BioC 3.3: CHECK report for FourCSeq on linux2.bioconductor.org

Package: FourCSeq

Version: 1.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings FourCSeq_1.5.0.tar.gz

StartedAt: 2015-10-27 03:57:31 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:04:24 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 413.0 seconds

RetCode: 0

Status:  OK

CheckDir: FourCSeq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings FourCSeq_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/FourCSeq.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘FourCSeq’ can be installed ... [24s/24s] 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’
Undefined global functions or variables:
  DataFrame IRanges Rle Seqinfo SimpleList aes change count
  differentialInteraction element_blank fit fitDown fitUp geom_path
  geom_point keepSeqlevels labs metadata mid peak rel
  scale_fill_gradient2 scale_y_continuous seqlengths seqlevels
  seqlevels<- theme theme_bw theme_set
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [175s/175s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getZScores      66.155  0.176  66.388
plotScatter     47.658  0.384  48.744
writeTrackFiles 16.683  0.244  17.078
plotDifferences  8.714  0.004   8.730
plotZScores      5.164  0.016   5.188
* 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
  ‘/home/biocbuild/bbs-3.3-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	0.27	0.00	0.27
addFragments	0.600	0.024	0.626
addViewpointFrags	0.454	0.000	0.458
combineFragEnds	0.553	0.012	0.566
countFragmentOverlaps	1.679	0.040	1.720
countFragmentOverlapsSecondCutter	0	0	0
fc	0.136	0.004	0.139
fcf	0.250	0.004	0.254
findViewpointFragments	0.663	0.004	0.667
getAllResults	4.233	0.008	4.245
getDifferences	3.189	0.024	3.218
getDistAroundVp	0.589	0.000	0.592
getNormalizationFactors	0.279	0.004	0.283
getReferenceSeq	0.127	0.000	0.127
getZScores	66.155	0.176	66.388
normalizeRPM	0.141	0.004	0.144
plotDifferences	8.714	0.004	8.730
plotFits	0.542	0.004	0.546
plotNormalizationFactors	2.299	0.020	2.319
plotScatter	47.658	0.384	48.744
plotZScores	5.164	0.016	5.188
smoothCounts	0.232	0.000	0.231
smoothHitPerCent	1.433	0.020	1.454
writeTrackFiles	16.683	0.244	17.078