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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HDF5Array.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings HDF5Array_1.18.1.tar.gz |
| StartedAt: 2021-05-06 03:33:31 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:07:12 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 2020.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HDF5Array.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HDF5Array.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings HDF5Array_1.18.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/HDF5Array.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HDF5Array/DESCRIPTION' ... OK
* this is package 'HDF5Array' version '1.18.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'HDF5Array' can be installed ... WARNING
Found the following significant warnings:
h5mread_helpers.c:534:23: warning: too many arguments for format [-Wformat-extra-args]
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/HDF5Array/man/HDF5Array-class.Rd:105: 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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/HDF5Array/man/HDF5ArraySeed-class.Rd:47: 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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/HDF5Array/man/ReshapedHDF5Array-class.Rd:75: 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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/HDF5Array/man/ReshapedHDF5ArraySeed-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-3.12-bioc/tmpdir/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/HDF5Array/man/TENxMatrix-class.Rd:113: 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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/HDF5Array/man/TENxMatrixSeed-class.Rd:55: 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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/HDF5Array/man/dump-management.Rd:216: 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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/HDF5Array/man/h5mread.Rd:105: 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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/HDF5Array/man/saveHDF5SummarizedExperiment.Rd:234: file link 'saveRDS' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpO448lv/R.INSTALLd0876775d67/HDF5Array/man/writeHDF5Array.Rd:172: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/HDF5Array.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 16.3Mb
sub-directories of 1Mb or more:
extdata 7.7Mb
libs 7.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'BiocGenerics:::testPackage' 'S4Vectors:::anyMissingOrOutside'
'S4Vectors:::extract_data_frame_rows' 'S4Vectors:::sapply_isNULL'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/HDF5Array/libs/i386/HDF5Array.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/HDF5Array/libs/x64/HDF5Array.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
h5mread 47.27 6.03 809.12
TENxMatrix-class 37.09 12.47 461.77
writeTENxMatrix 24.78 1.72 27.35
TENxMatrixSeed-class 7.09 1.85 9.74
HDF5Array-class 5.64 0.44 12.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
h5mread 47.94 1.67 50.50
TENxMatrix-class 31.67 8.95 228.90
writeTENxMatrix 23.08 1.00 24.50
TENxMatrixSeed-class 7.69 0.70 8.82
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
OK
** running tests for arch 'x64' ...
Running 'run_unitTests.R'
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/HDF5Array.Rcheck/00check.log'
for details.
HDF5Array.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/HDF5Array_1.18.1.tar.gz && 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 && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL HDF5Array_1.18.1.zip && rm HDF5Array_1.18.1.tar.gz HDF5Array_1.18.1.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
50 7881k 50 4000k 0 0 26.8M 0 --:--:-- --:--:-- --:--:-- 26.9M
100 7881k 100 7881k 0 0 37.4M 0 --:--:-- --:--:-- --:--:-- 37.5M
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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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/RtmpO448lv/R.INSTALLd0876775d67/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)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'HDF5Array' successfully unpacked and MD5 sums checked
|
HDF5Array.Rcheck/tests_i386/run_unitTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("HDF5Array") || stop("unable to load HDF5Array package")
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:Matrix':
expand
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: rhdf5
[1] TRUE
> HDF5Array:::.test()
RUNIT TEST PROTOCOL -- Thu May 06 04:06:27 2021
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
HDF5Array RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
18.00 3.28 58.17
|
HDF5Array.Rcheck/tests_x64/run_unitTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("HDF5Array") || stop("unable to load HDF5Array package")
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:Matrix':
expand
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: rhdf5
[1] TRUE
> HDF5Array:::.test()
RUNIT TEST PROTOCOL -- Thu May 06 04:07:05 2021
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
HDF5Array RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
22.29 4.12 38.32
|
|
HDF5Array.Rcheck/examples_i386/HDF5Array-Ex.timings
|
HDF5Array.Rcheck/examples_x64/HDF5Array-Ex.timings
|