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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TarSeqQC.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TarSeqQC_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/TarSeqQC.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘TarSeqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TarSeqQC’ version ‘1.28.0’
* 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 ... 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 ... 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  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")
Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
of ggplot2 3.3.4.
ℹ The deprecated feature was likely used in the TarSeqQC package.
  Please report the issue to the authors.
> 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)
Error in aggregate.formula(formula = xmin ~ seqnames, data = df_panel,  : 
  argument 'x' is  missing -- it has been renamed from 'formula'
Calls: plot -> plot -> .local -> aggregate -> aggregate.formula
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 ...
  ‘TarSeqQC-vignette.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/TarSeqQC.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL TarSeqQC
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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:stats':

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, 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.max, which.min


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


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 11 00:33:39 2023 
*********************************************** 
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 
Warning message:
The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
of ggplot2 3.3.4.
ℹ The deprecated feature was likely used in the TarSeqQC package.
  Please report the issue to the authors. 
> 
> proc.time()
   user  system elapsed 
 19.231   4.845  17.671