BioC 3.5: CHECK report for TarSeqQC on malbec2

Package: TarSeqQC

Version: 1.6.2

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.6.2.tar.gz

StartedAt: 2017-10-18 02:49:51 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:55:02 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 311.3 seconds

RetCode: 0

Status:  OK

CheckDir: TarSeqQC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.6.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.2’
* 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 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             10.660  1.236  47.297
TargetExperiment-plotRegion         0.364  0.216   9.262
TargetExperiment-plotFeature        0.228  0.252   7.885
pileupCounts                        0.160  0.140   5.279
TargetExperiment-plotNtdPercentage  0.180  0.120   5.321
* 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	0.092	0.000	0.091
TargetExperiment-buildFeaturePanel	1.432	0.012	1.444
TargetExperiment-buildReport	1.700	0.020	1.742
TargetExperiment-class	10.660	1.236	47.297
TargetExperiment-constructor	1.036	0.104	3.540
TargetExperiment-getters	0.372	0.036	0.410
TargetExperiment-initialize	0.004	0.000	0.001
TargetExperiment-plot	0.236	0.000	0.239
TargetExperiment-plotAttrExpl	0.100	0.000	0.103
TargetExperiment-plotAttrPerform	0.064	0.000	0.067
TargetExperiment-plotFeatPerform	0.764	0.000	0.765
TargetExperiment-plotFeature	0.228	0.252	7.885
TargetExperiment-plotGeneAttrPerFeat	0.896	0.016	0.913
TargetExperiment-plotMetaDataExpl	0.036	0.000	0.037
TargetExperiment-plotNtdPercentage	0.180	0.120	5.321
TargetExperiment-plotRegion	0.364	0.216	9.262
TargetExperiment-print	0.048	0.004	0.054
TargetExperiment-readFrequencies	0.292	0.052	2.789
TargetExperiment-setters	0.004	0.000	0.007
TargetExperiment-show	0.052	0.004	0.059
TargetExperiment-statistics	0.108	0.004	0.114
TargetExperiment-summarizePanel	0.080	0.060	2.781
TargetExperimentList-class	0.592	0.012	0.607
TargetExperimentList-constructor	0.068	0.000	0.067
TargetExperimentList-initialize	0.052	0.004	0.053
TargetExperimentList-plotGlobalAttrExpl	0.164	0.000	0.163
TargetExperimentList-plotPoolPerformance	0.164	0.000	0.165
checkBedFasta	0.036	0.000	0.034
pileupCounts	0.160	0.140	5.279
plotInOutFeatures	0.240	0.096	2.838