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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings IsoformSwitchAnalyzeR_2.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ version ‘2.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'limma', 'DEXSeq', 'satuRn', 'sva', 'ggplot2', 'pfamAnalyzeR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘IsoformSwitchAnalyzeR’ can be installed ... OK
* used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    data      1.1Mb
    extdata   4.4Mb
* 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 code 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
analyzeNovelIsoformORF: no visible binding for global variable
  'orf_origin'
analyzeNovelIsoformORF: no visible binding for global variable
  'orfStartGenomic'
analyzeNovelIsoformORF: no visible binding for global variable
  'isoform_id'
analyzeNovelIsoformORF: no visible binding for global variable
  'orfEndGenomic'
expressionAnalysisPlot: no visible binding for global variable
  'Condition'
expressionAnalysisPlot: no visible binding for global variable
  'gene_expression'
expressionAnalysisPlot: no visible binding for global variable 'CI_up'
expressionAnalysisPlot: no visible binding for global variable
  'CI_down'
expressionAnalysisPlot: no visible binding for global variable
  'sigLevelPos'
expressionAnalysisPlot: no visible binding for global variable
  'sigLevel'
expressionAnalysisPlot: no visible binding for global variable 'CI_hi'
expressionAnalysisPlot: no visible binding for global variable 'CI_low'
expressionAnalysisPlot: no visible binding for global variable 'ymax'
expressionAnalysisPlot: no visible binding for global variable
  'sigEval'
expressionAnalysisPlot: no visible binding for global variable 'idNr'
expressionAnalysisPlot: no visible binding for global variable 'IF'
extractConsequenceEnrichment: no visible binding for global variable
  'feature2'
extractConsequenceEnrichment: no visible binding for global variable
  'propOfRelevantEvents'
extractConsequenceEnrichment: no visible binding for global variable
  'Significant'
extractConsequenceEnrichment: no visible binding for global variable
  'propCiLo'
extractConsequenceEnrichment: no visible binding for global variable
  'propCiHi'
extractConsequenceEnrichment: no visible binding for global variable
  'nTot'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'Comparison'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'propOfRelevantEvents'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'Significant'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'nTot'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'propCiHi'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'propCiLo'
extractConsequenceGenomeWide: no visible binding for global variable
  'isoform_feature'
extractConsequenceGenomeWide: no visible binding for global variable
  'value'
extractConsequenceGenomeWide: no visible binding for global variable
  'variable'
extractConsequenceGenomeWide: no visible binding for global variable
  'ymax'
extractConsequenceGenomeWide: no visible binding for global variable
  'significance'
extractConsequenceGenomeWide: no visible binding for global variable
  'idNr'
extractConsequenceSummary: no visible binding for global variable
  'switchConsequence'
extractConsequenceSummary: no visible binding for global variable
  'geneFraction'
extractConsequenceSummary: no visible binding for global variable
  'nrGenesWithConsequences'
extractConsequenceSummary: no visible binding for global variable
  'isoFraction'
extractConsequenceSummary: no visible binding for global variable
  'nrIsoWithConsequences'
extractSplicingEnrichment: no visible binding for global variable
  'AStype'
extractSplicingEnrichment: no visible binding for global variable
  'propUp'
extractSplicingEnrichment: no visible binding for global variable
  'Significant'
extractSplicingEnrichment: no visible binding for global variable
  'nTot'
extractSplicingEnrichment: no visible binding for global variable
  'propUpCiHi'
extractSplicingEnrichment: no visible binding for global variable
  'propUpCiLo'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'Comparison'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'propUp'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'Significant'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'nTot'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'propUpCiHi'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'propUpCiLo'
extractSplicingGenomeWide: no visible binding for global variable
  'isoform_feature'
extractSplicingGenomeWide: no visible binding for global variable
  'value'
extractSplicingGenomeWide: no visible binding for global variable
  'variable'
extractSplicingGenomeWide: no visible binding for global variable
  'ymax'
extractSplicingGenomeWide: no visible binding for global variable
  'significance'
extractSplicingGenomeWide: no visible binding for global variable
  'idNr'
extractSplicingSummary: no visible binding for global variable
  'splicingResult'
extractSplicingSummary: no visible binding for global variable
  'geneFraction'
extractSplicingSummary: no visible binding for global variable
  'nrGenesWithConsequences'
extractSplicingSummary: no visible binding for global variable
  'isoFraction'
extractSplicingSummary: no visible binding for global variable
  'nrIsoWithConsequences'
extractSubCellShifts: no visible binding for global variable 'gene_ref'
extractSubCellShifts: no visible binding for global variable 'gene_id'
extractSubCellShifts: no visible binding for global variable
  'condition_1'
extractSubCellShifts: no visible binding for global variable
  'condition_2'
extractSubCellShifts: no visible binding for global variable
  'isoformUpregulated'
extractSubCellShifts: no visible binding for global variable
  'isoformDownregulated'
extractSubCellShifts: no visible binding for global variable
  'featureCompared'
extractSubCellShifts: no visible binding for global variable
  'isoformsDifferent'
extractSubCellShifts: no visible binding for global variable
  'isoform_id'
extractSubCellShifts: no visible binding for global variable
  'Localizations'
extractSubCellShifts: no visible binding for global variable
  'location_gain'
extractSubCellShifts: no visible binding for global variable
  'location_loss'
extractSubCellShifts: no visible binding for global variable 'n_genes'
extractSubCellShifts: no visible binding for global variable 'n_switch'
extractSubCellShifts: no visible binding for global variable 'Genes'
extractSubCellShifts: no visible binding for global variable 'Switch'
importGTF: no visible binding for global variable 'gene_id'
importGTF: no visible binding for global variable 'gene_name'
importRdata: no visible binding for global variable 'isoform_id'
importRdata: no visible binding for global variable 'gene_id'
importRdata: no visible binding for global variable 'ref_gene_id'
importRdata: no visible binding for global variable 'n_ref_gene_ids'
importRdata: no visible binding for global variable 'n_iso_na'
importRdata: no visible binding for global variable 'novel_iso'
importRdata: no visible binding for global variable 'known_ref_gene_id'
importRdata: no visible binding for global variable 'nt_overlap'
importRdata: no visible binding for global variable 'frac_overlap'
importRdata: no visible binding for global variable
  'log2_overlap_ratio'
importRdata: no visible binding for global variable 'has_ref_gene_id'
importRdata: no visible binding for global variable 'has_novel_iso'
importRdata: no visible binding for global variable 'gene_name'
importRdata: no visible binding for global variable 'n_ref'
isoformToGeneExp: no visible binding for global variable 'gene_id'
isoformToGeneExp: no visible binding for global variable 'gene_name'
preFilter: no visible global function definition for 'setdff'
switchPlotTranscript: no visible binding for global variable 'topology'
switchPlotTranscript: no visible binding for global variable 'idNr'
switchPlotTranscript: no visible binding for global variable 'Topology'
switchPlotTranscript: no visible binding for global variable 'topGroup'
switchPlotTranscript: no visible binding for global variable 'y'
switchPlotTranscript: no visible binding for global variable 'yend'
switchPlotTranscript: no visible binding for global variable 'x'
switchPlotTranscript: no visible binding for global variable 'ymin'
switchPlotTranscript: no visible binding for global variable 'xmin'
switchPlotTranscript: no visible binding for global variable 'ymax'
switchPlotTranscript: no visible binding for global variable 'xmax'
switchPlotTranscript: no visible binding for global variable 'Domain'
switchPlotTranscript: no visible binding for global variable 'value'
Undefined global functions or variables:
  AStype CI_down CI_hi CI_low CI_up Comparison Condition Domain Genes
  IF Localizations Significant Switch Topology condition_1 condition_2
  feature2 featureCompared frac_overlap geneFraction gene_expression
  gene_id gene_name gene_ref has_novel_iso has_ref_gene_id idNr
  isoFraction isoformDownregulated isoformUpregulated isoform_feature
  isoform_id isoformsDifferent known_ref_gene_id location_gain
  location_loss log2_overlap_ratio nTot n_genes n_iso_na n_ref
  n_ref_gene_ids n_switch novel_iso nrGenesWithConsequences
  nrIsoWithConsequences nt_overlap orfEndGenomic orfStartGenomic
  orf_origin propCiHi propCiLo propOfRelevantEvents propUp propUpCiHi
  propUpCiLo ref_gene_id setdff sigEval sigLevel sigLevelPos
  significance splicingResult switchConsequence topGroup topology value
  variable x xmax xmin y yend ymax ymin
* checking Rd files ... NOTE
checkRd: (-1) isoformToGeneExp.Rd:22: Lost braces; missing escapes or markup?
    22 |     \item{Using the {isoformGeneAnnotation} argument}.
       |                     ^
checkRd: (-1) isoformToIsoformFraction.Rd:23: Lost braces; missing escapes or markup?
    23 |     \item{Using the {isoformGeneAnnotation} argument}.
       |                     ^
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
IsoformSwitchTestDEXSeq       94.218  0.821  95.448
isoformSwitchAnalysisCombined 65.026  1.816  67.027
importSalmonData              39.241  2.383  88.802
prepareSalmonFilesDataFrame   20.605  1.461  33.265
extractSequence               13.496  0.063  13.589
analyzeORF                    12.252  0.016  12.290
extractSwitchSummary          11.555  0.028  11.606
extractTopSwitches            11.189  0.012  11.224
isoformSwitchAnalysisPart1    10.501  0.151  10.676
analyzeAlternativSplicing     10.225  0.004  10.292
extractGenomeWideAnalysis      5.903  0.084   6.000
isoformSwitchAnalysisPart2     4.962  0.104   5.067
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.