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CHECK report for rhdf5 on tokay1

This page was generated on 2019-04-13 11:22:00 -0400 (Sat, 13 Apr 2019).

Package 1305/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5 2.26.2
Mike Smith
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/rhdf5
Branch: RELEASE_3_8
Last Commit: 81e1125
Last Changed Date: 2019-01-02 10:53:12 -0400 (Wed, 02 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rhdf5
Version: 2.26.2
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rhdf5.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rhdf5_2.26.2.tar.gz
StartedAt: 2019-04-13 05:02:05 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:04:28 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 142.8 seconds
RetCode: 0
Status:  OK  
CheckDir: rhdf5.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rhdf5.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rhdf5_2.26.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/rhdf5.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rhdf5/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rhdf5' version '2.26.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
* 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
* 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 ... 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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-3.8-bioc/R/library/rhdf5/libs/i386/rhdf5.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/rhdf5.Rcheck/00check.log'
for details.



Installation output

rhdf5.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/rhdf5_2.26.2.tar.gz && rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rhdf5.buildbin-libdir rhdf5_2.26.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL rhdf5_2.26.2.zip && rm rhdf5_2.26.2.tar.gz rhdf5_2.26.2.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
100  195k  100  195k    0     0  4610k      0 --:--:-- --:--:-- --:--:-- 5004k

install for i386

* installing *source* package 'rhdf5' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5.c -o H5.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5A.c -o H5A.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5D.c -o H5D.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5E.c -o H5E.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5F.c -o H5F.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5G.c -o H5G.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5I.c -o H5I.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5L.c -o H5L.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5O.c -o H5O.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5P.c -o H5P.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5S.c -o H5S.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5T.c -o H5T.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5constants.c -o H5constants.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c HandleList.cpp -o HandleList.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c HandleListWrap.c -o HandleListWrap.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c h5dump.c -o h5dump.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c h5ls.c -o h5ls.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c h5testLock.c -o h5testLock.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c h5writeDataFrame.c -o h5writeDataFrame.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c printdatatype.c -o printdatatype.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c wrap.c -o wrap.o
C:/Rtools/mingw_32/bin/g++ -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 H5S.o H5T.o H5constants.o HandleList.o HandleListWrap.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o wrap.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rhdf5'
    finding HTML links ... done
    H5                                      html  
    H5A                                     html  
    H5D                                     html  
    H5F                                     html  
    H5G                                     html  
    H5I                                     html  
    H5IdComponent-class                     html  
    H5L                                     html  
    H5O                                     html  
    H5P                                     html  
    H5P_DATASET_ACCESS                      html  
    H5P_DATASET_CREATE                      html  
    H5P_LINK_CREATE                         html  
    H5S                                     html  
    H5T                                     html  
    h5closeAll                              html  
    h5const                                 html  
    h5createAttribute                       html  
    h5createDataset                         html  
    h5createFile                            html  
    h5createGroup                           html  
    h5delete                                html  
    h5errorHandling                         html  
    h5fileLocking                           html  
    h5listIdentifier                        html  
    h5ls                                    html  
    h5save                                  html  
    h5set_extent                            html  
    h5version                               html  
    h5write                                 html  
    methods-And                             html  
    methods-Dollar1                         html  
    methods-Dollar2                         html  
    methods-subset1                         html  
    methods-subset2                         html  
    rhdf5                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'rhdf5' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5.c -o H5.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5A.c -o H5A.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5D.c -o H5D.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5E.c -o H5E.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5F.c -o H5F.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5G.c -o H5G.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5I.c -o H5I.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5L.c -o H5L.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5O.c -o H5O.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5P.c -o H5P.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5S.c -o H5S.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5T.c -o H5T.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5constants.c -o H5constants.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c HandleList.cpp -o HandleList.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c HandleListWrap.c -o HandleListWrap.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c h5dump.c -o h5dump.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c h5ls.c -o h5ls.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c h5testLock.c -o h5testLock.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c h5writeDataFrame.c -o h5writeDataFrame.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c printdatatype.c -o printdatatype.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c wrap.c -o wrap.o
C:/Rtools/mingw_64/bin/g++ -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 H5S.o H5T.o H5constants.o HandleList.o HandleListWrap.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o wrap.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rhdf5' as rhdf5_2.26.2.zip
* DONE (rhdf5)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'rhdf5' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

rhdf5.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> library(testthat)
> library(rhdf5)
> 
> test_check("rhdf5")
== testthat results  ===========================================================
OK: 557 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.73    0.26    4.54 

rhdf5.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
== testthat results  ===========================================================
OK: 557 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.34    0.29    6.78 

Example timings

rhdf5.Rcheck/examples_i386/rhdf5-Ex.timings

nameusersystemelapsed
H5000
H5A0.070.000.08
H5D0.030.000.03
H5F0.020.000.02
H5G0.000.000.01
H5I0.000.000.08
H5IdComponent-class000
H5L000
H5O0.020.000.01
H5P000
H5P_DATASET_ACCESS000
H5P_DATASET_CREATE0.010.000.02
H5P_LINK_CREATE000
H5S000
H5T000
h5closeAll0.000.020.01
h5const000
h5createAttribute0.020.000.02
h5createDataset0.040.000.05
h5createFile0.020.000.01
h5createGroup0.020.000.02
h5errorHandling000
h5fileLocking000
h5listIdentifier000
h5ls0.010.000.03
h5save0.030.000.03
h5set_extent0.020.000.02
h5version0.010.000.01
h5write0.020.010.03
rhdf50.050.000.05

rhdf5.Rcheck/examples_x64/rhdf5-Ex.timings

nameusersystemelapsed
H5000
H5A0.140.000.22
H5D0.050.020.07
H5F0.000.000.06
H5G0.020.000.01
H5I0.030.000.04
H5IdComponent-class000
H5L0.000.010.01
H5O0.030.000.03
H5P000
H5P_DATASET_ACCESS000
H5P_DATASET_CREATE0.010.000.02
H5P_LINK_CREATE0.020.000.01
H5S000
H5T000
h5closeAll0.020.000.02
h5const000
h5createAttribute0.030.000.03
h5createDataset0.070.020.09
h5createFile0.020.000.02
h5createGroup0.000.020.02
h5errorHandling000
h5fileLocking0.020.000.01
h5listIdentifier000
h5ls0.040.000.05
h5save0.070.000.06
h5set_extent0.020.000.01
h5version0.010.000.02
h5write0.050.010.06
rhdf50.080.000.08