BioC 3.5: CHECK report for TarSeqQC on toluca2

Package: TarSeqQC

Version: 1.5.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TarSeqQC_1.5.3.tar.gz

StartedAt: 2017-04-23 10:37:50 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 10:45:27 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 456.9 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_1.5.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TarSeqQC.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.5.3’
* 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             112.866 31.049  67.489
TargetExperiment-plotRegion         68.106 21.123  12.954
TargetExperiment-constructor         1.361  0.114   5.040
TargetExperiment-plotFeature         0.300  0.327  10.734
TargetExperiment-plotNtdPercentage   0.247  0.239   7.400
pileupCounts                         0.150  0.069   7.122
* 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	0.150	0.024	0.175
TargetExperiment-buildFeaturePanel	2.233	0.019	2.439
TargetExperiment-buildReport	2.593	0.038	3.013
TargetExperiment-class	112.866	31.049	67.489
TargetExperiment-constructor	1.361	0.114	5.040
TargetExperiment-getters	0.398	0.067	0.485
TargetExperiment-initialize	0.003	0.000	0.006
TargetExperiment-plot	0.414	0.031	0.509
TargetExperiment-plotAttrExpl	0.161	0.012	0.196
TargetExperiment-plotAttrPerform	0.115	0.006	0.135
TargetExperiment-plotFeatPerform	1.222	0.010	1.395
TargetExperiment-plotFeature	0.300	0.327	10.734
TargetExperiment-plotGeneAttrPerFeat	0.989	0.067	1.248
TargetExperiment-plotMetaDataExpl	0.045	0.005	0.062
TargetExperiment-plotNtdPercentage	0.247	0.239	7.400
TargetExperiment-plotRegion	68.106	21.123	12.954
TargetExperiment-print	0.080	0.019	0.098
TargetExperiment-readFrequencies	0.293	0.152	3.901
TargetExperiment-setters	0.007	0.005	0.012
TargetExperiment-show	0.052	0.013	0.066
TargetExperiment-statistics	0.118	0.020	0.153
TargetExperiment-summarizePanel	0.066	0.105	3.738
TargetExperimentList-class	0.940	0.089	1.081
TargetExperimentList-constructor	0.097	0.009	0.106
TargetExperimentList-initialize	0.071	0.011	0.089
TargetExperimentList-plotGlobalAttrExpl	0.270	0.006	0.279
TargetExperimentList-plotPoolPerformance	0.218	0.005	0.223
checkBedFasta	0.046	0.001	0.046
pileupCounts	0.150	0.069	7.122
plotInOutFeatures	0.337	0.183	4.011