BioC 3.5: CHECK report for TarSeqQC on oaxaca

Package: TarSeqQC

Version: 1.5.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TarSeqQC_1.5.3.tar.gz

StartedAt: 2017-03-04 09:53:58 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 10:00:43 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 405.4 seconds

RetCode: 0

Status:  OK

CheckDir: TarSeqQC.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 TarSeqQC_1.5.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TarSeqQC.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TarSeqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TarSeqQC’ version ‘1.5.3’
* 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 ‘TarSeqQC’ can be installed ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
TargetExperiment-class             13.225  2.205  58.280
TargetExperiment-plotRegion         0.445  0.424  11.944
TargetExperiment-plotFeature        0.280  0.318   8.921
TargetExperiment-plotNtdPercentage  0.225  0.215   6.758
pileupCounts                        0.183  0.199   6.986
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: OK

* installing *source* package ‘TarSeqQC’ ...
** 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 (TarSeqQC)

name	user	system	elapsed
TargetExperiment-biasExploration	0.160	0.023	0.183
TargetExperiment-buildFeaturePanel	2.380	0.033	2.415
TargetExperiment-buildReport	2.323	0.035	2.377
TargetExperiment-class	13.225	2.205	58.280
TargetExperiment-constructor	1.354	0.115	4.428
TargetExperiment-getters	0.279	0.035	0.313
TargetExperiment-initialize	0.003	0.000	0.003
TargetExperiment-plot	0.35	0.03	0.38
TargetExperiment-plotAttrExpl	0.103	0.003	0.107
TargetExperiment-plotAttrPerform	0.068	0.002	0.070
TargetExperiment-plotFeatPerform	0.761	0.005	0.766
TargetExperiment-plotFeature	0.280	0.318	8.921
TargetExperiment-plotGeneAttrPerFeat	0.763	0.059	0.822
TargetExperiment-plotMetaDataExpl	0.034	0.002	0.037
TargetExperiment-plotNtdPercentage	0.225	0.215	6.758
TargetExperiment-plotRegion	0.445	0.424	11.944
TargetExperiment-print	0.055	0.010	0.065
TargetExperiment-readFrequencies	0.256	0.137	3.594
TargetExperiment-setters	0.004	0.002	0.006
TargetExperiment-show	0.052	0.008	0.059
TargetExperiment-statistics	0.112	0.014	0.126
TargetExperiment-summarizePanel	0.065	0.093	3.594
TargetExperimentList-class	0.931	0.081	1.013
TargetExperimentList-constructor	0.114	0.005	0.120
TargetExperimentList-initialize	0.088	0.005	0.093
TargetExperimentList-plotGlobalAttrExpl	0.268	0.004	0.271
TargetExperimentList-plotPoolPerformance	0.231	0.003	0.235
checkBedFasta	0.046	0.001	0.048
pileupCounts	0.183	0.199	6.986
plotInOutFeatures	0.320	0.172	3.840