############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL HDF5Array ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'HDF5Array' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c H5File.c -o H5File.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c global_errmsg_buf.c -o global_errmsg_buf.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c H5DSetDescriptor.c -o H5DSetDescriptor.o H5DSetDescriptor.c: In function 'print_H5TypeDescriptor': H5DSetDescriptor.c:720:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=] 720 | Rprintf("%s * h5type_id = %ld\n", margin, h5type->h5type_id); | ~~^ ~~~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld H5DSetDescriptor.c:722:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 722 | Rprintf("%s * h5type_size = %lu\n", margin, h5type->h5type_size); | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int size_t {aka long long unsigned int} | %llu H5DSetDescriptor.c:762:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 762 | Rprintf("%s * Rtype_size = %lu\n", margin, h5type->Rtype_size); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long unsigned int size_t {aka long long unsigned int} | %llu H5DSetDescriptor.c:777:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 777 | Rprintf("%s * native_type_size = %lu\n", margin, | ~~^ | | | long unsigned int | %llu 778 | h5type->native_type_size); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long long unsigned int} H5DSetDescriptor.c: In function 'C_show_H5DSetDescriptor_xp': H5DSetDescriptor.c:1204:32: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] 1204 | Rprintf("- dset_id = %ld\n", h5dset->dset_id); | ~~^ ~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld H5DSetDescriptor.c:1222:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] 1222 | Rprintf("- h5space_id = %ld\n", h5dset->h5space_id); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld H5DSetDescriptor.c:1226:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] 1226 | Rprintf("- h5plist_id = %ld\n", h5dset->h5plist_id); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5dimscales.c -o h5dimscales.o In file included from h5dimscales.c:7: H5File.h:11: warning: "__USE_MINGW_ANSI_STDIO" redefined 11 | #define __USE_MINGW_ANSI_STDIO 1 | In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/include/corecrt.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/crtdefs.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/stddef.h:7, from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/stddef.h:1, from F:/biocbuild/bbs-3.19-bioc/R/include/R_ext/Memory.h:36, from F:/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:37, from h5dimscales.h:4, from h5dimscales.c:5: C:/rtools44/x86_64-w64-mingw32.static.posix/include/_mingw.h:434: note: this is the location of the previous definition 434 | #define __USE_MINGW_ANSI_STDIO 0 /* was not defined so it should be 0 */ | gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c uaselection.c -o uaselection.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5mread_helpers.c -o h5mread_helpers.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5mread_startscounts.c -o h5mread_startscounts.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ChunkIterator.c -o ChunkIterator.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5mread_index.c -o h5mread_index.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5mread_sparse.c -o h5mread_sparse.o h5mread_sparse.c:206:13: warning: 'NOT_USED_make_nzindex_from_bufs' defined but not used [-Wunused-function] 206 | static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ h5mread_sparse.c:179:13: warning: 'NOT_USED_make_nzdata_from_IntAE_bufs' defined but not used [-Wunused-function] 179 | static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ h5mread_sparse.c:123:13: warning: 'NOT_USED_make_nzindex_from_buf' defined but not used [-Wunused-function] 123 | static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5mread.c -o h5mread.o In file included from h5mread.c:7: H5File.h:11: warning: "__USE_MINGW_ANSI_STDIO" redefined 11 | #define __USE_MINGW_ANSI_STDIO 1 | In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/include/corecrt.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/crtdefs.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/stddef.h:7, from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/stddef.h:1, from F:/biocbuild/bbs-3.19-bioc/R/include/R_ext/Memory.h:36, from F:/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:37, from h5mread.h:4, from h5mread.c:5: C:/rtools44/x86_64-w64-mingw32.static.posix/include/_mingw.h:434: note: this is the location of the previous definition 434 | #define __USE_MINGW_ANSI_STDIO 0 /* was not defined so it should be 0 */ | gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c h5summarize.c -o h5summarize.o In file included from h5summarize.c:7: H5File.h:11: warning: "__USE_MINGW_ANSI_STDIO" redefined 11 | #define __USE_MINGW_ANSI_STDIO 1 | In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/include/corecrt.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/crtdefs.h:10, from C:/rtools44/x86_64-w64-mingw32.static.posix/include/stddef.h:7, from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/stddef.h:1, from F:/biocbuild/bbs-3.19-bioc/R/include/R_ext/Memory.h:36, from F:/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:37, from h5summarize.h:4, from h5summarize.c:5: C:/rtools44/x86_64-w64-mingw32.static.posix/include/_mingw.h:434: note: this is the location of the previous definition 434 | #define __USE_MINGW_ANSI_STDIO 0 /* was not defined so it should be 0 */ | gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_HDF5Array.c -o R_init_HDF5Array.o gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o -LF:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_hl -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-HDF5Array/00new/HDF5Array/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 * DONE (HDF5Array)