Package: TarSeqQC

Version: 1.8.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.8.0.tar.gz

StartedAt: 2018-04-12 03:16:29 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:20:01 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 212.5 seconds

RetCode: 0

Status:  OK

CheckDir: TarSeqQC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.0’
* 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 ... 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 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 9.928  1.148  14.105
* 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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("TarSeqQC")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'plyr'

The following object is masked from 'package:XVector':

    compact

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename



RUNIT TEST PROTOCOL -- Thu Apr 12 03:19:58 2018 
*********************************************** 
Number of test functions: 33 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TarSeqQC RUnit Tests - 33 test functions, 0 errors, 0 failures
Number of test functions: 33 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 23.800   1.032  25.916 

name	user	system	elapsed
TargetExperiment-biasExploration	0.092	0.000	0.092
TargetExperiment-buildFeaturePanel	1.748	0.028	1.777
TargetExperiment-buildReport	1.444	0.020	1.475
TargetExperiment-class	9.928	1.148	14.105
TargetExperiment-constructor	0.896	0.080	1.164
TargetExperiment-getters	0.296	0.020	0.317
TargetExperiment-initialize	0.004	0.000	0.001
TargetExperiment-plot	0.244	0.016	0.261
TargetExperiment-plotAttrExpl	0.100	0.000	0.101
TargetExperiment-plotAttrPerform	0.064	0.004	0.068
TargetExperiment-plotFeatPerform	0.708	0.004	0.712
TargetExperiment-plotFeature	0.236	0.180	0.617
TargetExperiment-plotGeneAttrPerFeat	0.560	0.056	0.616
TargetExperiment-plotMetaDataExpl	0.028	0.000	0.028
TargetExperiment-plotNtdPercentage	0.176	0.116	0.438
TargetExperiment-plotRegion	0.328	0.188	2.124
TargetExperiment-print	0.048	0.004	0.053
TargetExperiment-readFrequencies	0.212	0.048	0.332
TargetExperiment-setters	0.004	0.000	0.004
TargetExperiment-show	0.032	0.004	0.038
TargetExperiment-statistics	0.076	0.000	0.076
TargetExperiment-summarizePanel	0.056	0.044	0.281
TargetExperimentList-class	0.948	0.028	0.974
TargetExperimentList-constructor	0.100	0.000	0.102
TargetExperimentList-initialize	0.080	0.004	0.085
TargetExperimentList-plotGlobalAttrExpl	0.284	0.000	0.287
TargetExperimentList-plotPoolPerformance	0.132	0.000	0.134
checkBedFasta	0.032	0.000	0.035
pileupCounts	0.144	0.120	0.454
plotInOutFeatures	0.304	0.088	0.502