Package: motifRG

Version: 1.26.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifRG.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings motifRG_1.26.0.tar.gz

StartedAt: 2019-04-13 03:58:46 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:05:46 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 420.2 seconds

RetCode: 0

Status:  OK

CheckDir: motifRG.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifRG.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings motifRG_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/motifRG.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'motifRG/DESCRIPTION' ... OK
* this is package 'motifRG' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Depends: includes the non-default packages:
  'Biostrings' 'IRanges' 'seqLogo' 'parallel' 'grid' 'BSgenome'
  'XVector' 'BSgenome.Hsapiens.UCSC.hg19'
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 'motifRG' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biostrings' 'IRanges' 'seqLogo' 'parallel' 'methods' 'grid' 'graphics' 'XVector'
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
* 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 ... NOTE
'library' or 'require' call to 'parallel' which was already attached by Depends.
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  'graphics' 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'BSgenome.Hsapiens.UCSC.hg19' 'methods'
  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
bestPWMMatch: no visible global function definition for 'Rle'
discretize.glm: no visible global function definition for 'glm.fit'
findMotif : refinePattern: no visible global function definition for
  't.test'
findMotif : refinePattern: no visible global function definition for
  'new'
findPatternView: no visible global function definition for 'as'
getScore: no visible global function definition for 'binomial'
getScore : <anonymous>: no visible global function definition for
  'glm.fit'
getScore : <anonymous>: no visible global function definition for
  'summary.glm'
matchPWMCoor: no visible global function definition for 'as'
matchPWMCoor: no visible global function definition for 'GRanges'
motifHtmlTable: no visible global function definition for 'png'
motifHtmlTable: no visible global function definition for 'par'
motifHtmlTable: no visible global function definition for 'dev.off'
motifLatexTable: no visible global function definition for 'pdf'
motifLatexTable: no visible global function definition for 'par'
motifLatexTable: no visible global function definition for 'dev.off'
my.pvec: no visible global function definition for 'mc.reset.stream'
my.pvec : <anonymous>: no visible global function definition for
  'mcparallel'
my.pvec: no visible global function definition for 'mccollect'
plotPWM: no visible global function definition for 'axis'
plotPWM: no visible global function definition for 'par'
plotPWM: no visible global function definition for 'col2rgb'
plotPWM: no visible global function definition for 'rgb'
plotPWM: no visible global function definition for 'points'
plotPair: no visible global function definition for 'rgb'
plotPair: no visible global function definition for 'lines'
Undefined global functions or variables:
  GRanges Rle as axis binomial col2rgb dev.off glm.fit lines
  mc.reset.stream mccollect mcparallel new par pdf png points rgb
  summary.glm t.test
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "pdf", "png", "rgb")
  importFrom("graphics", "axis", "lines", "par", "points")
  importFrom("methods", "as", "new")
  importFrom("stats", "binomial", "glm.fit", "summary.glm", "t.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: YY1.control.Rd:8-9: Dropping empty section \details
prepare_Rd: YY1.peak.Rd:8-9: Dropping empty section \details
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
findMotif 59.65   0.42    60.4
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
findMotif 66.37   0.06   66.57
* 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-3.8-bioc/meat/motifRG.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/motifRG_1.26.0.tar.gz && rm -rf motifRG.buildbin-libdir && mkdir motifRG.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifRG.buildbin-libdir motifRG_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL motifRG_1.26.0.zip && rm motifRG_1.26.0.tar.gz motifRG_1.26.0.zip
###
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install for i386

* installing *source* package 'motifRG' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'motifRG'
    finding HTML links ... done
    Motif                                   html  
    YY1.control                             html  
    YY1.peak                                html  
    ctcf.motifs                             html  
    findMotif                               html  
    findMotifFasta                          html  
    findMotifFgBg                           html  
    getSequence                             html  
    motifLatexTable                         html  
    plotMotif                               html  
    finding level-2 HTML links ... done

    refinePWMMotif                          html  
    refinePWMMotifExtend                    html  
    summaryMotif                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'motifRG' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifRG' as motifRG_1.26.0.zip
* DONE (motifRG)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'motifRG' successfully unpacked and MD5 sums checked
In R CMD INSTALL