| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:47 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the rhdf5 package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1653/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rhdf5 2.43.0 (landing page) Mike Smith
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: rhdf5 |
| Version: 2.43.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rhdf5.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings rhdf5_2.43.0.tar.gz |
| StartedAt: 2022-12-29 02:51:46 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 02:53:05 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 79.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rhdf5.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rhdf5.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings rhdf5_2.43.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/rhdf5.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rhdf5/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rhdf5' version '2.43.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'rhdf5' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
libs 6.6Mb
* checking package directory ... OK
* checking 'build' 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
* 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 ... OK
* 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 shell scripts ... 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 x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/rhdf5/libs/x64/rhdf5.dll':
Found '_assert', possibly from 'assert' (C)
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 nor [v]sprintf. 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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/rhdf5.Rcheck/00check.log'
for details.
rhdf5.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL rhdf5 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'rhdf5' ... ** using staged installation ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture using C compiler: 'gcc.exe (GCC) 12.2.0' using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5.c -o H5.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5A.c -o H5A.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5D.c -o H5D.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5E.c -o H5E.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5F.c -o H5F.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5G.c -o H5G.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5I.c -o H5I.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5L.c -o H5L.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5O.c -o H5O.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5P.c -o H5P.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5R.c -o H5R.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5S.c -o H5S.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5S_extras.c -o H5S_extras.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5T.c -o H5T.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5Z.c -o H5Z.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c H5constants.c -o H5constants.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HandleList.cpp -o HandleList.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HandleListWrap.c -o HandleListWrap.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bit64conversion.c -o bit64conversion.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c external_filters.c -o external_filters.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5dump.c -o h5dump.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5ls.c -o h5ls.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5testLock.c -o h5testLock.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c printdatatype.c -o printdatatype.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D__USE_MINGW_ANSI_STDIO -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c wrap.c -o wrap.o g++ -std=gnu++11 -shared -s -static-libgcc -o rhdf5.dll tmp.def H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5R.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o -LF:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rhdf5/00new/rhdf5/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** 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 * DONE (rhdf5)
rhdf5.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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.
> library(testthat)
> library(rhdf5)
>
> test_check("rhdf5")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 1014 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (2)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 1014 ]
>
> proc.time()
user system elapsed
6.26 1.53 9.09
rhdf5.Rcheck/rhdf5-Ex.timings
| name | user | system | elapsed | |
| H5Dopen | 0.02 | 0.00 | 0.03 | |
| H5Fget_name | 0 | 0 | 0 | |
| H5Gget_info | 0 | 0 | 0 | |
| H5Iget_type | 0 | 0 | 0 | |
| H5Iis_valid | 0 | 0 | 0 | |
| H5Lcreate_external | 0.01 | 0.00 | 0.02 | |
| H5Ldelete | 0.00 | 0.02 | 0.01 | |
| H5Lmove | 0.03 | 0.00 | 0.05 | |
| H5Ocopy | 0.00 | 0.00 | 0.01 | |
| H5Olink | 0.00 | 0.01 | 0.02 | |
| H5Oopen | 0.02 | 0.00 | 0.02 | |
| H5P_create_intermediate_group | 0.02 | 0.00 | 0.01 | |
| H5Pset_fapl_ros3 | 0 | 0 | 0 | |
| H5R | 0.01 | 0.00 | 0.02 | |
| H5Scombine_hyperslab | 0.02 | 0.00 | 0.01 | |
| H5Scombine_select | 0 | 0 | 0 | |
| H5Sselect_hyperslab | 0 | 0 | 0 | |
| H5Sselect_index | 0 | 0 | 0 | |
| H5functions | 0 | 0 | 0 | |
| h5_FileLocking | 0.00 | 0.02 | 0.02 | |
| h5_createAttribute | 0.00 | 0.00 | 0.01 | |
| h5_createDataset | 0.11 | 0.02 | 0.18 | |
| h5_createFile | 0.01 | 0.00 | 0.01 | |
| h5_createGroup | 0.00 | 0.00 | 0.02 | |
| h5_dump | 0.00 | 0.01 | 0.01 | |
| h5_errorHandling | 0 | 0 | 0 | |
| h5_read | 0.03 | 0.00 | 0.06 | |
| h5_save | 0.00 | 0.00 | 0.03 | |
| h5_set_extent | 0.01 | 0.00 | 0.05 | |
| h5_write | 0.02 | 0.00 | 0.01 | |
| h5closeAll | 0 | 0 | 0 | |
| h5constants | 0 | 0 | 0 | |
| h5listObjects | 0 | 0 | 0 | |
| h5ls | 0.01 | 0.00 | 0.02 | |
| h5version | 0 | 0 | 0 | |