Multiple platform build/check report for BioC 3.6 - CHECK report for Rhdf5lib on tokay1

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### Running command:
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###   rm -rf Rhdf5lib.buildbin-libdir Rhdf5lib.Rcheck && mkdir Rhdf5lib.buildbin-libdir Rhdf5lib.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rhdf5lib.buildbin-libdir Rhdf5lib_1.0.0.tar.gz >Rhdf5lib.Rcheck\00install.out 2>&1 && cp Rhdf5lib.Rcheck\00install.out Rhdf5lib-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Rhdf5lib.buildbin-libdir --install="check:Rhdf5lib-install.out" --force-multiarch --no-vignettes --timings Rhdf5lib_1.0.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rhdf5lib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rhdf5lib' version '1.0.0'
* 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 'Rhdf5lib' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.1Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib      11.7Mb
    libs      5.9Mb
* 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 ... NOTE
pkgconfig: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
* 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 ... 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-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/i386/Rhdf5lib.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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. 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'Rhdf5lib' ...
untarring hdf5_headers_1.8.19.tar.gz ...
** libs
mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/i386/" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include/c++"
cp "winlib/i386/libhdf5.a" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/i386/libhdf5.a"
cp "winlib/i386/libhdf5_cpp.a" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/i386/libhdf5_cpp.a"
cp "winlib/i386/libszip.a" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/i386/libszip.a"
cp ./hdf5/*.h "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include"
cp ./hdf5/c++/*.h "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include/c++"
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I./hdf5   -O3 -Wall  -std=gnu99 -mtune=generic -c Rhdf5lib.c -o Rhdf5lib.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Rhdf5lib.dll tmp.def Rhdf5lib.o winlib/i386/libhdf5.a winlib/i386/libszip.a -lpsapi -lz -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Rhdf5lib'
    finding HTML links ... done
    Rhdf5lib                                html  
    getHdf5Version                          html  
    pkgconfig                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Rhdf5lib' ...
untarring hdf5_headers_1.8.19.tar.gz ...
** libs
mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/x64/" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include/c++"
cp "winlib/x64/libhdf5.a" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/x64/libhdf5.a"
cp "winlib/x64/libhdf5_cpp.a" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/x64/libhdf5_cpp.a"
cp "winlib/x64/libszip.a" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/x64/libszip.a"
cp ./hdf5/*.h "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include"
cp ./hdf5/c++/*.h "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include/c++"
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I./hdf5   -O2 -Wall  -std=gnu99 -mtune=generic -c Rhdf5lib.c -o Rhdf5lib.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Rhdf5lib.dll tmp.def Rhdf5lib.o winlib/x64/libhdf5.a winlib/x64/libszip.a -lpsapi -lz -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rhdf5lib' as Rhdf5lib_1.0.0.zip
* DONE (Rhdf5lib)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for Rhdf5lib on tokay1

Summary

Command output

Installation output

Tests output

Example timings