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###
### Running command:
###
### rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=HDF5Array.buildbin-libdir HDF5Array_1.35.2.tar.gz
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* installing *source* package 'HDF5Array' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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\13.3.0\include\stddef.h:1,
from E:/biocbuild/bbs-3.21-bioc/R/include/R_ext/Memory.h:36,
from E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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\13.3.0\include\stddef.h:1,
from E:/biocbuild/bbs-3.21-bioc/R/include/R_ext/Memory.h:36,
from E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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\13.3.0\include\stddef.h:1,
from E:/biocbuild/bbs-3.21-bioc/R/include/R_ext/Memory.h:36,
from E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-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 -LE:/biocbuild/bbs-3.21-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 -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-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_1.35.2.zip
* DONE (HDF5Array)
