BioC 3.4: CHECK report for TarSeqQC on morelia

Package: TarSeqQC

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TarSeqQC_1.4.1.tar.gz

StartedAt: 2017-04-15 08:46:25 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:52:02 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 337.4 seconds

RetCode: 0

Status:  OK

CheckDir: TarSeqQC.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TarSeqQC_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.1’
* 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 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-plotRegion        158.882 44.257   9.952
plotInOutFeatures                   53.344 15.300   2.891
TargetExperiment-class               7.437  1.596  48.004
TargetExperiment-plotFeature         0.211  0.246   7.817
TargetExperiment-plotNtdPercentage   0.147  0.161   5.326
pileupCounts                         0.119  0.162   5.557
* 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	0.071	0.010	0.079
TargetExperiment-buildFeaturePanel	1.787	0.082	1.870
TargetExperiment-buildReport	0.690	0.038	0.789
TargetExperiment-class	7.437	1.596	48.004
TargetExperiment-constructor	1.212	0.097	4.024
TargetExperiment-getters	0.254	0.042	0.296
TargetExperiment-initialize	0.003	0.000	0.003
TargetExperiment-plot	0.132	0.020	0.152
TargetExperiment-plotAttrExpl	0.048	0.013	0.060
TargetExperiment-plotAttrPerform	0.037	0.005	0.042
TargetExperiment-plotFeatPerform	0.657	0.009	0.665
TargetExperiment-plotFeature	0.211	0.246	7.817
TargetExperiment-plotGeneAttrPerFeat	0.530	0.032	0.562
TargetExperiment-plotMetaDataExpl	0.040	0.006	0.046
TargetExperiment-plotNtdPercentage	0.147	0.161	5.326
TargetExperiment-plotRegion	158.882	44.257	9.952
TargetExperiment-print	0.056	0.017	0.073
TargetExperiment-readFrequencies	0.263	0.119	2.957
TargetExperiment-setters	0.007	0.005	0.013
TargetExperiment-show	0.050	0.015	0.065
TargetExperiment-statistics	0.073	0.015	0.088
TargetExperiment-summarizePanel	0.107	0.178	2.872
TargetExperimentList-class	0.305	0.048	0.353
TargetExperimentList-constructor	0.080	0.012	0.091
TargetExperimentList-initialize	0.070	0.009	0.080
TargetExperimentList-plotGlobalAttrExpl	0.030	0.005	0.035
TargetExperimentList-plotPoolPerformance	0.017	0.005	0.021
checkBedFasta	0.041	0.001	0.041
pileupCounts	0.119	0.162	5.557
plotInOutFeatures	53.344	15.300	2.891