BUILD BIN results for HDF5Array on palomino4
To the developers/maintainers of the HDF5Array package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HDF5Array.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
|
raw results
Summary
Command output
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### Running command:
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### rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=HDF5Array.buildbin-libdir HDF5Array_1.33.0.tar.gz
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* installing *source* package 'HDF5Array' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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: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-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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 F:/biocbuild/bbs-3.20-bioc/R/include/R_ext/Memory.h:36,
from F:/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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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
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-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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 F:/biocbuild/bbs-3.20-bioc/R/include/R_ext/Memory.h:36,
from F:/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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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 F:/biocbuild/bbs-3.20-bioc/R/include/R_ext/Memory.h:36,
from F:/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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/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 -LF:/biocbuild/bbs-3.20-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-3.20-bioc/R/bin/x64 -lR
installing to F:/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_1.33.0.zip
* DONE (HDF5Array)
