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jariani.abb
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@jarianiabb-9953
Last seen 7.2 years ago
Hi,
For an obscure reason I cannot get rhdf5 to install on my ubuntu 16 machine. When I try to install it on another computer with the same version of Ubuntu it works. I am wondering if you could help me out. Many thanks!
Here is the start and the end of installation log which fitted here:
Kind regards,
Abbas Jariani
PhD student, VIB center for microbiology, KU Leuven
> source("https://bioconductor.org/biocLite.R";)
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
version of R; see http://bioconductor.org/install
> biocLite("rhdf5")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘rhdf5’
trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/rhdf5_2.18.0.tar.gz';
Content type 'application/x-gzip' length 5397112 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
-
installing source package ‘rhdf5’ ...
** libs
cd hdf5source && \
gunzip -dc hdf5small.tgz | tar xf -;
rm -rf hdf5
mv hdf5source/hdf5 .
cd hdf5 && \
./configure CC="gcc" CPP="gcc -E" CXX="g++" CXXCPP="g++ -E" F77="f95" --build="" --with-pic
checking for a BSD-compatible install... /usr/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 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
.
.
.
.
config.status: creating src/H5config.h
config.status: executing default-1 commands
creating src/H5pubconf.h
Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
chmod: cannot access 'tools/misc/h5cc': No such file or directory
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
HDF5 Version: 1.8.7
Configured on: Tue Oct 3 18:06:04 CEST 2017
Configured by: abbas@abbas-desktop
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux abbas-desktop 4.10.0-35-generic #39~16.04.1-Ubuntu SMP Wed Sep 13 09:02:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /tmp/Rtmpl31CV7/R.INSTALL12bf7934f2e4/rhdf5/src/hdf5/hdf5
Compiling Options:
Compilation Mode: production
C Compiler: /usr/bin/gcc
CFLAGS:
H5_CFLAGS: -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -w -O -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
Fortran: no
C++: no
Features:
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
H5dump Packed Bits: yes
cd hdf5/src && \
make
make[1]: Entering directory '/tmp/Rtmpl31CV7/R.INSTALL12bf7934f2e4/rhdf5/src/hdf5/src'
make all-am
make[2]: Entering directory '/tmp/Rtmpl31CV7/R.INSTALL12bf7934f2e4/rhdf5/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 H5B.lo
CC H5Bcache.lo
CC H5Bdbg.lo
CC H5B2.lo
CC H5B2cache.lo
CC H5B2dbg.lo
CC H5B2hdr.lo
CC H5B2int.lo
CC H5B2stat.lo
CC H5B2test.lo
CC H5C.lo
CC H5CS.lo
CC H5D.lo
CC H5Dbtree.lo
CC H5Dchunk.lo
CC H5Dcompact.lo
CC H5Dcontig.lo
CC H5Ddbg.lo
CC H5Ddeprec.lo
CC H5Defl.lo
CC H5Dfill.lo
CC H5Dint.lo
CC H5Dio.lo
CC H5Dlayout.lo
CC H5Dmpio.lo
CC H5Doh.lo
CC H5Dscatgath.lo
CC H5Dselect.lo
CC H5Dtest.lo
CC H5E.lo
CC H5Edeprec.lo
CC H5Eint.lo
CC H5F.lo
CC H5Faccum.lo
CC H5Fdbg.lo
CC H5Fefc.lo
CC H5Ffake.lo
CC H5Fio.lo
CC H5Fmount.lo
CC H5Fmpi.lo
CC H5Fquery.lo
CC H5Fsfile.lo
CC H5Fsuper.lo
CC H5Fsuper_cache.lo
CC H5Ftest.lo
CC H5FD.lo
CC H5FDcore.lo
CC H5FDdirect.lo
CC H5FDfamily.lo
CC H5FDint.lo
CC H5FDlog.lo
CC H5FDmpi.lo
CC H5FDmpio.lo
CC H5FDmpiposix.lo
CC H5FDmulti.lo
CC H5FDsec2.lo
CC H5FDspace.lo
CC H5FDstdio.lo
CC H5FL.lo
CC H5FO.lo
CC H5FS.lo
CC H5FScache.lo
CC H5FSdbg.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 H5HL.lo
CC H5HLcache.lo
CC H5HLdbg.lo
CC H5HLint.lo
CC H5HP.lo
CC H5I.lo
CC H5Itest.lo
CC H5L.lo
CC H5Lexternal.lo
CC H5make_libsettings.o
CCLD H5make_libsettings
../libtool: eval: line 6449: unexpected EOF while looking for matching `''
../libtool: eval: line 6450: syntax error: unexpected end of file
Makefile:689: recipe for target 'H5make_libsettings' failed
make[2]: * [H5make_libsettings] Error 2
make[2]: Leaving directory '/tmp/Rtmpl31CV7/R.INSTALL12bf7934f2e4/rhdf5/src/hdf5/src'
Makefile:590: recipe for target 'all' failed
make[1]: * [all] Error 2
make[1]: Leaving directory '/tmp/Rtmpl31CV7/R.INSTALL12bf7934f2e4/rhdf5/src/hdf5/src'
Makevars:27: recipe for target 'libhdf5ForBioC.a' failed
make: * [libhdf5ForBioC.a] Error 2
ERROR: compilation failed for package ‘rhdf5’
-
removing ‘/home/abbas/R/x86_64-pc-linux-gnu-library/3.3/rhdf5’
The downloaded source packages are in ‘/tmp/RtmpWQrrTE/downloaded_packages’ installation path not writeable, unable to update packages: boot, cluster, foreign, lattice, MASS, Matrix, mgcv, nlme, rpart, survival Warning message: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘rhdf5’ had non-zero exit status
This is a strange problem, as it looks like it's problem compiling the version of libhdf5 that is distributed with the package. Just to confirm it isn't a corrupted download, can you try downloading the rhdf5 source tarball (http://bioconductor.org/packages/release/bioc/src/contrib/rhdf5_2.20.0.tar.gz) and install directly from that. Similarly you can try installing from the package's github repo:
BiocInstaller::biocLite('grimbough/rhdf5')If neither of those works then I suspect it's a problem with the build tools you've got installed on that machine, but it might take a bit of trial and error to find them. Let me know how you get on.
For good measure, try with a more recent version of R and perhaps also update the rest of your system before hunting quirks of a possibly obsolete system configuration.
There is a couple of oddities, e.g. "installation path not writeable, unable to update packages: boot, ... survival" (problem with permissions?) and the fact that you want to build R packages from source but have no C++ and Fortran installed. It's not clear whether they are causative, but tracing down a problem like the one you describe tends to be easier if the build system is well-maintained.
Thank you Mike Smith and Wolfgang Huber for your replies.
I tried copying the tarball from a another computer where it installed correctly, however it did not work. Regarding the permission issues I tried to start the R session with sudo however it did not help.
After few days of struggle I ended up formating my pc and re-instaling the Ubuntu and it did the trick. I suspect that at some point I might have manually messed up something in Ubuntu that I shouldn't have and it caused the problem.
Kind regards,
Abbas