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CHECK report for TarSeqQC on malbec2

This page was generated on 2020-10-17 11:55:54 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TarSeqQC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1781/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TarSeqQC 1.18.0
Gabriela Merino
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/TarSeqQC
Branch: RELEASE_3_11
Last Commit: f0f86ab
Last Changed Date: 2020-04-27 14:51:30 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  TIMEOUT  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TarSeqQC
Version: 1.18.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:TarSeqQC.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings TarSeqQC_1.18.0.tar.gz
StartedAt: 2020-10-17 05:59:12 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:03:49 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 276.1 seconds
RetCode: 0
Status:  OK 
CheckDir: TarSeqQC.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:TarSeqQC.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings TarSeqQC_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/TarSeqQC.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.18.0’
* 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 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 (user + system) or elapsed time > 5s
                              user system elapsed
TargetExperiment-class      15.289  5.336  13.553
TargetExperiment-plotRegion  3.799  1.277   1.966
* 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-3.11-bioc/meat/TarSeqQC.Rcheck/00check.log’
for details.



Installation output

TarSeqQC.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL TarSeqQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-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 version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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, 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 -- Sat Oct 17 06:03:42 2020 
*********************************************** 
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 
 18.848   3.595  18.686 

Example timings

TarSeqQC.Rcheck/TarSeqQC-Ex.timings

nameusersystemelapsed
TargetExperiment-biasExploration0.0650.0000.065
TargetExperiment-buildFeaturePanel1.2830.1081.421
TargetExperiment-buildReport1.9190.0071.926
TargetExperiment-class15.289 5.33613.553
TargetExperiment-constructor2.4190.3962.242
TargetExperiment-getters0.5590.1230.412
TargetExperiment-initialize0.0020.0000.001
TargetExperiment-plot0.3340.0280.363
TargetExperiment-plotAttrExpl0.1010.0120.113
TargetExperiment-plotAttrPerform0.0420.0080.049
TargetExperiment-plotFeatPerform0.4110.0120.423
TargetExperiment-plotFeature0.3440.6860.463
TargetExperiment-plotGeneAttrPerFeat0.7010.0680.769
TargetExperiment-plotMetaDataExpl0.0630.0010.063
TargetExperiment-plotNtdPercentage0.3640.5020.460
TargetExperiment-plotRegion3.7991.2771.966
TargetExperiment-print0.0480.0040.052
TargetExperiment-readFrequencies0.3580.2630.419
TargetExperiment-setters0.0030.0000.004
TargetExperiment-show0.0440.0040.048
TargetExperiment-statistics0.0650.0070.072
TargetExperiment-summarizePanel0.5920.3160.392
TargetExperimentList-class0.6760.1470.541
TargetExperimentList-constructor0.0750.0000.075
TargetExperimentList-initialize0.0760.0040.080
TargetExperimentList-plotGlobalAttrExpl0.0190.0040.023
TargetExperimentList-plotPoolPerformance0.0130.0000.014
checkBedFasta0.0370.0040.041
pileupCounts0.3560.3370.340
plotInOutFeatures0.5640.3820.571