Hervé Pagès
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/HDF5Array |
| Branch: RELEASE_3_12 |
| Last Commit: 5bc12e4 |
| Last Changed Date: 2021-02-04 13:15:08 -0400 (Thu, 04 Feb 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:44 -0400 (Thu, 06 May 2021).
|
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 819/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HDF5Array 1.18.1 (landing page) Hervé Pagès
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: HDF5Array |
| Version: 1.18.1 |
| Command: rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HDF5Array.buildbin-libdir HDF5Array_1.18.1.tar.gz |
| StartedAt: 2021-05-06 09:16:04 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 09:17:11 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 67.0 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: HDF5Array_1.18.1.zip |
| PackageFileSize: 10.95 MiB |
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###
### Running command:
###
### rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HDF5Array.buildbin-libdir HDF5Array_1.18.1.tar.gz
###
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install for i386
* installing *source* package 'HDF5Array' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-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:239:6: 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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c global_errmsg_buf.c -o global_errmsg_buf.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread.c -o h5mread.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread_helpers.c -o h5mread_helpers.o
In file included from h5mread_helpers.c:17:
h5mread_helpers.c: In function '_read_h5chunk':
h5mread_helpers.c:534:23: warning: unknown conversion type character 'l' in format [-Wformat=]
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
h5mread_helpers.c:534:46: note: format string is defined here
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^
In file included from h5mread_helpers.c:17:
h5mread_helpers.c:534:23: 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_helpers.c:536:9:
chunk_storage_size,
~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
h5mread_helpers.c:535:27: note: format string is defined here
"than expected (%lu + %d)",
~~^
%I64u
In file included from h5mread_helpers.c:17:
h5mread_helpers.c:534:23: warning: too many arguments for format [-Wformat-extra-args]
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
At top level:
h5mread_helpers.c:25:13: warning: 'print_chunk_data' defined but not used [-Wunused-function]
static void print_chunk_data(const H5DSetDescriptor *h5dset,
^~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:263:13: warning: 'NOT_USED_make_nzindex_from_bufs' defined but not used [-Wunused-function]
static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:236:13: warning: 'NOT_USED_make_nzdata_from_IntAE_bufs' defined but not used [-Wunused-function]
static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:181:13: warning: 'NOT_USED_make_nzindex_from_buf' defined but not used [-Wunused-function]
static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread_starts.c -o h5mread_starts.o
h5mread_starts.c:438:22: warning: 'NOT_USED_select_elements_from_chunk' defined but not used [-Wunused-function]
static long long int NOT_USED_select_elements_from_chunk(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread_startscounts.c -o h5mread_startscounts.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c uaselection.c -o uaselection.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def H5DSetDescriptor.o R_init_HDF5Array.o S4Vectors_stubs.o global_errmsg_buf.o h5dimscales.o h5mread.o h5mread_helpers.o h5mread_sparse.o h5mread_starts.o h5mread_startscounts.o uaselection.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/library/Rhdf5lib/lib/i386 -lhdf5_hl -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/HDF5Array-class.Rd:24: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/HDF5Array-class.Rd:27: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/HDF5Array-class.Rd:60: file link 'type' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/HDF5Array-class.Rd:87: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/HDF5Array-class.Rd:90: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/HDF5Array-class.Rd:93: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/HDF5Array-class.Rd:105: 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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/HDF5ArraySeed-class.Rd:44: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/HDF5ArraySeed-class.Rd:47: 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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/TENxMatrix-class.Rd:105: file link 'colAutoGrid' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/h5mread.Rd:103: file link 'h5read' in package 'rhdf5' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/h5mread.Rd:105: 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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:31: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:39: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:133: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:148: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:149: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:152: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:201: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:226: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:227: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:234: 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-3.12-bioc/tmpdir/RtmpCgFbjR/R.INSTALL1d345c0e158c/HDF5Array/man/writeHDF5Array.Rd:172: 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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-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:239:6: 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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c global_errmsg_buf.c -o global_errmsg_buf.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread.c -o h5mread.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread_helpers.c -o h5mread_helpers.o
In file included from h5mread_helpers.c:17:
h5mread_helpers.c: In function '_read_h5chunk':
h5mread_helpers.c:534:23: warning: unknown conversion type character 'l' in format [-Wformat=]
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
h5mread_helpers.c:534:46: note: format string is defined here
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^
In file included from h5mread_helpers.c:17:
h5mread_helpers.c:534:23: 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_helpers.c:536:9:
chunk_storage_size,
~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
h5mread_helpers.c:535:27: note: format string is defined here
"than expected (%lu + %d)",
~~^
%I64u
In file included from h5mread_helpers.c:17:
h5mread_helpers.c:534:23: 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_helpers.c:537:9:
h5dset->chunk_data_buf_size,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
h5mread_helpers.c:535:32: note: format string is defined here
"than expected (%lu + %d)",
~^
%I64d
In file included from h5mread_helpers.c:17:
h5mread_helpers.c:534:23: warning: too many arguments for format [-Wformat-extra-args]
PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
global_errmsg_buf.h:9:62: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
^~~~~~~~~~~
At top level:
h5mread_helpers.c:25:13: warning: 'print_chunk_data' defined but not used [-Wunused-function]
static void print_chunk_data(const H5DSetDescriptor *h5dset,
^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:263:13: warning: 'NOT_USED_make_nzindex_from_bufs' defined but not used [-Wunused-function]
static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:236:13: warning: 'NOT_USED_make_nzdata_from_IntAE_bufs' defined but not used [-Wunused-function]
static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:181:13: warning: 'NOT_USED_make_nzindex_from_buf' defined but not used [-Wunused-function]
static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread_starts.c -o h5mread_starts.o
h5mread_starts.c:438:22: warning: 'NOT_USED_select_elements_from_chunk' defined but not used [-Wunused-function]
static long long int NOT_USED_select_elements_from_chunk(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5mread_startscounts.c -o h5mread_startscounts.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c uaselection.c -o uaselection.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def H5DSetDescriptor.o R_init_HDF5Array.o S4Vectors_stubs.o global_errmsg_buf.o h5dimscales.o h5mread.o h5mread_helpers.o h5mread_sparse.o h5mread_starts.o h5mread_startscounts.o uaselection.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/library/Rhdf5lib/lib/x64 -lhdf5_hl -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/HDF5Array.buildbin-libdir/HDF5Array/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HDF5Array' as HDF5Array_1.18.1.zip
* DONE (HDF5Array)