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This page was generated on 2018-04-12 13:45:11 -0400 (Thu, 12 Apr 2018).
Package 1174/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Rhdf5lib 1.0.0 Mike Smith
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] |
Package: Rhdf5lib |
Version: 1.0.0 |
Command: rm -rf Rhdf5lib.buildbin-libdir && mkdir Rhdf5lib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhdf5lib_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhdf5lib.buildbin-libdir |
StartedAt: 2018-04-12 12:07:55 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 12:11:03 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 188.2 seconds |
RetCode: 0 |
Status: OK |
PackageFile: Rhdf5lib_1.0.0.tgz |
PackageFileSize: 5.185 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Rhdf5lib.buildbin-libdir && mkdir Rhdf5lib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhdf5lib_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhdf5lib.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rhdf5lib.buildbin-libdir Rhdf5lib_1.0.0.tar.gz' >>>>>>> * installing *source* package ‘Rhdf5lib’ ... checking for gcc... clang 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... yes checking whether clang accepts -g... yes checking for clang option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes untarring hdf5small_cxx_1.8.19.tar.gz ... building the szip library... 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/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... x86_64-apple-darwin15.6.0 checking host system type... x86_64-apple-darwin15.6.0 checking for config x86_64-apple-darwin15.6.0... no checking for config x86_64-apple-darwin15.6.0... no checking for config apple-darwin15.6.0... no checking for config apple-darwin15.6.0... no checking for config x86_64-darwin15.6.0... no checking for config x86_64-darwin15.6.0... no checking for config x86_64-apple... no checking for config darwin15.6.0... no checking for config darwin15.6.0... no checking for config apple... no checking for config x86_64... no checking for gcc... clang 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... yes checking whether clang accepts -g... yes checking for clang option to accept ISO C89... none needed checking whether clang understands -c and -o together... rm: conftest.dSYM: is a directory yes checking for style of include used by make... 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(cached) yes checking whether the clang linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin15.6.0 dyld checking how to hardcode library paths into programs... immediate checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for build mode... production checking for math library support... no checking for ANSI C header files... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for error_at_line... no checking for working memcmp... yes checking for vprintf... yes checking for _doprnt... no checking for memset... yes checking if encoding enabled... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/SZconfig.h config.status: executing depfiles commands config.status: executing libtool commands Making all in src make all-am /bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Wall -O2 -w -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c -o rice.lo rice.c libtool: compile: clang -DHAVE_CONFIG_H -I. -Wall -O2 -w -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c rice.c -fno-common -DPIC -o rice.o mv -f .deps/rice.Tpo .deps/rice.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Wall -O2 -w -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c -o sz_api.lo sz_api.c libtool: compile: clang -DHAVE_CONFIG_H -I. -Wall -O2 -w -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c sz_api.c -fno-common -DPIC -o sz_api.o mv -f .deps/sz_api.Tpo .deps/sz_api.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -Wall -O2 -w -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c -o encoding.lo encoding.c libtool: compile: clang -DHAVE_CONFIG_H -I. -Wall -O2 -w -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c encoding.c -fno-common -DPIC -o encoding.o mv -f .deps/encoding.Tpo .deps/encoding.Plo /bin/sh ../libtool --tag=CC --mode=link clang -Wall -O2 -w -version-info 2:0:0 -o libsz.la -rpath /private/tmp/Rtmpsn8RD8/R.INSTALL5978178d7f93/Rhdf5lib/src/hdf5/szip/szip/lib rice.lo sz_api.lo encoding.lo -lm libtool: link: ar cru .libs/libsz.a rice.o sz_api.o encoding.o libtool: link: ranlib .libs/libsz.a libtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" ) make[1]: Nothing to be done for `all-am'. building the bundled hdf5 library... 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/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... 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BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking how to convert i386-apple-darwin15.6.0 file names to i386-apple-darwin15.6.0 format... func_convert_file_noop checking how to convert i386-apple-darwin15.6.0 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... no checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from clang object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... clang -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if clang supports -fno-rtti -fno-exceptions... yes checking for clang option to produce PIC... -fno-common -DPIC checking if clang PIC flag -fno-common -DPIC works... yes checking if clang static flag -static works... no checking if clang supports -c -o file.o... yes checking if clang supports -c -o file.o... 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checking for __FUNCTION__ extension... yes checking for C99 designated initialization support... yes checking how to print long long... %ld and %lu checking Threads support system scope... yes checking for debug flags... none checking whether function stack tracking is enabled... no checking whether metadata trace file code is enabled... no checking for API tracing... no checking for instrumented library... no checking whether to clear file buffers... yes checking whether a memory checking tool will be used... no checking for parallel support files... skipped checking whether O_DIRECT is declared... no checking for posix_memalign... yes checking if the direct I/O virtual file driver (VFD) is enabled... no checking for custom plugin default path definition... /usr/local/hdf5/lib/plugin checking whether exception handling functions is checked during data conversions... yes checking whether data accuracy is guaranteed during data conversions... yes checking if the machine has window style path name... no checking if using special algorithm to convert long double to (unsigned) long values... no checking if using special algorithm to convert (unsigned) long to long double values... no checking if correctly converting long double to (unsigned) long long values... yes checking if correctly converting (unsigned) long long to long double values... yes checking additional programs should be built... no checking if deprecated public symbols are available... yes checking which version of public symbols to use by default... v18 checking whether to perform strict file format checks... no checking whether to have library information embedded in the executables... yes checking if alignment restrictions are strictly enforced... no configure: creating ./config.lt config.lt: creating libtool checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating src/libhdf5.settings config.status: creating Makefile config.status: creating src/Makefile config.status: creating c++/Makefile config.status: creating c++/src/Makefile config.status: creating c++/src/h5c++ config.status: creating src/H5config.h config.status: executing pubconf commands creating src/H5pubconf.h Post process src/libhdf5.settings config.status: executing depfiles commands config.status: executing libtool commands SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.8.19 Configured on: Thu Apr 12 12:08:35 EDT 2018 Configured by: biocbuild@veracruz1.bioconductor.org Configure mode: production Host system: i386-apple-darwin15.6.0 Uname information: Darwin veracruz1.bioconductor.org 15.6.0 Darwin Kernel Version 15.6.0: Tue Jan 9 20:12:05 PST 2018; root:xnu-3248.73.5˜1/RELEASE_X86_64 x86_64 Byte sex: little-endian Libraries: static Installation point: /private/tmp/Rtmpsn8RD8/R.INSTALL5978178d7f93/Rhdf5lib/src/hdf5/hdf5 Compiling Options: ------------------ Compilation Mode: production C Compiler: /usr/local/clang4/bin/clang CFLAGS: -Wall -g -O2 -w -L../szip/src/.libs -I../szip/src H5_CFLAGS: AM_CFLAGS: CPPFLAGS: 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 -ldl -lm Archiver: ar Ranlib: ranlib Debugged Packages: API Tracing: no Languages: ---------- Fortran: no C++: yes C++ Compiler: /usr/bin/g++ C++ Flags: H5 C++ Flags: AM C++ Flags: Shared C++ Library: no Static C++ Library: yes 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) MPE: no Direct VFD: no dmalloc: no Clear file buffers before write: yes Using memory checker: no Function Stack Tracing: no Strict File Format Checks: no Optimization Instrumentation: no for d in src . c++; do \ if test $d != .; then \ (cd $d && make lib) || exit 1; \ fi; \ done CC H5.lo CC H5checksum.lo CC H5dbg.lo CC H5system.lo CC H5timer.lo CC H5trace.lo CC H5A.lo CC H5Abtree2.lo CC H5Adense.lo CC H5Adeprec.lo CC H5Aint.lo CC H5Atest.lo CC H5AC.lo CC H5B.lo CC H5Bcache.lo CC H5Bdbg.lo CC H5B2.lo CC H5B2cache.lo CC H5B2dbg.lo CC H5B2hdr.lo CC H5B2int.lo CC H5B2stat.lo CC H5B2test.lo CC H5C.lo CC H5CS.lo CC H5D.lo CC H5Dbtree.lo CC H5Dchunk.lo CC H5Dcompact.lo CC H5Dcontig.lo CC H5Ddbg.lo CC H5Ddeprec.lo CC H5Defl.lo CC H5Dfill.lo CC H5Dint.lo CC H5Dio.lo CC H5Dlayout.lo CC H5Dmpio.lo CC H5Doh.lo CC H5Dscatgath.lo CC H5Dselect.lo CC H5Dtest.lo CC H5E.lo CC H5Edeprec.lo CC H5Eint.lo CC H5F.lo CC H5Fint.lo CC H5Faccum.lo CC H5Fcwfs.lo CC H5Fdbg.lo CC H5Fefc.lo CC H5Ffake.lo CC H5Fio.lo CC H5Fmount.lo CC H5Fmpi.lo CC H5Fquery.lo CC H5Fsfile.lo CC H5Fsuper.lo CC H5Fsuper_cache.lo CC H5Ftest.lo CC H5FD.lo CC H5FDcore.lo CC H5FDdirect.lo CC H5FDfamily.lo CC H5FDint.lo CC H5FDlog.lo CC H5FDmpi.lo CC H5FDmpio.lo CC H5FDmulti.lo CC H5FDsec2.lo CC H5FDspace.lo CC H5FDstdio.lo CC H5FL.lo CC H5FO.lo CC H5FS.lo CC H5FScache.lo CC H5FSdbg.lo CC H5FSsection.lo CC H5FSstat.lo CC H5FStest.lo CC H5G.lo CC H5Gbtree2.lo CC H5Gcache.lo CC H5Gcompact.lo CC H5Gdense.lo CC H5Gdeprec.lo CC H5Gent.lo CC H5Gint.lo CC H5Glink.lo CC H5Gloc.lo CC H5Gname.lo CC H5Gnode.lo CC H5Gobj.lo CC H5Goh.lo CC H5Groot.lo CC H5Gstab.lo CC H5Gtest.lo CC H5Gtraverse.lo CC H5HF.lo CC H5HFbtree2.lo CC H5HFcache.lo CC H5HFdbg.lo CC H5HFdblock.lo CC H5HFdtable.lo CC H5HFhdr.lo CC H5HFhuge.lo CC H5HFiblock.lo CC H5HFiter.lo CC H5HFman.lo CC H5HFsection.lo CC H5HFspace.lo CC H5HFstat.lo CC H5HFtest.lo CC H5HFtiny.lo CC H5HG.lo CC H5HGcache.lo CC H5HGdbg.lo CC H5HGquery.lo CC H5HL.lo CC H5HLcache.lo CC H5HLdbg.lo CC H5HLint.lo CC H5HP.lo CC H5I.lo CC H5Itest.lo CC H5L.lo CC H5Lexternal.lo CC H5make_libsettings.o CCLD H5make_libsettings LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \ sed -e 's/-L/:/g' -e 's/ //g'`" \ ./H5make_libsettings > H5lib_settings.c || \ (test $HDF5_Make_Ignore && echo "*** Error ignored") || \ (rm -f H5lib_settings.c ; exit 1) CC H5lib_settings.lo CC H5MF.lo CC H5MFaggr.lo CC H5MFdbg.lo CC H5MFsection.lo CC H5MM.lo CC H5MP.lo CC H5MPtest.lo CC H5O.lo CC H5Oainfo.lo CC H5Oalloc.lo CC H5Oattr.lo CC H5Oattribute.lo CC H5Obogus.lo CC H5Obtreek.lo CC H5Ocache.lo CC H5Ochunk.lo CC H5Ocont.lo CC H5Ocopy.lo CC H5Odbg.lo CC H5Odrvinfo.lo CC H5Odtype.lo CC H5Oefl.lo CC H5Ofill.lo CC H5Oginfo.lo CC H5Olayout.lo CC H5Olinfo.lo CC H5Olink.lo CC H5Omessage.lo CC H5Omtime.lo CC H5Oname.lo CC H5Onull.lo CC H5Opline.lo CC H5Orefcount.lo CC H5Osdspace.lo CC H5Oshared.lo CC H5Ostab.lo CC H5Oshmesg.lo CC H5Otest.lo CC H5Ounknown.lo CC H5P.lo CC H5Pacpl.lo CC H5Pdapl.lo CC H5Pdcpl.lo CC H5Pdeprec.lo CC H5Pdxpl.lo CC H5Pfapl.lo CC H5Pfcpl.lo CC H5Pfmpl.lo CC H5Pgcpl.lo CC H5Pint.lo CC H5Plapl.lo CC H5Plcpl.lo CC H5Pocpl.lo CC H5Pocpypl.lo CC H5Pstrcpl.lo CC H5Ptest.lo CC H5PL.lo CC H5R.lo CC H5Rdeprec.lo CC H5RC.lo CC H5RS.lo CC H5S.lo CC H5Sall.lo CC H5Sdbg.lo CC H5Shyper.lo CC H5Smpio.lo CC H5Snone.lo CC H5Spoint.lo CC H5Sselect.lo CC H5Stest.lo CC H5SL.lo CC H5SM.lo CC H5SMbtree2.lo CC H5SMcache.lo CC H5SMmessage.lo CC H5SMtest.lo CC H5ST.lo CC H5T.lo CC H5Tarray.lo CC H5Tbit.lo CC H5Tcommit.lo CC H5Tcompound.lo CC H5Tconv.lo CC H5Tcset.lo CC H5Tdbg.lo CC H5Tdeprec.lo CC H5Tenum.lo CC H5Tfields.lo CC H5Tfixed.lo CC H5Tfloat.lo CC H5detect.o CCLD H5detect LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \ sed -e 's/-L/:/g' -e 's/ //g'`" \ ./H5detect > H5Tinit.c || \ (test $HDF5_Make_Ignore && echo "*** Error ignored") || \ (rm -f H5Tinit.c ; exit 1) CC H5Tinit.lo CC H5Tnative.lo CC H5Toffset.lo CC H5Toh.lo CC H5Topaque.lo CC H5Torder.lo CC H5Tpad.lo CC H5Tprecis.lo CC H5Tstrpad.lo CC H5Tvisit.lo CC H5Tvlen.lo CC H5TS.lo CC H5VM.lo CC H5WB.lo CC H5Z.lo CC H5Zdeflate.lo CC H5Zfletcher32.lo CC H5Znbit.lo CC H5Zshuffle.lo CC H5Zszip.lo CC H5Zscaleoffset.lo CC H5Ztrans.lo CCLD libhdf5.la /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5CS.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Dmpio.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Fmpi.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDdirect.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDmpi.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDmpio.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5MFdbg.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Obogus.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Smpio.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5TS.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Zszip.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5CS.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Dmpio.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Fmpi.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDdirect.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDmpi.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDmpio.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5MFdbg.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Obogus.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Smpio.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5TS.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Zszip.o) has no symbols make[2]: Nothing to be done for `build-lib'. + cd src + make lib CXX H5Exception.lo CXX H5IdComponent.lo CXX H5DataSpace.lo CXX H5PropList.lo CXX H5Library.lo CXX H5FaccProp.lo CXX H5FcreatProp.lo CXX H5LaccProp.lo CXX H5DxferProp.lo CXX H5DcreatProp.lo CXX H5Location.lo CXX H5AbstractDs.lo CXX H5Attribute.lo CXX H5Object.lo CXX H5OcreatProp.lo CXX H5DataType.lo CXX H5AtomType.lo CXX H5PredType.lo CXX H5EnumType.lo CXX H5IntType.lo CXX H5FloatType.lo CXX H5StrType.lo CXX H5ArrayType.lo CXX H5VarLenType.lo CXX H5CompType.lo CXX H5DataSet.lo CXX H5CommonFG.lo CXX H5Group.lo CXX H5File.lo CXXLD libhdf5_cpp.la configure: HDF5_INCLUDE=hdf5/src configure: HDF5_CXX_INCLUDE=hdf5/c++/src configure: HDF5_LIB=hdf5/src/.libs/libhdf5.a configure: HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a configure: SZIP_LIB=hdf5/szip/src/.libs/libsz.a configure: creating ./config.status config.status: creating src/Makevars ** libs mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include" cp hdf5/src/*.h /Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include/c++" cp hdf5/c++/src/*.h /Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include/c++ mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/" cp hdf5/src/.libs/libhdf5.a /Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/ cp hdf5/c++/src/.libs/libhdf5_cpp.a /Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/ cp hdf5/szip/src/.libs/libsz.a /Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/ clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c Rhdf5lib.c -o Rhdf5lib.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rhdf5lib.so Rhdf5lib.o hdf5/src/.libs/libhdf5.a hdf5/szip/src/.libs/libsz.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Rhdf5lib) >>>>>>> >>>>>>> FIXING LINKS FOR Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so" install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so" install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so" install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so"