BioC 3.2: CHECK report for FourCSeq on perceval

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: 2015-08-24 00:48:17 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:00:45 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 747.7 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 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [41s/43s] 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
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’
FourC: no visible global function definition for ‘SimpleList’
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 ... [325s/328s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
getZScores      112.120 18.358 131.086
plotScatter     103.943  4.525 109.134
writeTrackFiles  19.500  1.179  20.908
plotDifferences   9.838  0.123  10.020
plotZScores       6.797  0.144   6.955
getAllResults     5.947  0.067   6.037
* 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	0.286	0.038	0.323
addFragments	0.748	0.048	0.866
addViewpointFrags	0.843	0.007	0.861
combineFragEnds	1.119	0.042	1.195
countFragmentOverlaps	2.475	0.150	2.651
countFragmentOverlapsSecondCutter	0.001	0.000	0.001
fc	0.125	0.012	0.138
fcf	0.278	0.034	0.313
findViewpointFragments	1.741	0.018	1.785
getAllResults	5.947	0.067	6.037
getDifferences	3.847	0.034	3.892
getDistAroundVp	0.166	0.023	0.191
getNormalizationFactors	0.272	0.021	0.299
getReferenceSeq	0.120	0.002	0.122
getZScores	112.120	18.358	131.086
normalizeRPM	0.230	0.100	0.334
plotDifferences	9.838	0.123	10.020
plotFits	0.605	0.060	0.675
plotNormalizationFactors	3.437	0.049	3.495
plotScatter	103.943	4.525	109.134
plotZScores	6.797	0.144	6.955
smoothCounts	0.239	0.066	0.306
smoothHitPerCent	3.602	0.727	4.348
writeTrackFiles	19.500	1.179	20.908