BioC 3.5: CHECK report for TarSeqQC on malbec2

Package: TarSeqQC

Version: 1.6.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.6.1.tar.gz

StartedAt: 2017-08-16 02:36:34 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:41:33 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 298.9 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_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.6.1’
* 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             9.500  1.160  45.443
TargetExperiment-plotRegion        0.388  0.268   9.070
TargetExperiment-plotFeature       0.244  0.196   7.598
TargetExperiment-plotNtdPercentage 0.188  0.132   5.222
pileupCounts                       0.152  0.092   5.095
* 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	1.388	0.016	1.405
TargetExperiment-buildReport	1.504	0.012	1.521
TargetExperiment-class	9.500	1.160	45.443
TargetExperiment-constructor	1.000	0.108	3.498
TargetExperiment-getters	0.232	0.020	0.252
TargetExperiment-initialize	0.000	0.000	0.001
TargetExperiment-plot	0.236	0.016	0.250
TargetExperiment-plotAttrExpl	0.104	0.000	0.103
TargetExperiment-plotAttrPerform	0.068	0.000	0.070
TargetExperiment-plotFeatPerform	0.752	0.000	0.756
TargetExperiment-plotFeature	0.244	0.196	7.598
TargetExperiment-plotGeneAttrPerFeat	0.592	0.028	0.621
TargetExperiment-plotMetaDataExpl	0.032	0.000	0.032
TargetExperiment-plotNtdPercentage	0.188	0.132	5.222
TargetExperiment-plotRegion	0.388	0.268	9.070
TargetExperiment-print	0.052	0.000	0.052
TargetExperiment-readFrequencies	0.276	0.060	2.858
TargetExperiment-setters	0.004	0.004	0.007
TargetExperiment-show	0.064	0.000	0.063
TargetExperiment-statistics	0.116	0.008	0.124
TargetExperiment-summarizePanel	0.084	0.048	2.787
TargetExperimentList-class	0.656	0.036	0.695
TargetExperimentList-constructor	0.064	0.000	0.066
TargetExperimentList-initialize	0.048	0.004	0.052
TargetExperimentList-plotGlobalAttrExpl	0.172	0.000	0.173
TargetExperimentList-plotPoolPerformance	0.116	0.000	0.117
checkBedFasta	0.032	0.000	0.030
pileupCounts	0.152	0.092	5.095
plotInOutFeatures	0.276	0.076	2.783