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CHECK report for TarSeqQC on malbec2

This page was generated on 2019-04-09 11:43:46 -0400 (Tue, 09 Apr 2019).

Package 1594/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TarSeqQC 1.13.1
Gabriela Merino
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/TarSeqQC
Branch: master
Last Commit: 35b7373
Last Changed Date: 2019-03-13 09:23:16 -0400 (Wed, 13 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: TarSeqQC
Version: 1.13.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TarSeqQC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TarSeqQC_1.13.1.tar.gz
StartedAt: 2019-04-09 03:59:30 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:04:08 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 277.6 seconds
RetCode: 0
Status:  OK 
CheckDir: TarSeqQC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TarSeqQC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TarSeqQC_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/TarSeqQC.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.13.1’
* 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 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 ... NOTE
plotNtdPercentage,TargetExperiment: no visible global function
  definition for ‘path’
plotRegion,TargetExperiment: no visible global function definition for
  ‘path’
readFrequencies,TargetExperiment: no visible global function definition
  for ‘path’
Undefined global functions or variables:
  path
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
TargetExperiment-class      16.218  5.782  12.025
TargetExperiment-plotRegion  7.009  1.787   2.860
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/TarSeqQC.Rcheck/00check.log’
for details.



Installation output

TarSeqQC.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL TarSeqQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘TarSeqQC’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TarSeqQC)

Tests output

TarSeqQC.Rcheck/tests/runTests.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, 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 -- Tue Apr  9 04:04:02 2019 
*********************************************** 
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 
 16.213   3.287  15.586 

Example timings

TarSeqQC.Rcheck/TarSeqQC-Ex.timings

nameusersystemelapsed
TargetExperiment-biasExploration0.0880.0000.088
TargetExperiment-buildFeaturePanel1.2880.0341.364
TargetExperiment-buildReport2.2950.0562.352
TargetExperiment-class16.218 5.78212.025
TargetExperiment-constructor1.3610.1671.760
TargetExperiment-getters1.0000.3860.267
TargetExperiment-initialize0.0010.0010.001
TargetExperiment-plot0.4220.0110.434
TargetExperiment-plotAttrExpl0.1730.0160.189
TargetExperiment-plotAttrPerform0.050.000.05
TargetExperiment-plotFeatPerform0.7310.0310.763
TargetExperiment-plotFeature1.2601.2811.072
TargetExperiment-plotGeneAttrPerFeat0.6300.0400.671
TargetExperiment-plotMetaDataExpl0.0570.0000.056
TargetExperiment-plotNtdPercentage0.4950.5800.617
TargetExperiment-plotRegion7.0091.7872.860
TargetExperiment-print0.0390.0150.054
TargetExperiment-readFrequencies0.4640.3260.504
TargetExperiment-setters0.0050.0000.005
TargetExperiment-show0.0510.0040.055
TargetExperiment-statistics0.0840.0040.088
TargetExperiment-summarizePanel0.1010.1230.418
TargetExperimentList-class1.2240.4490.666
TargetExperimentList-constructor0.0830.0040.087
TargetExperimentList-initialize0.0920.0000.092
TargetExperimentList-plotGlobalAttrExpl0.0270.0000.027
TargetExperimentList-plotPoolPerformance0.020.000.02
checkBedFasta0.0470.0080.055
pileupCounts0.6140.4820.605
plotInOutFeatures0.6370.5160.554