BioC 3.3: CHECK report for SGSeq on morelia

Package: SGSeq

Version: 1.5.15

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SGSeq_1.5.15.tar.gz

StartedAt: 2016-04-21 07:31:05 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:37:45 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 400.0 seconds

RetCode: 0

Status:  OK

CheckDir: SGSeq.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 SGSeq_1.5.15.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SGSeq.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SGSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SGSeq’ version ‘1.5.15’
* 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 ‘SGSeq’ can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Unexported objects imported by ':::' calls:
  ‘GenomicRanges:::extraColumnSlotNames’
  ‘GenomicRanges:::extraColumnSlotsAsDF’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addAlpha: no visible global function definition for ‘col2rgb’
addAlpha: no visible global function definition for ‘rgb’
annotateFeatures: no visible global function definition for ‘setNames’
collapseFeatures: no visible global function definition for ‘setNames’
exportFeatures: no visible global function definition for ‘rgb’
exportFeatures: no visible global function definition for ‘col2rgb’
extractExons: no visible global function definition for ‘setNames’
extractJunctions: no visible global function definition for ‘setNames’
extractSplicesitesFromJunctions: no visible global function definition
  for ‘setNames’
filterExonsTerminal: no visible global function definition for
  ‘setNames’
filterIntrons: no visible global function definition for ‘setNames’
findEvents: no visible global function definition for ‘setNames’
findSGSegments: no visible global function definition for ‘setNames’
findSGSegmentsPerGene: no visible global function definition for
  ‘setNames’
findSGVariantsFromSGFeatures: no visible global function definition for
  ‘setNames’
getLayoutParameters: no visible global function definition for
  ‘dev.size’
getPadding: no visible global function definition for ‘dev.size’
mapEventToProtein: no visible global function definition for ‘setNames’
mergeExonsTerminal: no visible global function definition for
  ‘setNames’
plotCoverage: no visible global function definition for ‘plot’
plotCoverage: no visible global function definition for ‘text’
plotExonGraph: no visible global function definition for ‘par’
plotExonGraph: no visible global function definition for ‘plot’
plotExonGraph: no visible global function definition for ‘text’
plotExonGraph: no visible global function definition for ‘mtext’
plotFeatures: no visible binding for global variable ‘dist’
plotFeatures: no visible binding for global variable ‘hclust’
plotFeatures: no visible global function definition for
  ‘colorRampPalette’
plotFeatures: no visible global function definition for ‘layout’
plotFeatures: no visible global function definition for ‘par’
plotImage: no visible global function definition for ‘par’
plotImage: no visible global function definition for ‘mtext’
plotRanges: no visible binding for global variable ‘rect’
plotSpliceGraph: no visible global function definition for ‘plot’
plotSpliceGraph: no visible global function definition for ‘text’
plotTrackRanges: no visible global function definition for ‘text’
plotTrackScore: no visible binding for global variable ‘rect’
plotTrackScore: no visible global function definition for ‘axis’
plotTrackScore: no visible global function definition for ‘mtext’
plotTrackScore: no visible global function definition for ‘par’
plotVariants: no visible binding for global variable ‘dist’
plotVariants: no visible binding for global variable ‘hclust’
plotVariants: no visible global function definition for
  ‘colorRampPalette’
plotVariants: no visible global function definition for ‘layout’
plotVariants: no visible global function definition for ‘par’
predictExonsTerminal: no visible global function definition for
  ‘setNames’
predictTxFeaturesPerSample: no visible global function definition for
  ‘setNames’
processFeatures: no visible global function definition for ‘setNames’
splicesiteOverlap: no visible global function definition for ‘setNames’
splitCharacterList: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  axis col2rgb colorRampPalette dev.size dist hclust layout mtext par
  plot rect rgb setNames text
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.size",
             "rgb")
  importFrom("graphics", "axis", "layout", "mtext", "par", "plot",
             "rect", "text")
  importFrom("stats", "dist", "hclust", "setNames")
to your NAMESPACE file.
* 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 ... [85s/86s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
predictVariantEffects 28.577  0.085  29.287
analyzeFeatures       17.661  0.248  17.919
predictTxFeatures     10.817  0.106  10.930
getSGVariantCounts     6.316  0.096   6.417
getSGFeatureCounts     5.704  0.107   5.819
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [143s/143s]
 [143s/143s] OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/SGSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘SGSeq’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SGSeq)

name	user	system	elapsed
SGFeatureCounts	0.198	0.015	0.213
SGFeatures	0.033	0.000	0.033
SGVariantCounts	0.145	0.000	0.145
SGVariants	0.143	0.000	0.142
TxFeatures	0.043	0.000	0.043
analyzeFeatures	17.661	0.248	17.919
analyzeVariants	1.319	0.007	1.326
annotate	1.475	0.002	1.476
assays	0.008	0.000	0.007
convertToSGFeatures	1.304	0.004	1.310
convertToTxFeatures	0.251	0.001	0.251
exportFeatures	0.000	0.000	0.001
findSGVariants	1.085	0.002	1.088
getBamInfo	1.352	0.149	1.521
getSGFeatureCounts	5.704	0.107	5.819
getSGVariantCounts	6.316	0.096	6.417
importTranscripts	0	0	0
makeSGFeatureCounts	0.053	0.000	0.053
makeVariantNames	0.007	0.000	0.006
mergeTxFeatures	0.328	0.001	0.329
plotCoverage	0	0	0
plotFeatures	0.000	0.001	0.001
plotSpliceGraph	0.000	0.000	0.001
plotVariants	0	0	0
predictTxFeatures	10.817	0.106	10.930
predictVariantEffects	28.577	0.085	29.287
processTerminalExons	0.274	0.000	0.274
slots	0.003	0.000	0.003