############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=HDF5Array.buildbin-libdir HDF5Array_1.33.3.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'HDF5Array' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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:698:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=] 698 | Rprintf("%s * h5type_id = %ld\n", margin, h5type->h5type_id); | ~~^ ~~~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld H5DSetDescriptor.c:700:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 700 | Rprintf("%s * h5type_size = %lu\n", margin, h5type->h5type_size); | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int size_t {aka long long unsigned int} | %llu H5DSetDescriptor.c:740:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 740 | Rprintf("%s * Rtype_size = %lu\n", margin, h5type->Rtype_size); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long unsigned int size_t {aka long long unsigned int} | %llu H5DSetDescriptor.c:755:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 755 | Rprintf("%s * native_type_size = %lu\n", margin, | ~~^ | | | long unsigned int | %llu 756 | h5type->native_type_size); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long long unsigned int} H5DSetDescriptor.c: In function 'C_show_H5DSetDescriptor_xp': H5DSetDescriptor.c:1166:32: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] 1166 | Rprintf("- dset_id = %ld\n", h5dset->dset_id); | ~~^ ~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld H5DSetDescriptor.c:1184:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] 1184 | Rprintf("- h5space_id = %ld\n", h5dset->h5space_id); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld H5DSetDescriptor.c:1188:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=] 1188 | Rprintf("- h5plist_id = %ld\n", h5dset->h5plist_id); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long int hid_t {aka long long int} | %lld H5DSetDescriptor.c:1210:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 1210 | Rprintf(" %lu", h5dset->h5nchunk[h5along]); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int size_t {aka long long unsigned int} | %llu gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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 C:/Users/biocbuild/bbs-3.20-bioc/R/include/R_ext/Memory.h:36, from C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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 In file included from uaselection.c:7: uaselection.c: In function 'get_untrusted_elt': uaselection.c:53:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1); | ^~~~~~~~~~~~~~~ ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:53:51: note: format string is defined here 53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1); | ~~^ | | | long int | %lld uaselection.c:53:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1); | ^~~~~~~~~~~~~~~ ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:53:51: note: format string is defined here 53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1); | ~~^ | | | long int | %lld uaselection.c:55:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA", | ^~~~~~~~~~~~~~~~~~~~~ 56 | what, along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:55:57: note: format string is defined here 55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA", | ~~^ | | | long int | %lld uaselection.c:55:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA", | ^~~~~~~~~~~~~~~~~~~~~ 56 | what, along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:55:57: note: format string is defined here 55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA", | ~~^ | | | long int | %lld uaselection.c:64:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN " | ^~~~~~~~~~~~~~~~~~~~~~~ 65 | "or not a finite number", 66 | what, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:64:51: note: format string is defined here 64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN " | ~~^ | | | long int | %lld uaselection.c:64:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN " | ^~~~~~~~~~~~~~~~~~~~~~~ 65 | "or not a finite number", 66 | what, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:64:51: note: format string is defined here 64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN " | ~~^ | | | long int | %lld uaselection.c:68:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | "or not a finite number", 70 | what, along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:68:57: note: format string is defined here 68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN " | ~~^ | | | long int | %lld uaselection.c:68:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | "or not a finite number", 70 | what, along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:68:57: note: format string is defined here 68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN " | ~~^ | | | long int | %lld uaselection.c:75:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 | what, i + 1, tmp2); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:75:51: note: format string is defined here 75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)", | ~~^ | | | long int | %lld uaselection.c:75:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 | what, i + 1, tmp2); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:75:51: note: format string is defined here 75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)", | ~~^ | | | long int | %lld uaselection.c:78:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 | what, along + 1, i + 1, tmp2); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:78:57: note: format string is defined here 78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)", | ~~^ | | | long int | %lld uaselection.c:78:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 | what, along + 1, i + 1, tmp2); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:78:57: note: format string is defined here 78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)", | ~~^ | | | long int | %lld uaselection.c: In function 'set_errmsg_for_uaselection_beyond_dim': uaselection.c:199:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 199 | "%s starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~ 200 | "> dimension %d in array", 201 | msg, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:199:44: note: format string is defined here 199 | "%s starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:199:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 199 | "%s starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~ 200 | "> dimension %d in array", 201 | msg, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:199:44: note: format string is defined here 199 | "%s starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "> dimension %d in array", 206 | msg, along1, i + 1, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:204:44: note: format string is defined here 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ~~^ | | | long int | %lld uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "> dimension %d in array", 206 | msg, along1, i + 1, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:204:64: note: format string is defined here 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ~~^ | | | long int | %lld uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "> dimension %d in array", 206 | msg, along1, i + 1, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:204:44: note: format string is defined here 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ~~^ | | | long int | %lld uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | "> dimension %d in array", 206 | msg, along1, i + 1, along1, i + 1, along1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:204:64: note: format string is defined here 204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 " | ~~^ | | | long int | %lld uaselection.c: In function 'set_errmsg_for_non_strictly_ascending_uaselection': uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | msg, along1, i + 1, along1, i); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:217:56: note: format string is defined here 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ~~^ | | | long int | %lld uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | msg, along1, i + 1, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:217:77: note: format string is defined here 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ~~^ | | | long int | %lld uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | msg, along1, i + 1, along1, i); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:217:56: note: format string is defined here 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ~~^ | | | long int | %lld uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | msg, along1, i + 1, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:217:77: note: format string is defined here 217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]", | ~~^ | | | long int | %lld uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:220:56: note: format string is defined here 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:220:76: note: format string is defined here 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 10 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:220:56: note: format string is defined here 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:220:76: note: format string is defined here 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ~~^ | | | long int | %lld uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 10 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | " + counts[[%d]][%ld]", 222 | msg, along1, i + 1, along1, i, along1, i); | ~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c: In function 'get_untrusted_start': uaselection.c:233:37: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:233:53: note: format string is defined here 233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1", | ~~^ | | | long int | %lld uaselection.c:233:37: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:233:53: note: format string is defined here 233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1", | ~~^ | | | long int | %lld uaselection.c: In function 'check_uaselection_along': uaselection.c:288:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:288:61: note: format string is defined here 288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ~~^ | | | long int | %lld uaselection.c:288:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:288:61: note: format string is defined here 288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ~~^ | | | long int | %lld uaselection.c: In function 'check_ordered_uaselection_along': uaselection.c:428:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 429 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:428:69: note: format string is defined here 428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ~~^ | | | long int | %lld uaselection.c:428:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 429 | along + 1, i + 1); | ~~~~~ | | | R_xlen_t {aka long long int} global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF' 9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__) | ^~~~~~~~~~~ uaselection.c:428:69: note: format string is defined here 428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0", | ~~^ | | | long int | %lld gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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 ChunkIterator.c: In function '_print_tchunk_info': ChunkIterator.c:457:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 457 | Rprintf("%lu/%lu", i, chunk_iter->num_tchunks[along]); | ~~^ ~ | | | | | size_t {aka long long unsigned int} | long unsigned int | %llu ChunkIterator.c:457:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=] 457 | Rprintf("%lu/%lu", i, chunk_iter->num_tchunks[along]); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int size_t {aka long long unsigned int} | %llu gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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 gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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 C:/Users/biocbuild/bbs-3.20-bioc/R/include/R_ext/Memory.h:36, from C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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 C:/Users/biocbuild/bbs-3.20-bioc/R/include/R_ext/Memory.h:36, from C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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 -LC:/Users/BIOCBU~1/BBS-3~1.20-/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 -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc/meat/HDF5Array.buildbin-libdir/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 * MD5 sums packaged installation of 'HDF5Array' as HDF5Array_1.33.3.zip * DONE (HDF5Array)