CHECK report for TarSeqQC on celaya2
This page was generated on 2020-01-16 13:43:23 -0500 (Thu, 16 Jan 2020).
TarSeqQC 1.17.1
Gabriela Merino
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/TarSeqQC |
| Branch: master |
| Last Commit: fe4252e |
| Last Changed Date: 2019-12-20 11:25:31 -0500 (Fri, 20 Dec 2019) |
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | NA | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK | |
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TarSeqQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TarSeqQC_1.17.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TarSeqQC.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.17.1’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TarSeqQC-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TargetExperiment-class
> ### Title: TargetExperiment S4 class implementation in R
> ### Aliases: TargetExperiment-class
>
> ### ** Examples
>
> ## Defining bam file, bed file and fasta file names and paths
> bamFile<-system.file("extdata", "mybam.bam", package="TarSeqQC",
+ mustWork=TRUE)
> bedFile<-system.file("extdata", "mybed.bed", package="TarSeqQC",
+ mustWork=TRUE)
> fastaFile<-system.file("extdata", "myfasta.fa", package="TarSeqQC",
+ mustWork=TRUE)
>
> ## Creating a TargetExperiment object
>
> # Defining feature parameter
> feature<-"amplicon"
> # Defining attribute parameter
> attribute<-"coverage"
> ampliPanel<-TargetExperiment(bedFile, bamFile, fastaFile, attribute=attribute,
+ feature=feature)
>
> ## Alternative object creation
> # Creating the TargetExperiment object
> ampliPanel<-TargetExperiment(bedFile, bamFile, fastaFile)
Warning in .local(.Object, ...) : The 'attribute' slot is empty
Warning in .local(.Object, ...) : The 'feature' slot is empty
> # Set feature slot value
> setFeature(ampliPanel)<-"amplicon"
> # Set attribute slot value
> setAttribute(ampliPanel)<-"coverage"
> # Set pileupP slot value in order to set the maximum depth at 1000
> setPileupP(ampliPanel)<-PileupParam(max_depth=1000)
> # Set the featurePanel slot but now using the new pileupP definition
> setFeaturePanel(ampliPanel)<-buildFeaturePanel(ampliPanel)
> ## Early exploration
> # show/print
> ampliPanel
TargetExperiment
amplicon panel:
GRanges object with 3 ranges and 6 metadata columns:
seqnames ranges strand | gene GC.gc coverage sdCoverage
<Rle> <IRanges> <Rle> | <character> <numeric> <numeric> <numeric>
AMPL1 chr1 463-551 * | gene1 0.674 320 19
AMPL2 chr1 1553-1603 * | gene2 0.451 550 90
AMPL3 chr1 3766-3814 * | gene2 0.531 455 12
medianCounts IQRCounts
<numeric> <numeric>
AMPL1 326 24
AMPL2 574 14
AMPL3 463 27
-------
seqinfo: 4 sequences from an unspecified genome; no seqlengths
gene panel:
GRanges object with 3 ranges and 4 metadata columns:
seqnames ranges strand | medianCounts IQRCounts coverage sdCoverage
<Rle> <IRanges> <Rle> | <numeric> <numeric> <numeric> <numeric>
gene1 chr1 463-551 * | 326 0 320 0
gene2 chr1 1553-3814 * | 518 56 502 67
gene3 chr3 1-59 * | 0 0 0 0
-------
seqinfo: 4 sequences from an unspecified genome; no seqlengths
selected attribute:
coverage
> # summary
> summary(ampliPanel)
Min. 1st Qu. Median Mean 3rd Qu. Max.
gene 0 261 328 312 396 502
amplicon 0 143 288 316 472 931
> # summary at feature level
> summaryFeatureLev(ampliPanel)
Min. 1st Qu. Median Mean 3rd Qu. Max.
amplicon 0 143 288 316 472 931
> # summary at gene level
> summaryGeneLev(ampliPanel)
Min. 1st Qu. Median Mean 3rd Qu. Max.
gene 0 261 328 312 396 502
> # attribute boxplot and density plot exploration
> g<-plotAttrExpl(ampliPanel,level="feature",join=TRUE, log=FALSE, color="blue")
> if(interactive()){
+ x11(type="cairo");g
+ }
> # explore amplicon length distribution
> g<-plotMetaDataExpl(ampliPanel, "length", log=FALSE, join=FALSE, color=
+ "blueviolet")
> if(interactive()){
+ g
+ }
> # explore gene's relative frequencies
> g<-plotMetaDataExpl(ampliPanel, "gene", abs=FALSE)
> if(interactive()){
+ g
+ }
> ## Deep exploration and Quality Control
> myfrequencies<-readFrequencies(ampliPanel)
> g<-plotInOutFeatures(readFrequencies(ampliPanel))
> if(interactive()){
+ g
+ }
> # definition of the interval extreme values
> attributeThres<-c(0,1,50,200,500, Inf)
> # plot panel overview
> g<-plot(ampliPanel, attributeThres, chrLabels =TRUE)
> if(interactive()){
+ x11(type="cairo");g
+ }
> # plot panel overview in a feature performance plot
> g<-plotFeatPerform(ampliPanel, attributeThres, complete=TRUE, log=FALSE,
+ featureLabs=TRUE, sepChr=TRUE, legend=TRUE)
> if(interactive()){
+ g
+ }
> # explore possible attribute bias
> g<-biasExploration(ampliPanel, source="gc", dens=TRUE)
Error in `colnames<-`(`*tmp*`, value = `*vtmp*`) :
attempt to set 'colnames' on an object with less than two dimensions
Calls: biasExploration -> biasExploration -> colnames<-
Execution halted
* 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 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/TarSeqQC.Rcheck/00check.log’
for details.
Installation output
TarSeqQC.Rcheck/00install.out
Tests output
TarSeqQC.Rcheck/tests/runTests.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 -- Thu Jan 16 09:30:51 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
30.005 8.393 29.507
Example timings
TarSeqQC.Rcheck/TarSeqQC-Ex.timings