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

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### Running command:
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###   rm -rf ChIPseqR.buildbin-libdir ChIPseqR.Rcheck && mkdir ChIPseqR.buildbin-libdir ChIPseqR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPseqR.buildbin-libdir ChIPseqR_1.32.0.tar.gz >ChIPseqR.Rcheck\00install.out 2>&1 && cp ChIPseqR.Rcheck\00install.out ChIPseqR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ChIPseqR.buildbin-libdir --install="check:ChIPseqR-install.out" --force-multiarch --no-vignettes --timings ChIPseqR_1.32.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPseqR.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 'ChIPseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPseqR' 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 'ChIPseqR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8qd39V/R.INSTALL22e01aea255a/ChIPseqR/man/strandPileup.Rd:29: missing file link 'coverage'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8qd39V/R.INSTALL22e01aea255a/ChIPseqR/man/strandPileup.Rd:46: missing file link 'coverage'
  Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
  Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
  Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPseqR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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
** 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 ... 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 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/ChIPseqR.buildbin-libdir/ChIPseqR/libs/i386/ChIPseqR.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
Examples with CPU or elapsed time > 5s
                    user system elapsed
alignFeature       32.64   4.44   37.09
callBindingSites   13.89   0.22   14.11
simpleNucCall      13.75   0.15   13.90
BindScore          13.23   0.36   13.60
RLEBindScore-class 12.28   0.20   12.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
alignFeature       44.02   4.36   48.38
BindScore          14.70   0.35   15.05
callBindingSites   12.73   0.15   12.89
RLEBindScore-class 12.56   0.28   12.84
simpleNucCall      12.61   0.22   12.83
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPseqR.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'ChIPseqR' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable]
  double stat, tmp_stat;
               ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.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/ChIPseqR.buildbin-libdir/ChIPseqR/libs/i386
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
** help
*** installing help indices
  converting help for package 'ChIPseqR'
    finding HTML links ... done
    BindScore                               html  
    ChIPseqR-package                        html  
    RLEBindScore-class                      html  
    finding level-2 HTML links ... done

    RLEReadCounts-class                     html  
    ReadCounts                              html  
    accessors                               html  
    alignFeature                            html  
    callBindingSites                        html  
    compress-BindScore                      html  
    compress-ReadCounts                     html  
    compress-methods                        html  
    decompress-methods                      html  
    decompress                              html  
    exportBindSequence                      html  
    getBindCor                              html  
    getBindLen                              html  
    getCutoff                               html  
    internal                                html  
    pickPeak                                html  
    plot-BindScore                          html  
    plot-ReadCounts                         html  
    plotReads                               html  
    plotWindow                              html  
    pos2gff                                 html  
    simpleNucCall                           html  
    startScore                              html  
    strandPileup                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8qd39V/R.INSTALL22e01aea255a/ChIPseqR/man/strandPileup.Rd:29: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8qd39V/R.INSTALL22e01aea255a/ChIPseqR/man/strandPileup.Rd:46: missing file link 'coverage'
    windowCounts                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
In R CMD INSTALL

install for x64

* installing *source* package 'ChIPseqR' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable]
  double stat, tmp_stat;
               ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.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/ChIPseqR.buildbin-libdir/ChIPseqR/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
* MD5 sums
packaged installation of 'ChIPseqR' as ChIPseqR_1.32.0.zip
* DONE (ChIPseqR)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for ChIPseqR on tokay1

Summary

Command output

Installation output

Tests output

Example timings