BioC 3.4: CHECK report for TarSeqQC on zin1

Package: TarSeqQC

Version: 1.3.13

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.3.13.tar.gz

StartedAt: 2016-09-20 13:14:09 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:17:59 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 229.6 seconds

RetCode: 0

Status:  OK

CheckDir: TarSeqQC.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.3.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.3.13’
* 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 5.284  0.576  29.502
* 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
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-biasExploration	0.044	0.000	0.046
TargetExperiment-buildFeaturePanel	0.940	0.008	0.949
TargetExperiment-buildReport	0.396	0.016	0.418
TargetExperiment-class	5.284	0.576	29.502
TargetExperiment-constructor	0.964	0.040	2.818
TargetExperiment-getters	0.148	0.008	0.159
TargetExperiment-initialize	0.000	0.000	0.001
TargetExperiment-plot	0.084	0.008	0.092
TargetExperiment-plotAttrExpl	0.032	0.000	0.034
TargetExperiment-plotAttrPerform	0.024	0.004	0.028
TargetExperiment-plotFeatPerform	0.472	0.008	0.480
TargetExperiment-plotFeature	0.132	0.080	3.553
TargetExperiment-plotGeneAttrPerFeat	0.036	0.000	0.034
TargetExperiment-plotMetaDataExpl	0.020	0.012	0.033
TargetExperiment-plotNtdPercentage	0.092	0.104	4.103
TargetExperiment-plotRegion	0.208	0.084	4.852
TargetExperiment-print	0.036	0.000	0.037
TargetExperiment-readFrequencies	0.236	0.044	2.262
TargetExperiment-setters	0.008	0.000	0.005
TargetExperiment-show	0.032	0.004	0.036
TargetExperiment-statistics	0.060	0.000	0.059
TargetExperiment-summarizePanel	0.040	0.036	2.030
TargetExperimentList-class	0.264	0.012	0.287
TargetExperimentList-constructor	0.052	0.004	0.055
TargetExperimentList-initialize	0.052	0.004	0.058
TargetExperimentList-plotGlobalAttrExpl	0.024	0.000	0.022
TargetExperimentList-plotPoolPerformance	0.012	0.000	0.012
pileupCounts	0.084	0.100	4.229
plotInOutFeatures	0.228	0.036	2.091