############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=rhdf5.buildbin-libdir rhdf5_2.39.6.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'rhdf5' ... ** using staged installation ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5.c -o H5.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5A.c -o H5A.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5D.c -o H5D.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5E.c -o H5E.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5F.c -o H5F.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5G.c -o H5G.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5I.c -o H5I.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5L.c -o H5L.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5O.c -o H5O.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5P.c -o H5P.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5R.c -o H5R.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5S.c -o H5S.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5S_extras.c -o H5S_extras.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5T.c -o H5T.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5Z.c -o H5Z.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c H5constants.c -o H5constants.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c HandleList.cpp -o HandleList.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c HandleListWrap.c -o HandleListWrap.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c bit64conversion.c -o bit64conversion.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c external_filters.c -o external_filters.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c h5dump.c -o h5dump.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c h5ls.c -o h5ls.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c h5testLock.c -o h5testLock.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c h5writeDataFrame.c -o h5writeDataFrame.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c printdatatype.c -o printdatatype.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c utils.c -o utils.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c wrap.c -o wrap.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o rhdf5.dll tmp.def H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5R.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o -LD:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/x64 -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/meat/rhdf5.buildbin-libdir/00LOCK-rhdf5/00new/rhdf5/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rhdf5' finding HTML links ... done H5Aclose html H5Acreate html H5Adelete html H5Aexists html H5Aget_name html H5Aget_space html H5Aget_type html H5Aopen html H5Aread html H5Awrite html H5Dchunk_dims html H5Dclose html H5Dcreate html H5Dget_create_plist html H5Dget_space html H5Dget_storage_size html H5Dget_type html H5Dopen html H5Dread html H5Dset_extent html H5Dwrite html H5Fclose html H5Fcreate html H5Fflush html H5Fget_filesize html H5Fget_name html H5Fget_plist html H5Fis_hdf5 html H5Fopen html H5Gclose html H5Gcreate html H5Gcreate_anon html H5Gget_info html H5Gopen html H5IdComponent-class html H5Iget_name html H5Iget_type html H5Iis_valid html H5Lcopy html H5Lcreate_external html H5Ldelete html H5Lexists html H5Lget_info html H5Lmove html H5Oclose html H5Oget_num_attrs html H5Olink html H5Oopen html H5P_chunk html H5P_chunk_cache html H5P_fill_time html H5P_fill_value html H5P_filters html H5P_istore_k html H5P_layout html H5P_libver_bounds html H5P_shared_mesg_nindexes html H5P_shared_mesg_phase_change html H5P_sizes html H5P_sym_k html H5P_userblock html H5Pclose html H5Pcopy html H5Pcreate html H5Pfill_value_defined html H5Pget_class html H5Pget_version html H5Pobject_track_times html H5Pset_blosc html H5Pset_bzip2 html H5Pset_deflate html H5Pset_fapl_ros3 html H5Pset_lzf html H5Pset_nbit html H5Pset_shuffle html H5Pset_szip html H5Pshared_mesg_index html H5R html H5Rcreate html H5Rdereference html H5Ref-class html H5Rget_name html H5Rget_obj_type html H5Rget_region html H5Sclose html H5Scombine_hyperslab html H5Scombine_select html H5Scopy html H5Screate html H5Screate_simple html H5Sget_select_npoints html H5Sget_simple_extent_dims html H5Sis_simple html H5Sselect_all html H5Sselect_hyperslab html H5Sselect_index html H5Sselect_none html H5Sselect_valid html H5Sset_extent_simple html H5Sunlimited html H5T_cset html H5T_precision html H5T_size html H5T_strpad html H5Tcopy html H5Tis_variable_str html H5Zfilter_avail html H5functions html h5_FileLocking html h5_createAttribute html h5_createDataset html h5_createFile html h5_createGroup html h5_delete html h5_deleteAttribute html h5_dump html h5_errorHandling html h5_read html h5_readAttributes html h5_save html h5_set_extent html h5_write html h5_writeAttribute html h5checkFilters html h5closeAll html h5constants html h5listObjects html h5ls html h5version html rhdf5 html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * MD5 sums packaged installation of 'rhdf5' as rhdf5_2.39.6.zip * DONE (rhdf5)