf5/src
configure:    HDF5_CXX_INCLUDE=hdf5/c++/src
configure:    HDF5_HL_INCLUDE=hdf5/hl/src
configure:    HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src
configure:    HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure:    HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure:    HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a
configure:    HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a
configure:    SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"*.h "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src/"*.h "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src/"*.h "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src/"*.h "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp: cannot stat ‘hdf5/src/.libs/libhdf5.a’: No such file or directory
make: *** [copying] Error 1
grimbough commented 4 years ago

The original error was due to me including the file src/COPYING in 283de8c40c9224059143bfb493cbf19fed77c861. How're this only seemed to break Mac OS X & had now been reverted, so it shouldn't be an issue anymore.

I suspect the problem is that the compilation of libhdf5.a is failing, but we only find out when it tries to copy that file & it doesn't exist. Could you include everything that is printed to screen when you try to install the package?

annebozack commented 4 years ago

Below is what is printed upon installation. It may be an issue with the configuration of the server I'm using, although I have successfully installed other packages.

install_github('grimbough/Rhdf5lib') Downloading GitHub repo grimbough/Rhdf5lib@master ✔ checking for file ‘/tmp/10986214.1.int.q/RtmpswFUgJ/remotesc93c17886360/grimbough-Rhdf5lib-1b05e97/DESCRIPTION’ (424ms) ─ preparing ‘Rhdf5lib’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ running ‘cleanup’ ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘Rhdf5lib_1.9.2.tar.gz’

Installing package into ‘/ifs/scratch/msph/ehs/akb2134/R_libs’ (as ‘lib’ is unspecified)

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.

/bin/mkdir -p '/tmp/10986214.1.int.q/RtmpOrbK3h/R.INSTALL1aaf7a62e033/Rhdf5lib/src/hdf5/szip/szip/include' /bin/install -c -m 644 ricehdf.h szip_adpt.h szlib.h '/tmp/10986214.1.int.q/RtmpOrbK3h/R.INSTALL1aaf7a62e033/Rhdf5lib/src/hdf5/szip/szip/include' make[2]: Leaving directory /tmp/10986214.1.int.q/RtmpOrbK3h/R.INSTALL1aaf7a62e033/Rhdf5lib/src/hdf5/szip/src' make[1]: Leaving directory /tmp/10986214.1.int.q/RtmpOrbK3h/R.INSTALL1aaf7a62e033/Rhdf5lib/src/hdf5/szip/src' make[1]: Entering directory /tmp/10986214.1.int.q/RtmpOrbK3h/R.INSTALL1aaf7a62e033/Rhdf5lib/src/hdf5/szip' make[2]: Entering directory /tmp/10986214.1.int.q/RtmpOrbK3h/R.INSTALL1aaf7a62e033/Rhdf5lib/src/hdf5/szip' make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done forinstall-data-am'. make[2]: Leaving directory /tmp/10986214.1.int.q/RtmpOrbK3h/R.INSTALL1aaf7a62e033/Rhdf5lib/src/hdf5/szip' make[1]: Leaving directory /tmp/10986214.1.int.q/RtmpOrbK3h/R.INSTALL1aaf7a62e033/Rhdf5lib/src/hdf5/szip' building the hdf5 library... checking for a BSD-compatible install... /bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking shell variables initial values... done checking if basename works... yes checking if xargs works... yes checking for cached host... none checking for config x86_64-unknown-linux-gnu... no checking for config x86_64-unknown-linux-gnu... no checking for config unknown-linux-gnu... no checking for config unknown-linux-gnu... no checking for config x86_64-linux-gnu... no checking for config x86_64-linux-gnu... no checking for config x86_64-unknown... no checking for config linux-gnu... found compiler 'gcc -std=gnu99' is GNU gcc-4.8.5 compiler 'gfortran' is GNU gfortran-4.8.5 compiler 'g++ -std=gnu++11' is GNU g++-4.8.5 checking for config ./config/site-specific/host-hb1c6n8.hpc... no checking for config ./config/site-specific/host-hpc... no checking build mode... production checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking whether gcc -std=gnu99 understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc -std=gnu99... gcc3 checking if unsupported combinations of configure options are allowed... no checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for off_t... yes checking for size_t... yes checking for ssize_t... yes checking for ptrdiff_t... yes checking whether byte ordering is bigendian... no checking size of char... 1 checking size of short... 2 checking size of int... 4 checking size of unsigned... 4 checking size of long... 8 checking size of long long... 8 checking size of int64... 0 checking size of float... 4 checking size of double... 8 checking size of long double... 16 checking size of float128... 16 checking size of _Quad... 0 checking quadmath.h usability... yes checking quadmath.h presence... yes checking for quadmath.h... yes checking maximum decimal precision for C... 33 checking if Fortran interface enabled... no checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++11 accepts -g... yes checking dependency style of g++ -std=gnu++11... gcc3 checking how to run the C++ preprocessor... g++ -std=gnu++11 -E checking if c++ interface enabled... yes checking if g++ -std=gnu++11 needs old style header files in includes... no checking if g++ -std=gnu++11 can handle namespaces... yes checking if g++ -std=gnu++11 can handle static cast... yes checking if g++ -std=gnu++11 has offsetof extension... yes checking if the high-level library is enabled... yes checking for ar... ar checking whether make sets $(MAKE)... (cached) yes checking for tr... /bin/tr checking if srcdir= and time commands work together... yes checking if Java JNI interface enabled... no checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc -std=gnu99... /bin/ld checking if the linker (/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B checking the name lister (/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1966080 checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /bin/nm -B output from gcc -std=gnu99 object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... yes checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes checking if gcc -std=gnu99 static flag -static works... yes checking if gcc -std=gnu99 supports -c -o file.o... yes checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes checking whether the gcc -std=gnu99 linker (/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -std=gnu++11 -E checking for ld used by g++ -std=gnu++11... /bin/ld -m elf_x86_64 checking if the linker (/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ -std=gnu++11 linker (/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ -std=gnu++11 option to produce PIC... -fPIC -DPIC checking if g++ -std=gnu++11 PIC flag -fPIC -DPIC works... yes checking if g++ -std=gnu++11 static flag -static works... yes checking if g++ -std=gnu++11 supports -c -o file.o... yes checking if g++ -std=gnu++11 supports -c -o file.o... (cached) yes checking whether the g++ -std=gnu++11 linker (/bin/ld -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... error configure: error: \'no\' is not a valid rpath type sh configure checking for a BSD-compatible install... /bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking shell variables initial values... done checking if basename works... yes checking if xargs works... yes checking for cached host... none checking for config x86_64-unknown-linux-gnu... no checking for config x86_64-unknown-linux-gnu... no checking for config unknown-linux-gnu... no checking for config unknown-linux-gnu... no checking for config x86_64-linux-gnu... no checking for config x86_64-linux-gnu... no checking for config x86_64-unknown... no checking for config linux-gnu... found compiler 'gcc' is GNU gcc-4.8.5 compiler 'gfortran' is GNU gfortran-4.8.5 compiler 'g++' is GNU g++-4.8.5 checking for config ./config/site-specific/host-hb1c6n8.hpc... no checking for config ./config/site-specific/host-hpc... no checking build mode... production checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking if unsupported combinations of configure options are allowed... no checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for off_t... yes checking for size_t... yes checking for ssize_t... yes checking for ptrdiff_t... yes checking whether byte ordering is bigendian... no checking size of char... 1 checking size of short... 2 checking size of int... 4 checking size of unsigned... 4 checking size of long... 8 checking size of long long... 8 checking size of int64... 0 checking size of float... 4 checking size of double... 8 checking size of long double... 16 checking size of float128... 16 checking size of _Quad... 0 checking quadmath.h usability... yes checking quadmath.h presence... yes checking for quadmath.h... yes checking maximum decimal precision for C... 33 checking if Fortran interface enabled... no checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking if c++ interface enabled... no checking if the high-level library is enabled... yes checking for ar... ar checking whether make sets $(MAKE)... (cached) yes checking for tr... /bin/tr checking if srcdir= and time commands work together... yes checking if Java JNI interface enabled... no checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /bin/ld checking if the linker (/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B checking the name lister (/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1966080 checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 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... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking if we should install only statically linked executables... no checking if -Wl,-rpath should be used to link shared libs in nondefault directories... error configure: error: \'yes\' is not a valid rpath type make: * [_config] Error 1 configure: HDF5_INCLUDE=hdf5/src configure: HDF5_CXX_INCLUDE=hdf5/c++/src configure: HDF5_HL_INCLUDE=hdf5/hl/src configure: HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src configure: HDF5_LIB=hdf5/src/.libs/libhdf5.a configure: HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a configure: HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a configure: HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a configure: SZIP_LIB=hdf5/szip/src/.libs/libsz.a configure: creating ./config.status config.status: creating src/Makevars * libs mkdir -p "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src/".h "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/c++/src/".h "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/src/".h "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/c++/src/".h "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" mkdir -p "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/src/.libs/libhdf5.a" "/ifs/scratch/msph/ehs/akb2134/R_libs/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp: cannot stat ‘hdf5/src/.libs/libhdf5.a’: No such file or directory make: [copying] Error 1 ERROR: compilation failed for package ‘Rhdf5lib’

On Sat, Apr 11, 2020 at 12:37 PM Mike Smith notifications@github.com wrote:

The original error was due to me including the file src/COPYING in 283de8c https://github.com/grimbough/Rhdf5lib/commit/283de8c40c9224059143bfb493cbf19fed77c861. How're this only seemed to break Mac OS X & had now been reverted, so it shouldn't be an issue anymore.

I suspect the problem is that the compilation of libhdf5.a is failing, but we only find out when it tries to copy that file & it doesn't exist. Could you include everything that is printed to screen when you try to install the package?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/grimbough/Rhdf5lib/issues/26#issuecomment-612460348, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACQQDI6PODF7NXUONOQWBPDRMCMFZANCNFSM4KUM7NNA .

grimbough commented 4 years ago

Thanks for that. It looks like there's at least two errors in there:

checking if -Wl,-rpath should be used to link shared libs in nondefault
directories... error
configure: error: \'no\' is not a valid rpath type

and 

checking if -Wl,-rpath should be used to link shared libs in nondefault
directories... error
configure: error: \'yes\' is not a valid rpath type

So I think this is more closely related to #25. Could you follow the instructions in https://github.com/grimbough/Rhdf5lib/issues/25#issuecomment-575926331 and then reply to that issue?

annebozack commented 4 years ago

That solved the problem - thanks so much for your help!

On Mon, Apr 13, 2020 at 5:43 AM Mike Smith notifications@github.com wrote:

Thanks for that. It looks like there's at least two errors in there:

checking if -Wl,-rpath should be used to link shared libs in nondefault directories... error configure: error: \'no\' is not a valid rpath type

and

checking if -Wl,-rpath should be used to link shared libs in nondefault directories... error configure: error: \'yes\' is not a valid rpath type

So I think this is more closely related to #25 https://github.com/grimbough/Rhdf5lib/issues/25. Could you follow the instructions in #25 (comment) https://github.com/grimbough/Rhdf5lib/issues/25#issuecomment-575926331 and then reply to that issue?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/grimbough/Rhdf5lib/issues/26#issuecomment-612831420, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACQQDIZXNY5DLQPYGYXFIALRMLNEHANCNFSM4KUM7NNA .

grimbough commented 4 years ago

Can you just confirm for me which of the two commands was needed? Then I'll make the necessary changes to the version on Bioconductor so you don't have to do a weird install from GitHub everytime it changes

annebozack commented 4 years ago

This one did it:

BiocManager::install("grimbough/Rhdf5lib", ref = "disable-rpath")

On Wed, Apr 15, 2020 at 2:46 AM Mike Smith notifications@github.com wrote:

Can you just confirm for me which of the two commands was needed? Then I'll make the necessary changes to the version on Bioconductor so you don't have to do a weird install from GitHub everytime it changes

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/grimbough/Rhdf5lib/issues/26#issuecomment-613849949, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACQQDIY3RCTXJRIYY4TVDETRMVJ47ANCNFSM4KUM7NNA .