BioC 3.2: CHECK report for TarSeqQC on perceval

Package: TarSeqQC

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TarSeqQC_1.0.0.tar.gz

StartedAt: 2015-10-27 12:49:10 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 12:53:34 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 264.1 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.0.0’
* 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 ... [14s/14s] 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 ... [453s/60s] OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
TargetExperiment-initialize        50.534 24.244  14.489
TargetExperiment-setters           37.342 19.797  14.553
TargetExperiment-buildFeaturePanel 25.067  8.669  11.667
pileupCounts                       20.439  6.582   9.326
TargetExperiment-buildReport        4.360  2.659   0.783
TargetExperiment-summarizePanel     4.010  2.899   2.030
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [270s/56s]
 [270s/56s] 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
Creating a generic function for ‘print’ from package ‘base’ in package ‘TarSeqQC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TarSeqQC)

name	user	system	elapsed
TargetExperiment-buildFeaturePanel	25.067	8.669	11.667
TargetExperiment-buildReport	4.360	2.659	0.783
TargetExperiment-constructor	0.003	0.000	0.004
TargetExperiment-getters	0.191	0.005	0.196
TargetExperiment-initialize	50.534	24.244	14.489
TargetExperiment-plot	0.002	0.000	0.002
TargetExperiment-plotAttrExpl	0.002	0.000	0.001
TargetExperiment-plotFeatPerform	0.002	0.000	0.002
TargetExperiment-plotFeature	0.002	0.001	0.003
TargetExperiment-plotGeneAttrPerFeat	0.002	0.000	0.002
TargetExperiment-plotNtdPercentage	0.003	0.000	0.004
TargetExperiment-plotRegion	0.004	0.001	0.005
TargetExperiment-print	0.059	0.014	0.073
TargetExperiment-setters	37.342	19.797	14.553
TargetExperiment-show	0.064	0.016	0.079
TargetExperiment-statistics	0.039	0.009	0.047
TargetExperiment-summarizePanel	4.010	2.899	2.030
pileupCounts	20.439	6.582	9.326