BioC 3.2: CHECK report for FourCSeq on oaxaca

Package: FourCSeq

Version: 1.3.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FourCSeq_1.3.5.tar.gz

StartedAt: 2015-08-23 23:59:09 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-24 00:08:07 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 538.2 seconds

RetCode: 0

Status:  OK

CheckDir: FourCSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FourCSeq_1.3.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/FourCSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FourCSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FourCSeq’ version ‘1.3.5’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘FourCSeq’ can be installed ... [33s/33s] OK
* 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
* 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 ... 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’
addFragments: no visible global function definition for ‘metadata’
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’
findViewpointFragments: no visible global function definition for
  ‘metadata’
findViewpointFragments : <anonymous>: no visible global function
  definition for ‘Rle’
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 global function definition for ‘DataFrame’
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 ‘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’
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’
saveGR: no visible global function definition for ‘metadata’
saveGR: no visible global function definition for ‘seqlengths’
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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [185s/194s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getZScores      58.356  8.822  67.306
plotScatter     45.171  2.151  48.836
writeTrackFiles 17.297  0.698  18.778
plotDifferences  8.354  0.124   9.748
plotZScores      6.502  0.097   6.684
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/FourCSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘FourCSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FourCSeq)

name	user	system	elapsed
FourC	0.279	0.012	0.310
addFragments	0.591	0.020	0.644
addViewpointFrags	0.745	0.004	1.830
combineFragEnds	0.571	0.019	0.609
countFragmentOverlaps	2.009	0.083	2.179
countFragmentOverlapsSecondCutter	0.001	0.000	0.001
fc	0.114	0.006	0.134
fcf	0.209	0.014	0.245
findViewpointFragments	0.916	0.006	1.617
getAllResults	4.248	0.086	4.509
getDifferences	3.848	0.056	3.926
getDistAroundVp	0.136	0.014	0.214
getNormalizationFactors	0.263	0.013	0.300
getReferenceSeq	0.122	0.001	0.123
getZScores	58.356	8.822	67.306
normalizeRPM	0.218	0.044	0.263
plotDifferences	8.354	0.124	9.748
plotFits	0.567	0.028	0.611
plotNormalizationFactors	3.065	0.068	3.888
plotScatter	45.171	2.151	48.836
plotZScores	6.502	0.097	6.684
smoothCounts	0.247	0.037	0.285
smoothHitPerCent	1.689	0.407	2.098
writeTrackFiles	17.297	0.698	18.778