Search
Question: Problem installing rhdf5
0
gravatar for jariani.abb
7 weeks ago by
jariani.abb10
jariani.abb10 wrote:

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
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by jariani.abb10
1

 

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.

ADD REPLYlink written 6 weeks ago by Mike Smith2.1k
1

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.

ADD REPLYlink written 6 weeks ago by Wolfgang Huber13k
1

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

ADD REPLYlink written 6 weeks ago by jariani.abb10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 285 users visited in the last hour