Package: Guitar

Version: 1.16.0

Command: rm -rf Guitar.buildbin-libdir Guitar.Rcheck && mkdir Guitar.buildbin-libdir Guitar.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Guitar.buildbin-libdir Guitar_1.16.0.tar.gz >Guitar.Rcheck\00install.out 2>&1 && cp Guitar.Rcheck\00install.out Guitar-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Guitar.buildbin-libdir --install="check:Guitar-install.out" --force-multiarch --no-vignettes --timings Guitar_1.16.0.tar.gz

StartedAt: 2018-04-12 00:37:25 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:43:30 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 364.9 seconds

RetCode: 0

Status:  OK

CheckDir: Guitar.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf Guitar.buildbin-libdir Guitar.Rcheck && mkdir Guitar.buildbin-libdir Guitar.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Guitar.buildbin-libdir Guitar_1.16.0.tar.gz >Guitar.Rcheck\00install.out 2>&1 && cp Guitar.Rcheck\00install.out Guitar-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Guitar.buildbin-libdir --install="check:Guitar-install.out" --force-multiarch --no-vignettes --timings Guitar_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Guitar.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 'Guitar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Guitar' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Rsamtools' 'GenomicFeatures' 'rtracklayer' 'GenomicAlignments'
  'GenomicRanges' 'ggplot2' 'grid' 'IRanges'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'Guitar' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
* 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
.makeFigure_fill: no visible global function definition for 'pdf'
.makeFigure_fill: no visible global function definition for 'dev.off'
.makeFigure_nofill: no visible global function definition for 'pdf'
.makeFigure_nofill: no visible global function definition for 'dev.off'
BED12toGRangesList: no visible global function definition for
  'read.table'
BED12toGRangesList: no visible global function definition for 'head'
narrowPeaktoGRanges: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  dev.off head pdf read.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "head", "read.table")
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 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
Guitar-package     11.11   0.15   11.26
combinedGuitarPlot  8.72   0.06    8.78
GuitarPlot          8.60   0.05    8.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
Guitar-package     15.24   0.10   15.32
combinedGuitarPlot 13.48   0.04   13.54
GuitarPlot         11.60   0.03   11.62
* 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/Guitar.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'Guitar' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Guitar'
    finding HTML links ... done
    BED12toGRangesList                      html  
    Guitar-package                          html  
    GuitarPlot                              html  
    combinedGuitarPlot                      html  
    getNeighborhood                         html  
    makeGuitarCoordsFromGRangesList         html  
    makeGuitarCoordsFromTxDb                html  
    narrowPeaktoGRanges                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Guitar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Guitar' as Guitar_1.16.0.zip
* DONE (Guitar)
In R CMD INSTALL
In R CMD INSTALL