Question: Problem installing rhdf5
gravatar for
14 months ago by
jariani.abb10 wrote:


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("";)

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

> biocLite("rhdf5")


Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).

Installing package(s) ‘rhdf5’

trying URL '';

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



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


     Installation point: /tmp/Rtmpl31CV7/R.INSTALL12bf7934f2e4/rhdf5/src/hdf5/hdf5

Compiling Options:

               Compilation Mode: production

                     C Compiler: /usr/bin/gcc


                      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





               Shared C Library: yes

               Static C Library: yes

  Statically Linked Executables: no




  Extra libraries:  -lz -lm 

         Archiver: ar

  Ranlib: ranlib

        Debugged Packages: 

    API Tracing: no


                        Fortran: no

                            C++: no


                  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[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


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 14 months ago • written 14 months ago by jariani.abb10


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 ( and install directly from that.  Similarly you can try installing from the package's github repo:


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 14 months ago by Mike Smith3.1k

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 14 months ago by Wolfgang Huber13k

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,



ADD REPLYlink written 14 months ago by jariani.abb10
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