Issue installing rhdf5 package on R-3.0.2
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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.
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Bernd Fischer ▴ 550
@bernd-fischer-5348
Last seen 7.9 years ago
Germany / Heidelberg / DKFZ
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]]
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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]]
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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]]
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Entering edit mode
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 <shivaliit05@gmail.com> 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 <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]]
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Dear Bernd, I also tried removing int from removehandle function and made that void Following changes - ====================HandleList.cpp====================== void removeHandle( hid_t id ) { HandleList::Instance().removeHandle( id ); } ===============HandleList.h========================== void removeHandle( hid_t fid ); ============================================= But still the Internal Compiler error is coming - 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]> Regards, Shivali On 11 December 2013 16:22, Bernd Fischer <bernd.fischer@embl.de> wrote: > 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 <shivaliit05@gmail.com> 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 <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]]
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