############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TarSeqQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TarSeqQC_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TarSeqQC.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TarSeqQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TarSeqQC’ version ‘1.30.0’ * 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 ... WARNING Found the following significant warnings: Warning: Package 'TarSeqQC' is deprecated and will be removed from Bioconductor See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TarSeqQC.Rcheck/00install.out’ for details. * 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 startup messages can be suppressed ... 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 coverage sdCoverage | 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 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 | 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 `` 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TarSeqQC.Rcheck/00check.log’ for details.