BioC 3.6: CHECK report for TarSeqQC on veracruz1

Package: TarSeqQC

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TarSeqQC_1.7.1.tar.gz

StartedAt: 2017-08-16 09:04:33 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 09:08:48 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 255.5 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_1.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.7.1’
* 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-class 11.288   1.18  15.904
* 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	0.121	0.002	0.129
TargetExperiment-buildFeaturePanel	1.758	0.031	1.850
TargetExperiment-buildReport	1.899	0.021	1.980
TargetExperiment-class	11.288	1.180	15.904
TargetExperiment-constructor	1.016	0.060	1.386
TargetExperiment-getters	0.250	0.033	0.299
TargetExperiment-initialize	0.002	0.000	0.002
TargetExperiment-plot	0.228	0.019	0.250
TargetExperiment-plotAttrExpl	0.103	0.004	0.111
TargetExperiment-plotAttrPerform	0.077	0.003	0.080
TargetExperiment-plotFeatPerform	0.981	0.007	1.023
TargetExperiment-plotFeature	0.237	0.157	0.625
TargetExperiment-plotGeneAttrPerFeat	0.648	0.040	0.696
TargetExperiment-plotMetaDataExpl	0.036	0.002	0.041
TargetExperiment-plotNtdPercentage	0.201	0.103	0.479
TargetExperiment-plotRegion	0.376	0.232	2.654
TargetExperiment-print	0.065	0.012	0.078
TargetExperiment-readFrequencies	0.244	0.079	0.399
TargetExperiment-setters	0.007	0.002	0.008
TargetExperiment-show	0.045	0.007	0.051
TargetExperiment-statistics	0.069	0.008	0.078
TargetExperiment-summarizePanel	0.060	0.054	0.387
TargetExperimentList-class	0.650	0.065	0.729
TargetExperimentList-constructor	0.080	0.003	0.087
TargetExperimentList-initialize	0.049	0.003	0.053
TargetExperimentList-plotGlobalAttrExpl	0.214	0.003	0.218
TargetExperimentList-plotPoolPerformance	0.199	0.007	0.210
checkBedFasta	0.042	0.001	0.042
pileupCounts	0.144	0.123	0.498
plotInOutFeatures	0.223	0.076	0.376