Hervé Pagès
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/HDF5Array |
| Branch: RELEASE_3_9 |
| Last Commit: 21c6077 |
| Last Changed Date: 2019-10-12 16:20:34 -0400 (Sat, 12 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:35:08 -0400 (Wed, 16 Oct 2019).
| Package 744/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HDF5Array 1.12.3 Hervé Pagès
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: HDF5Array |
| Version: 1.12.3 |
| Command: rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HDF5Array.buildbin-libdir HDF5Array_1.12.3.tar.gz |
| StartedAt: 2019-10-16 09:24:59 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 09:26:22 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 82.9 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: HDF5Array_1.12.3.zip |
| PackageFileSize: 10.78 MiB |
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### Running command:
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### rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HDF5Array.buildbin-libdir HDF5Array_1.12.3.tar.gz
###
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install for i386
* installing *source* package 'HDF5Array' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c DSet.c -o DSet.o
DSet.c: In function '_get_DSet':
DSet.c:269:7: warning: 'storage_mode_attr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (map_storage_mode_to_Rtype(storage_mode_attr, as_int,
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_HDF5Array.c -o R_init_HDF5Array.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c array_selection.c -o array_selection.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c h5mread.c -o h5mread.o
h5mread.c:1194:22: warning: 'select_elements_from_chunk' defined but not used [-Wunused-function]
static long long int select_elements_from_chunk(const DSet *dset,
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def DSet.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5mread.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/Rhdf5lib/lib/i386 -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/HDF5Array-class.Rd:67: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/HDF5Array-class.Rd:69: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/HDF5Array-class.Rd:81: 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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/HDF5ArraySeed-class.Rd:37: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/HDF5ArraySeed-class.Rd:40: 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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:26: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:30: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:65: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:66: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:84: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:86: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:98: file link 'setAutoBPPARAM' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:99: file link 'setAutoBlockSize' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:102: file link 'colGrid' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:103: file link 'blockApply' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:110: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrix-class.Rd:110: 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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrixSeed-class.Rd:49: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/TENxMatrixSeed-class.Rd:52: 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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/h5mread.Rd:53: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/h5mread.Rd:55: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/h5mread.Rd:90: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/h5mread.Rd:92: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
saveHDF5SummarizedExperiment html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/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-3.9-bioc/tmpdir/Rtmp0AnBN8/R.INSTALL130c701456fc/HDF5Array/man/writeHDF5Array.Rd:111: 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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c DSet.c -o DSet.o
DSet.c: In function '_get_DSet':
DSet.c:100:6: warning: 'storage_mode_attr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (strcmp(storage_mode, "integer") == 0) {
^
DSet.c:210:8: note: 'storage_mode_attr' was declared here
char *storage_mode_attr;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_HDF5Array.c -o R_init_HDF5Array.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c array_selection.c -o array_selection.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c h5mread.c -o h5mread.o
h5mread.c:1194:22: warning: 'select_elements_from_chunk' defined but not used [-Wunused-function]
static long long int select_elements_from_chunk(const DSet *dset,
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def DSet.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5mread.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/Rhdf5lib/lib/x64 -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/HDF5Array.buildbin-libdir/HDF5Array/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HDF5Array' as HDF5Array_1.12.3.zip
* DONE (HDF5Array)