But still following error is coming --

xlC_r: 1501-230 (S) Internal compiler error; please contact your Service
Representative. For more information visit:
http://www.ibm.com/support/docview.wss?uid=swg21110810
make: 1254-004 The error code from the last command is 41.


Stop.
ERROR: compilation failed for package 'rhdf5'
* removing '/gpfs1/home/shivali/R-3.0.2/
lib/R/library/rhdf5'
[ncmr0102][/gpfs1/home/shivali/R-3.0.2/bin]>




Hi Bernd,
>
> I executed the latest tar you shared as following -
>
>
> [ncmr0102][/gpfs1/home/shivali/R-3.0.2/bin]>  R CMD INSTALL
> /gpfs1/home/shivali/rhdf5_2.7.3.tar.gz
> * installing to library '/gpfs1/home/shivali/R-3.0.2/lib/R/library'
> * installing *source* package 'rhdf5' ...
> ** libs
>         cd hdf5source &&  gunzip -dc hdf5small.tgz | tar xf -;
>         mv hdf5source/hdf5 .
>         cd hdf5 &&  ./configure CC="xlc_r -q64" CPP="" CXX="xlC_r -q64"
> CXXCPP="xlC_r -q64 -E" F77="xlf_r -q64" --build="" --with-pic
> checking for a BSD-compatible install... bin/install-sh -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... bin/install-sh -c -d
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking whether to enable maintainer-specific portions of Makefiles... no
> checking build system type... powerpc-ibm-aix5.3.0.0
> checking host system type... powerpc-ibm-aix5.3.0.0
> checking shell variables initial values... done
> checking if basename works... yes
> checking if xargs works... yes
> checking for cached host... none
> checking for config powerpc-ibm-aix5.3.0.0... no
> checking for config powerpc-ibm-aix... no
> checking for config ibm-aix5.3.0.0... no
> checking for config ibm-aix... found
> compiler 'xlc_r -q64' is IBM XL-10.01.0000.0000
> checking for config ./config/site-specific/host-ncmr0102... no
> checking for gcc... xlc_r -q64
> 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... no
> checking whether xlc_r -q64 accepts -g... yes
> checking for xlc_r -q64 option to accept ISO C89... none needed
> checking for style of include used by make... GNU
> checking dependency style of xlc_r -q64... aix
> checking if unsupported combinations of configure options are allowed... no
> checking if Fortran interface enabled... no
> checking whether we are using the GNU C++ compiler... no
> checking whether xlC_r -q64 accepts -g... yes
> checking dependency style of xlC_r -q64... aix
> checking how to run the C++ preprocessor... xlC_r -q64 -E
> checking if c++ interface enabled... no
> checking whether make sets $(MAKE)... (cached) yes
> checking for tr... /bin/tr
> checking if srcdir= and time commands work together... yes
> checking how to print strings... print -r
> checking for a sed that does not truncate output... /bin/sed
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for fgrep... /bin/grep -F
> checking for non-GNU ld... /bin/ld
> checking if the linker (/bin/ld) is GNU ld... no
> 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... 1572864
> checking whether the shell understands some XSI constructs... yes
> checking whether the shell understands "+="... no
> checking how to convert powerpc-ibm-aix5.3.0.0 file names to
> powerpc-ibm-aix5.3.0.0 format... func_convert_file_noop
> checking how to convert powerpc-ibm-aix5.3.0.0 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... dlltool
> checking how to associate runtime and link libraries... print -r --
> checking for archiver @FILE support... no
> checking for strip... strip
> checking for ranlib... ranlib
> checking command to parse /bin/nm -B output from xlc_r -q64 object... ok
> checking for sysroot... no
> checking for mt... mt
> checking if mt is a manifest tool... no
> checking how to run the C preprocessor... xlc_r -q64 -E
> checking for ANSI C header files... (cached) yes
> checking for sys/types.h... yes
>
>
> ================================================================
>
>
> But now i am getting -
> ===============================================================
>
>              SUMMARY OF THE HDF5 CONFIGURATION
>             =================================
>
> General Information:
> -------------------
>                    HDF5 Version: 1.8.7
>                   Configured on: Wed Dec 11 15:36:10 IST 2013
>                   Configured by: shivali@ncmr0102
>                  Configure mode: production
>                     Host system: powerpc-ibm-aix5.3.0.0
>               Uname information: AIX ncmr0102 3 5 00CEBD134C00
>                        Byte sex: big-endian
>                       Libraries:
>              Installation point:
> /tmp/Rtmp4EW1Lb/R.INSTALLd200425b14009/rhdf5/src/hdf5/hdf5
>
> Compiling Options:
> ------------------
>                Compilation Mode: production
>                      C Compiler: /usr/vac/bin/xlc_r -q64 ( IBM XL C/C++
> 10.01.0000.0000)
>                          CFLAGS: -O -qstrict
>                       H5_CFLAGS: -qlanglvl=stdc99  -w
>                       AM_CFLAGS:
>                        CPPFLAGS:
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include
>                     H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
>                     AM_CPPFLAGS:
>                Shared C Library: no
>                Static C Library: yes
>   Statically Linked Executables: no
>                         LDFLAGS:
>                      H5_LDFLAGS:
>                      AM_LDFLAGS:
>                 Extra libraries:  -lz -lm
>                        Archiver: ar -X64
>                          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: yes
>                         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  all-am
>   CC     H5.lo
>   CC     H5checksum.lo
>   CC     H5dbg.lo
>
> Target "all-am" is up to date.
>         cp hdf5/src/.libs/libhdf5ForBioC.a .
>         xlc_r -q64 -I/gpfs1/home/shivali/R-3.0.2/lib/R/include -DNDEBUG
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include   -Ihdf5/src   -O
> -qstrict  -c H5A.c -o H5A.o
>         xlc_r -q64 -I/gpfs1/home/shivali/R-3.0.2/lib/R/include -DNDEBUG
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include   -Ihdf5/src   -O
> -qstrict  -c H5D.c -o H5D.o
>         xlc_r -q64 -I/gpfs1/home/shivali/R-3.0.2/lib/R/include -DNDEBUG
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include   -Ihdf5/src   -O
> -qstrict  -c H5F.c -o H5F.o
>         xlc_r -q64 -I/gpfs1/home/shivali/R-3.0.2/lib/R/include -DNDEBUG
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include   -Ihdf5/src   -O
> -qstrict  -c H5G.c -o H5G.o
>         xlc_r -q64 -I/gpfs1/home/shivali/R-3.0.2/lib/R/include -DNDEBUG
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include   -Ihdf5/src   -O
> -qstrict  -c H5I.c -o H5I.o
> "H5I.c", line 24.24: 1506-280 (W) Function argument assignment between
> types "char*" and "char(*)[]" is not allowed.
>         xlc_r -q64 -I/gpfs1/home/shivali/R-3.0.2/lib/R/include -DNDEBUG
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include   -Ihdf5/src   -O
> -qstrict  -c H5L.c -o H5L.o
>         xlc_r -q64 -I/gpfs1/home/shivali/R-3.0.2/lib/R/include -DNDEBUG
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include   -Ihdf5/src   -O
> -qstrict  -c H5O.c -o H5O.o
>         xlc_r -q64 -I/gpfs1/home/shivali/R-3.0.2/lib/R/include -DNDEBUG
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include   -Ihdf5/src   -O
> -qstrict  -c H5S.c -o H5S.o
>         xlc_r -q64 -I/gpfs1/home/shivali/R-3.0.2/lib/R/include -DNDEBUG
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include   -Ihdf5/src   -O
> -qstrict  -c H5T.c -o H5T.o
>         xlc_r -q64 -I/gpfs1/home/shivali/R-3.0.2/lib/R/include -DNDEBUG
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include   -Ihdf5/src   -O
> -qstrict  -c H5constants.c -o H5constants.o
>         xlC_r -q64 -I/gpfs1/home/shivali/R-3.0.2/lib/R/include -DNDEBUG
> -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
> -I/usr/lpp/X11/include/X11
> -I/gpfs1/home/shivali/software/gettext-0.18/include
> -I/gpfs1/home/shivali/software/libpng-1.6.2/include   -Ihdf5/src   -O
> -qstrict  -c HandleList.cpp -o HandleList.o
>
> xlC_r: 1501-230 (S) Internal compiler error; please contact your Service
> Representative. For more information visit:
> http://www.ibm.com/support/docview.wss?uid=swg21110810
> make: 1254-004 The error code from the last command is 41.
>
>
> Stop.
> ERROR: compilation failed for package 'rhdf5'
> * removing '/gpfs1/home/shivali/R-3.0.2/lib/R/library/rhdf5'
> [ncmr0102][/gpfs1/home/shivali/R-3.0.2/bin]>
>
>
> Thanks & Regards,
> Shivali Gangwar
>
>
>
>
> On 11 December 2013 15:20, Bernd Fischer <bernd.fischer@embl.de> wrote:
>
>> Dear Shivali!
>>
>> Can you please specify the command that you used to download and install
>> rhdf5 in your next post?
>>
>> 1.) I think, I solved a this issue already in current developmental
>> version.
>> Try to install the latest version of rhdf5 from the devel branch
>> (currently 2.7.3):
>> http://www.bioconductor.org/packages/2.14/bioc/html/rhdf5.html
>>
>> 2.) You added an include path to your local HDF5 installation:
>>
>>  -I/gpfs1/home/shivali/hdf5-1.8.12/include
>>
>> Remove this include path. There can be a clash between your the local
>> HDF5 installation and the HDF5 version that is used by rhdf5. You don't
>> need
>> to install HDF5 beforehand on your computer. rhdf5 brings its own HDF5
>> library.
>>
>> Best,
>>
>> Bernd
>>
>>
>>
>>
>> On 11.12.2013, at 10:23, shivali@embl-heidelberg.de wrote:
>>
>>
>> AIX- 5.3
>>
>>        xlC_r -q64 -I/gpfs1/home/shivali/R-Updated/R-3.0.2/lib/R/include
>> -DNDEBUG  -I/gpfs1/home/shivali/shivali/libiconv-1.14/include
>> -I/usr/lpp/X11/include/X11
>> -I/gpfs1/home/shivali/software/gettext-0.18/include
>> -I/gpfs1/home/shivali/software/libpng-1.6.2/include
>> -I/gpfs1/home/shivali/hdf5-1.8.12/include   -Ihdf5/src   -O -qstrict  -c
>> HandleList.cpp -o HandleList.o
>> "HandleList.cpp", line 175.1: 1540-1101 (W) A return value of type "int"
>> is expected.
>> xlC_r: 1501-230 (S) Internal compiler error; please contact your Service
>> Representative. For more information visit:
>> http://www.ibm.com/support/docview.wss?uid=swg21110810
>> make: 1254-004 The error code from the last command is 41.
>>
>>
>> Stop.
>> ERROR: compilation failed for package 'rhdf5'
>> * removing '/gpfs1/home/shivali/R-Updated/R-3.0.2/lib/R/library/rhdf5'
>> [ncmr0102][/gpfs1/home/shivali/R-Updated/R-3.0.2/bin]>
>>
>> -- output of sessionInfo():
>>
>> [ncmr0102][/gpfs1/home/shivali/R-Updated/R-3.0.2/bin]> R
>>
>> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
>> Copyright (C) 2013 The R Foundation for Statistical Computing
>> Platform: powerpc-ibm-aix5.3.0.0 (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>>  Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>> s> essionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: powerpc-ibm-aix5.3.0.0 (64-bit)
>>
>> locale:
>> [1] en_US en_US en_US C en_US en_US
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>>
>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
>>
>>
>

	[[alternative HTML version deleted]]

