Package: nucleR

Version: 2.10.0

Command: rm -rf nucleR.buildbin-libdir nucleR.Rcheck && mkdir nucleR.buildbin-libdir nucleR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nucleR.buildbin-libdir nucleR_2.10.0.tar.gz >nucleR.Rcheck\00install.out 2>&1 && cp nucleR.Rcheck\00install.out nucleR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=nucleR.buildbin-libdir --install="check:nucleR-install.out" --force-multiarch --no-vignettes --timings nucleR_2.10.0.tar.gz

StartedAt: 2018-04-12 01:51:37 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:55:51 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 254.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: nucleR.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf nucleR.buildbin-libdir nucleR.Rcheck && mkdir nucleR.buildbin-libdir nucleR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nucleR.buildbin-libdir nucleR_2.10.0.tar.gz >nucleR.Rcheck\00install.out 2>&1 && cp nucleR.Rcheck\00install.out nucleR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=nucleR.buildbin-libdir --install="check:nucleR-install.out" --force-multiarch --no-vignettes --timings nucleR_2.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/nucleR.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 'nucleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nucleR' version '2.10.0'
* 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 'nucleR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpY1mWOo/R.INSTALL11b86c4b6a6d/nucleR/man/processTilingArray.Rd:99: missing file link 'ExpressionSet'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/nucleR.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 ... NOTE
.buildGRSingle: no visible binding for global variable 'rname'
.buildGRSingle: no visible binding for global variable 'qwidth'
Undefined global functions or variables:
  qwidth rname
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/nucleR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'nucleR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'nucleR'
    finding HTML links ... done
    controlCorrection                       html  
    coverage.rpm                            html  
    finding level-2 HTML links ... done

    export.bed                              html  
    export.wig                              html  
    filterFFT                               html  
    fragmentLenDetect                       html  
    mergeCalls                              html  
    nucleR-package                          html  
    nucleosome_htseq                        html  
    nucleosome_tiling                       html  
    pcKeepCompDetect                        html  
    peakDetection                           html  
    peakScoring                             html  
    plotPeaks                               html  
    processReads                            html  
    processTilingArray                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpY1mWOo/R.INSTALL11b86c4b6a6d/nucleR/man/processTilingArray.Rd:99: missing file link 'ExpressionSet'
    readBAM                                 html  
    syntheticNucMap                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'nucleR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nucleR' as nucleR_2.10.0.zip
* DONE (nucleR)
In R CMD INSTALL
In R CMD INSTALL