Hervé Pagès
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/HDF5Array |
| Branch: RELEASE_3_11 |
| Last Commit: 0b5a293 |
| Last Changed Date: 2020-06-16 04:42:27 -0400 (Tue, 16 Jun 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:48 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE HDF5Array PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 805/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HDF5Array 1.16.1 Hervé Pagès
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: HDF5Array |
| Version: 1.16.1 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/HDF5Array_1.16.1.tar.gz && rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HDF5Array.buildbin-libdir HDF5Array_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL HDF5Array_1.16.1.zip && rm HDF5Array_1.16.1.tar.gz HDF5Array_1.16.1.zip |
| StartedAt: 2020-10-16 17:06:25 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 17:08:35 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 130.3 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/HDF5Array_1.16.1.tar.gz && rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HDF5Array.buildbin-libdir HDF5Array_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL HDF5Array_1.16.1.zip && rm HDF5Array_1.16.1.tar.gz HDF5Array_1.16.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
6 7872k 6 528k 0 0 718k 0 0:00:10 --:--:-- 0:00:10 724k
100 7872k 100 7872k 0 0 9557k 0 --:--:-- --:--:-- --:--:-- 9624k
install for i386
* installing *source* package 'HDF5Array' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5DSetDescriptor.c -o H5DSetDescriptor.o
H5DSetDescriptor.c: In function '_init_H5DSetDescriptor':
H5DSetDescriptor.c:238:6: warning: 'storage_mode_attr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (strcmp(storage_mode, "integer") == 0) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5DSetDescriptor.c:349:17: note: 'storage_mode_attr' was declared here
char *h5name, *storage_mode_attr;
^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_HDF5Array.c -o R_init_HDF5Array.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c array_selection.c -o array_selection.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5dimscales.c -o h5dimscales.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread.c -o h5mread.o
In file included from h5mread.c:14:
h5mread.c: In function 'load_chunk':
h5mread.c:857:23: warning: unknown conversion type character 'l' in format [-Wformat=]
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
HDF5Array.h:9:55: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
h5mread.c:857:46: note: format string is defined here
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^
In file included from h5mread.c:14:
h5mread.c:857:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=]
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread.c:859:9:
chunk_storage_size,
~~~~~~~~~~~~~~~~~~
HDF5Array.h:9:55: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
h5mread.c:858:27: note: format string is defined here
"than expected (%lu + %d)",
~~^
%I64u
In file included from h5mread.c:14:
h5mread.c:857:23: warning: too many arguments for format [-Wformat-extra-args]
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
HDF5Array.h:9:55: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
At top level:
h5mread.c:1309:22: warning: 'select_elements_from_chunk' defined but not used [-Wunused-function]
static long long int select_elements_from_chunk(
^~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def H5DSetDescriptor.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5dimscales.o h5mread.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/library/Rhdf5lib/lib/i386 -lhdf5_hl -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/HDF5Array.buildbin-libdir/00LOCK-HDF5Array/00new/HDF5Array/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'HDF5Array'
finding HTML links ... done
HDF5Array-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/HDF5Array-class.Rd:22: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/HDF5Array-class.Rd:25: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/HDF5Array-class.Rd:43: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/HDF5Array-class.Rd:70: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/HDF5Array-class.Rd:73: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/HDF5Array-class.Rd:76: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/HDF5Array-class.Rd:88: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
HDF5ArraySeed-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/HDF5ArraySeed-class.Rd:39: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/HDF5ArraySeed-class.Rd:42: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
ReshapedHDF5Array-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/ReshapedHDF5Array-class.Rd:22: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/ReshapedHDF5Array-class.Rd:26: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/ReshapedHDF5Array-class.Rd:63: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/ReshapedHDF5Array-class.Rd:66: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/ReshapedHDF5Array-class.Rd:75: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
ReshapedHDF5ArraySeed-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/ReshapedHDF5ArraySeed-class.Rd:36: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/ReshapedHDF5ArraySeed-class.Rd:39: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
TENxMatrix-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrix-class.Rd:29: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrix-class.Rd:33: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrix-class.Rd:68: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrix-class.Rd:69: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrix-class.Rd:87: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrix-class.Rd:89: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrix-class.Rd:101: file link 'setAutoBPPARAM' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrix-class.Rd:102: file link 'setAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrix-class.Rd:105: file link 'colGrid' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrix-class.Rd:113: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrix-class.Rd:113: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
TENxMatrixSeed-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrixSeed-class.Rd:52: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/TENxMatrixSeed-class.Rd:55: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
dump-management html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/dump-management.Rd:123: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/dump-management.Rd:216: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
h5mread html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/h5mread.Rd:63: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/h5mread.Rd:65: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/h5mread.Rd:100: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/h5mread.Rd:102: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
h5mread_from_reshaped html
h5writeDimnames html
saveHDF5SummarizedExperiment html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:12: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:30: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:38: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:117: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:132: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:133: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:136: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:185: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:210: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:211: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:218: file link 'saveRDS' in package 'base' does not exist and so has been treated as a topic
writeHDF5Array html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpkXYHDe/R.INSTALLeb848183069/HDF5Array/man/writeHDF5Array.Rd:154: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
writeTENxMatrix html
** 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
install for x64
* installing *source* package 'HDF5Array' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5DSetDescriptor.c -o H5DSetDescriptor.o
H5DSetDescriptor.c: In function '_init_H5DSetDescriptor':
H5DSetDescriptor.c:238:6: warning: 'storage_mode_attr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (strcmp(storage_mode, "integer") == 0) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5DSetDescriptor.c:349:17: note: 'storage_mode_attr' was declared here
char *h5name, *storage_mode_attr;
^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_HDF5Array.c -o R_init_HDF5Array.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c array_selection.c -o array_selection.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5dimscales.c -o h5dimscales.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread.c -o h5mread.o
In file included from h5mread.c:14:
h5mread.c: In function 'load_chunk':
h5mread.c:857:23: warning: unknown conversion type character 'l' in format [-Wformat=]
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
HDF5Array.h:9:55: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
h5mread.c:857:46: note: format string is defined here
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^
In file included from h5mread.c:14:
h5mread.c:857:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=]
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread.c:859:9:
chunk_storage_size,
~~~~~~~~~~~~~~~~~~
HDF5Array.h:9:55: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
h5mread.c:858:27: note: format string is defined here
"than expected (%lu + %d)",
~~^
%I64u
In file included from h5mread.c:14:
h5mread.c:857:23: warning: format '%d' expects argument of type 'int', but argument 5 has type 'size_t' {aka 'const long long unsigned int'} [-Wformat=]
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread.c:860:9:
h5dset->chunk_data_buf_size,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
HDF5Array.h:9:55: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
h5mread.c:858:32: note: format string is defined here
"than expected (%lu + %d)",
~^
%I64d
In file included from h5mread.c:14:
h5mread.c:857:23: warning: too many arguments for format [-Wformat-extra-args]
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
HDF5Array.h:9:55: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
At top level:
h5mread.c:1309:22: warning: 'select_elements_from_chunk' defined but not used [-Wunused-function]
static long long int select_elements_from_chunk(
^~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def H5DSetDescriptor.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5dimscales.o h5mread.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/library/Rhdf5lib/lib/x64 -lhdf5_hl -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/HDF5Array.buildbin-libdir/HDF5Array/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HDF5Array' as HDF5Array_1.16.1.zip
* DONE (HDF5Array)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'HDF5Array' successfully unpacked and MD5 sums checked