Dear Shivali! I checked in a new version 2.7.4 in SVN. It will appear by tomorrow 18:00 GMT on the bioconductor website. I removed the 'int' return value, since it is not used anyway. Best, Bernd On 11.12.2013, at 11:47, shivali gangwar wrote: > 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 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]]