BioC 3.5: CHECK report for TarSeqQC on veracruz2

Package: TarSeqQC

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TarSeqQC_1.6.2.tar.gz

StartedAt: 2017-10-18 09:37:02 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:43:22 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 379.7 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_1.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.2’
* 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 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             127.789 32.949  59.166
TargetExperiment-plotRegion          0.391  0.405  11.736
TargetExperiment-plotFeature         0.287  0.344  10.122
TargetExperiment-plotNtdPercentage   0.210  0.213   6.809
pileupCounts                         0.166  0.254   6.579
* 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	0.139	0.006	0.148
TargetExperiment-buildFeaturePanel	1.729	0.043	1.799
TargetExperiment-buildReport	2.066	0.037	2.163
TargetExperiment-class	127.789	32.949	59.166
TargetExperiment-constructor	1.167	0.133	4.558
TargetExperiment-getters	0.303	0.053	0.365
TargetExperiment-initialize	0.003	0.000	0.004
TargetExperiment-plot	0.334	0.027	0.366
TargetExperiment-plotAttrExpl	0.124	0.007	0.134
TargetExperiment-plotAttrPerform	0.091	0.004	0.103
TargetExperiment-plotFeatPerform	1.017	0.011	1.054
TargetExperiment-plotFeature	0.287	0.344	10.122
TargetExperiment-plotGeneAttrPerFeat	0.879	0.061	0.960
TargetExperiment-plotMetaDataExpl	0.044	0.005	0.049
TargetExperiment-plotNtdPercentage	0.210	0.213	6.809
TargetExperiment-plotRegion	0.391	0.405	11.736
TargetExperiment-print	0.079	0.018	0.098
TargetExperiment-readFrequencies	0.264	0.139	3.716
TargetExperiment-setters	0.005	0.004	0.010
TargetExperiment-show	0.055	0.014	0.071
TargetExperiment-statistics	0.104	0.017	0.126
TargetExperiment-summarizePanel	0.063	0.098	3.526
TargetExperimentList-class	0.809	0.078	0.908
TargetExperimentList-constructor	0.086	0.008	0.097
TargetExperimentList-initialize	0.075	0.009	0.086
TargetExperimentList-plotGlobalAttrExpl	0.222	0.004	0.230
TargetExperimentList-plotPoolPerformance	0.168	0.004	0.184
checkBedFasta	0.039	0.001	0.041
pileupCounts	0.166	0.254	6.579
plotInOutFeatures	0.284	0.150	3.534