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

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### Running command:
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###   rm -rf DEGseq.buildbin-libdir DEGseq.Rcheck && mkdir DEGseq.buildbin-libdir DEGseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGseq.buildbin-libdir DEGseq_1.32.0.tar.gz >DEGseq.Rcheck\00install.out 2>&1 && cp DEGseq.Rcheck\00install.out DEGseq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DEGseq.buildbin-libdir --install="check:DEGseq-install.out" --force-multiarch --no-vignettes --timings DEGseq_1.32.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DEGseq.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 'DEGseq/DESCRIPTION' ... OK
* this is package 'DEGseq' version '1.32.0'
* 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 'DEGseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
    libs      1.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'methods' 'qvalue' 'samr'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'qvalue' 'samr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DEGexp: no visible global function definition for 'dev.cur'
DEGexp2: no visible global function definition for 'dev.cur'
getQvalue2: no visible global function definition for 'qvalue'
samWrapper: no visible global function definition for 'check.format'
samWrapper: no visible global function definition for 'samr'
samWrapper: no visible global function definition for
  'samr.compute.delta.table'
samWrapper: no visible global function definition for
  'samr.compute.siggenes.table'
Undefined global functions or variables:
  check.format dev.cur qvalue samr samr.compute.delta.table
  samr.compute.siggenes.table
Consider adding
  importFrom("grDevices", "dev.cur")
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 C/C++/Fortran sources/headers ... 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/DEGseq.buildbin-libdir/DEGseq/libs/i386/DEGseq.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 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/DEGseq.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'DEGseq' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c getGeneExp.cpp -o getGeneExp.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o DEGseq.dll tmp.def getGeneExp.o -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/DEGseq.buildbin-libdir/DEGseq/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DEGseq'
    finding HTML links ... done
    DEGexp                                  html  
    DEGexp2                                 html  
    DEGseq                                  html  
    GeneExpExample1000                      html  
    GeneExpExample5000                      html  
    getGeneExp                              html  
    kidneyChr21.bed                         html  
    kidneyChr21Bowtie                       html  
    liverChr21.bed                          html  
    liverChr21Bowtie                        html  
    readGeneExp                             html  
    refFlatChr21                            html  
    samWrapper                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DEGseq' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c getGeneExp.cpp -o getGeneExp.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o DEGseq.dll tmp.def getGeneExp.o -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/DEGseq.buildbin-libdir/DEGseq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEGseq' as DEGseq_1.32.0.zip
* DONE (DEGseq)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for DEGseq on tokay1

Summary

Command output

Installation output

Tests output

Example timings