Package: FourCSeq

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FourCSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings FourCSeq_1.20.0.tar.gz

StartedAt: 2020-04-15 03:16:25 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:29:46 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 800.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: FourCSeq.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FourCSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings FourCSeq_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/FourCSeq.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FourCSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FourCSeq' version '1.20.0'
* 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 'FourCSeq' can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/FourCSeq.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'DESeq2' 'GenomicRanges'
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
Packages in Depends field not imported from:
  'ggplot2' '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
FourC: no visible global function definition for 'SimpleList'
FourC: no visible global function definition for 'formula'
FourC: no visible global function definition for 'new'
addFragments: no visible global function definition for 'metadata'
addFragments: no visible global function definition for
  'subsetByOverlaps'
addFragments: no visible global function definition for 'DataFrame'
addPeaks: no visible global function definition for 'metadata'
addPeaks: no visible global function definition for 'DataFrame'
addViewpointFrags: no visible global function definition for 'metadata'
addViewpointFrags: no visible global function definition for
  'DataFrame'
countFragmentOverlaps: no visible global function definition for
  'metadata'
countFragmentOverlaps: no visible global function definition for
  'DataFrame'
countFragmentOverlaps: no visible global function definition for
  'SimpleList'
countFragmentOverlapsSecondCutter: no visible global function
  definition for 'metadata'
countFragmentOverlapsSecondCutter: no visible global function
  definition for 'DataFrame'
countFragmentOverlapsSecondCutter: no visible global function
  definition for 'SimpleList'
distFitMonotone: no visible global function definition for 'predict'
distFitMonotoneSymmetric: no visible global function definition for
  'predict'
findViewpointFragments: no visible global function definition for
  'metadata'
findViewpointFragments : <anonymous>: no visible global function
  definition for 'Rle'
findViewpointFragments: no visible global function definition for
  'subjectHits'
findViewpointFragments: no visible global function definition for
  'write.table'
getDifferences: no visible global function definition for 'relevel'
getDifferences: no visible global function definition for 'formula'
getDistAroundVp: no visible global function definition for 'DataFrame'
getFragments: no visible global function definition for 'Rle'
getFragments: no visible global function definition for 'IRanges'
getFragments: no visible global function definition for 'seqlengths'
getReferenceSeq: no visible global function definition for 'metadata'
getSites: no visible global function definition for 'seqlevels<-'
getSites: no visible global function definition for 'seqlevels'
getSites: no visible global function definition for 'Seqinfo'
getSites: no visible global function definition for 'Rle'
getZScores: no visible binding for global variable 'mad'
getZScores: no visible binding for global variable 'median'
getZScores: no visible global function definition for 'DataFrame'
getZScores: no visible binding for global variable 'pnorm'
getZScores: no visible binding for global variable 'p.adjust'
getZScores: no visible global function definition for 'metadata'
getZScores: no visible global function definition for 'SimpleList'
plotDifferences: no visible global function definition for 'theme_bw'
plotDifferences: no visible global function definition for 'rel'
plotDifferences: no visible global function definition for 'theme_set'
plotDifferences: no visible global function definition for 'metadata'
plotDifferences: no visible global function definition for 'ggplot'
plotDifferences: no visible global function definition for
  'subsetByOverlaps'
plotDifferences: no visible global function definition for 'aes'
plotDifferences: no visible binding for global variable 'change'
plotDifferences: no visible global function definition for
  'scale_fill_gradient2'
plotDifferences: no visible global function definition for 'theme'
plotDifferences: no visible global function definition for
  'element_blank'
plotDifferences: no visible binding for global variable 'mid'
plotDifferences: no visible global function definition for 'labs'
plotDifferences: no visible global function definition for 'geom_path'
plotDifferences: no visible global function definition for 'geom_point'
plotDifferences: no visible global function definition for
  'scale_y_continuous'
plotDifferences: no visible binding for global variable 'peak'
plotDifferences: no visible binding for global variable
  'differentialInteraction'
plotFits: no visible global function definition for 'metadata'
plotFits: no visible global function definition for 'par'
plotFits: no visible global function definition for 'plot'
plotFits: no visible global function definition for 'axis'
plotFits: no visible global function definition for 'mtext'
plotFits: no visible global function definition for 'points'
plotNormalizationFactors: no visible global function definition for
  'plot'
plotNormalizationFactors: no visible global function definition for
  'points'
plotNormalizationFactors: no visible global function definition for
  'legend'
plotNormalizationFactors: no visible global function definition for
  'abline'
plotSmoothScatter: no visible binding for global variable 'blues9'
plotSmoothScatter: no visible global function definition for 'axis'
plotVp: no visible global function definition for 'ggplot'
plotVp: no visible global function definition for 'aes'
plotVp: no visible binding for global variable 'mid'
plotVp: no visible binding for global variable 'count'
plotVp: no visible global function definition for 'labs'
plotVp: no visible global function definition for 'geom_path'
plotVp: no visible binding for global variable 'fit'
plotVp: no visible binding for global variable 'fitUp'
plotVp: no visible binding for global variable 'fitDown'
plotVp: no visible global function definition for 'geom_point'
plotVp: no visible global function definition for 'scale_y_continuous'
plotVp: no visible binding for global variable 'peak'
plotVp: no visible binding for global variable
  'differentialInteraction'
plotZScores: no visible global function definition for 'theme_bw'
plotZScores: no visible global function definition for 'rel'
plotZScores: no visible global function definition for 'theme_set'
plotZScores: no visible global function definition for 'metadata'
plotZScores: no visible global function definition for 'ggplot'
plotZScores: no visible global function definition for
  'subsetByOverlaps'
saveGR: no visible global function definition for 'metadata'
saveGR: no visible global function definition for 'seqlengths'
saveGR: no visible global function definition for 'write.table'
smoothCounts: no visible global function definition for 'SimpleList'
smoothHitPerCent: no visible global function definition for
  'SimpleList'
writeTrackFiles: no visible global function definition for 'metadata'
writeTrackFiles: no visible global function definition for
  'keepSeqlevels'
updateObject,FourC: no visible global function definition for
  'callNextMethod'
Undefined global functions or variables:
  DataFrame IRanges Rle Seqinfo SimpleList abline aes axis blues9
  callNextMethod change count differentialInteraction element_blank fit
  fitDown fitUp formula geom_path geom_point ggplot keepSeqlevels labs
  legend mad median metadata mid mtext new p.adjust par peak plot pnorm
  points predict rel relevel scale_fill_gradient2 scale_y_continuous
  seqlengths seqlevels seqlevels<- subjectHits subsetByOverlaps theme
  theme_bw theme_set write.table
Consider adding
  importFrom("grDevices", "blues9")
  importFrom("graphics", "abline", "axis", "legend", "mtext", "par",
             "plot", "points")
  importFrom("methods", "callNextMethod", "new")
  importFrom("stats", "formula", "mad", "median", "p.adjust", "pnorm",
             "predict", "relevel")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotScatter              66.68   2.55   69.21
getZScores               44.59   3.36   47.95
plotDifferences           9.33   0.01    9.34
getAllResults             7.56   0.49    8.05
getDifferences            6.91   0.32    7.23
plotZScores               6.23   0.05    6.29
plotNormalizationFactors  4.96   0.04    5.04
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotScatter     61.27   2.99   64.25
getZScores      40.29   3.18   43.48
plotDifferences 12.63   0.06   12.68
plotZScores      6.92   0.03    6.95
getAllResults    6.38   0.01    6.39
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/FourCSeq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/FourCSeq_1.20.0.tar.gz && rm -rf FourCSeq.buildbin-libdir && mkdir FourCSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FourCSeq.buildbin-libdir FourCSeq_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL FourCSeq_1.20.0.zip && rm FourCSeq_1.20.0.tar.gz FourCSeq_1.20.0.zip
###
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100 2037k  100 2037k    0     0  7455k      0 --:--:-- --:--:-- --:--:-- 7573k

install for i386

* installing *source* package 'FourCSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
  converting help for package 'FourCSeq'
    finding HTML links ... done
    FourC                                   html  
    addFragments                            html  
    addPeaks                                html  
    addViewpointFrags                       html  
    combineFragEnds                         html  
    countFragmentOverlaps                   html  
    countFragmentOverlapsSecondCutter       html  
    distFitMonotone                         html  
    distFitMonotoneSymmetric                html  
    fc                                      html  
    fcf                                     html  
    findViewpointFragments                  html  
    getAllResults                           html  
    getDifferences                          html  
    getDistAroundVp                         html  
    getNormalizationFactors                 html  
    getReferenceSeq                         html  
    getZScores                              html  
    normalizeRPM                            html  
    plotDifferences                         html  
    plotFits                                html  
    plotNormalizationFactors                html  
    plotScatter                             html  
    plotZScores                             html  
    smoothCounts                            html  
    smoothHitPerCent                        html  
    writeTrackFiles                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'FourCSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FourCSeq' as FourCSeq_1.20.0.zip
* DONE (FourCSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'FourCSeq' successfully unpacked and MD5 sums checked