CRAN Package Check Results for Package RNAseqQC

Last updated on 2022-08-11 21:50:15 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.4 41.01 539.80 580.81 OK
r-devel-linux-x86_64-debian-gcc 0.1.4 36.06 404.44 440.50 OK
r-devel-linux-x86_64-fedora-clang 0.1.4 743.51 NOTE
r-devel-linux-x86_64-fedora-gcc 0.1.4 770.03 NOTE
r-devel-windows-x86_64 0.1.4 49.00 598.00 647.00 NOTE
r-patched-linux-x86_64 0.1.4 34.18 527.94 562.12 OK
r-release-linux-x86_64 0.1.4 31.41 534.29 565.70 OK
r-release-macos-arm64 0.1.4 190.00 NOTE
r-release-macos-x86_64 0.1.4 260.00 NOTE
r-release-windows-x86_64 0.1.4 54.00 599.00 653.00 NOTE
r-oldrel-macos-arm64 0.1.4 149.00 ERROR
r-oldrel-macos-x86_64 0.1.4 189.00 ERROR
r-oldrel-windows-ix86+x86_64 0.1.4 90.00 423.00 513.00 ERROR

Check Details

Version: 0.1.4
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘recount3’
    
    Imports includes 24 non-default packages.
    Importing from so many packages makes the package vulnerable to any of
    them becoming unavailable. Move as many as possible to Suggests and
    use conditionally.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.4
Check: installed package size
Result: NOTE
     installed size is 5.9Mb
     sub-directories of 1Mb or more:
     data 3.5Mb
     doc 2.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.1.4
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘recount3’
Flavors: r-devel-linux-x86_64-fedora-gcc, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 0.1.4
Check: dependencies in R code
Result: WARN
    Missing or unexported object: 'SummarizedExperiment::colnames'
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.1.4
Check: examples
Result: ERROR
    Running examples in ‘RNAseqQC-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: plot_library_complexity
    > ### Title: Plot the library complexity
    > ### Aliases: plot_library_complexity
    >
    > ### ** Examples
    >
    > library("DESeq2")
    Loading required package: S4Vectors
    Loading required package: stats4
    Loading required package: BiocGenerics
    Loading required package: parallel
    
    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.max, which.min
    
    
    Attaching package: ‘S4Vectors’
    
    The following objects are masked from ‘package:base’:
    
     I, expand.grid, unname
    
    Loading required package: IRanges
    Loading required package: GenomicRanges
    Loading required package: GenomeInfoDb
    Loading required package: SummarizedExperiment
    Loading required package: MatrixGenerics
    Loading required package: matrixStats
    
    Attaching package: ‘MatrixGenerics’
    
    The following objects are masked from ‘package:matrixStats’:
    
     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
     colWeightedMeans, colWeightedMedians, colWeightedSds,
     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
     rowWeightedSds, rowWeightedVars
    
    Loading required package: Biobase
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
    
    Attaching package: ‘Biobase’
    
    The following object is masked from ‘package:MatrixGenerics’:
    
     rowMedians
    
    The following objects are masked from ‘package:matrixStats’:
    
     anyMissing, rowMedians
    
    > set.seed(1)
    > dds <- makeExampleDESeqDataSet()
    > plot_library_complexity(dds)
    Error: 'colnames' is not an exported object from 'namespace:SummarizedExperiment'
    Execution halted
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 0.1.4
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘data.Rmd’ using rmarkdown
    --- finished re-building ‘data.Rmd’
    
    --- re-building ‘introduction.Rmd’ using rmarkdown
    Loading required package: S4Vectors
    Loading required package: stats4
    Loading required package: BiocGenerics
    Loading required package: parallel
    
    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.max, which.min
    
    
    Attaching package: 'S4Vectors'
    
    The following objects are masked from 'package:base':
    
     I, expand.grid, unname
    
    Loading required package: IRanges
    Loading required package: GenomicRanges
    Loading required package: GenomeInfoDb
    Loading required package: SummarizedExperiment
    Loading required package: MatrixGenerics
    Loading required package: matrixStats
    
    Attaching package: 'MatrixGenerics'
    
    The following objects are masked from 'package:matrixStats':
    
     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
     colWeightedMeans, colWeightedMedians, colWeightedSds,
     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
     rowWeightedSds, rowWeightedVars
    
    Loading required package: Biobase
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
    
    Attaching package: 'Biobase'
    
    The following object is masked from 'package:MatrixGenerics':
    
     rowMedians
    
    The following objects are masked from 'package:matrixStats':
    
     anyMissing, rowMedians
    
    Loading required package: GenomicFeatures
    Loading required package: AnnotationDbi
    Loading required package: AnnotationFilter
    
    Attaching package: 'ensembldb'
    
    The following object is masked from 'package:stats':
    
     filter
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:ensembldb':
    
     filter, select
    
    The following object is masked from 'package:AnnotationDbi':
    
     select
    
    The following object is masked from 'package:Biobase':
    
     combine
    
    The following object is masked from 'package:matrixStats':
    
     count
    
    The following objects are masked from 'package:GenomicRanges':
    
     intersect, setdiff, union
    
    The following object is masked from 'package:GenomeInfoDb':
    
     intersect
    
    The following objects are masked from 'package:IRanges':
    
     collapse, desc, intersect, setdiff, slice, union
    
    The following objects are masked from 'package:S4Vectors':
    
     first, intersect, rename, setdiff, setequal, union
    
    The following objects are masked from 'package:BiocGenerics':
    
     combine, intersect, setdiff, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
    Attaching package: 'purrr'
    
    The following object is masked from 'package:GenomicRanges':
    
     reduce
    
    The following object is masked from 'package:IRanges':
    
     reduce
    
    
    Attaching package: 'tidyr'
    
    The following object is masked from 'package:S4Vectors':
    
     expand
    
    
    Attaching package: 'magrittr'
    
    The following object is masked from 'package:tidyr':
    
     extract
    
    The following object is masked from 'package:purrr':
    
     set_names
    
    The following object is masked from 'package:AnnotationFilter':
    
     not
    
    Quitting from lines 88-89 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    'colnames' is not an exported object from 'namespace:SummarizedExperiment'
    --- failed re-building ‘introduction.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘introduction.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 0.1.4
Check: examples
Result: ERROR
    Running examples in 'RNAseqQC-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: plot_library_complexity
    > ### Title: Plot the library complexity
    > ### Aliases: plot_library_complexity
    >
    > ### ** Examples
    >
    > library("DESeq2")
    Loading required package: S4Vectors
    Loading required package: stats4
    Loading required package: BiocGenerics
    
    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, 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
    
    Loading required package: IRanges
    
    Attaching package: 'IRanges'
    
    The following object is masked from 'package:grDevices':
    
     windows
    
    Loading required package: GenomicRanges
    Loading required package: GenomeInfoDb
    Loading required package: SummarizedExperiment
    Loading required package: MatrixGenerics
    Loading required package: matrixStats
    
    Attaching package: 'MatrixGenerics'
    
    The following objects are masked from 'package:matrixStats':
    
     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
     colWeightedMeans, colWeightedMedians, colWeightedSds,
     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
     rowWeightedSds, rowWeightedVars
    
    Loading required package: Biobase
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
    
    Attaching package: 'Biobase'
    
    The following object is masked from 'package:MatrixGenerics':
    
     rowMedians
    
    The following objects are masked from 'package:matrixStats':
    
     anyMissing, rowMedians
    
    > set.seed(1)
    > dds <- makeExampleDESeqDataSet()
    > plot_library_complexity(dds)
    Error: 'colnames' is not an exported object from 'namespace:SummarizedExperiment'
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.1.4
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'data.Rmd' using rmarkdown
    --- finished re-building 'data.Rmd'
    
    --- re-building 'introduction.Rmd' using rmarkdown
    Loading required package: S4Vectors
    Loading required package: stats4
    Loading required package: BiocGenerics
    
    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, 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
    
    Loading required package: IRanges
    
    Attaching package: 'IRanges'
    
    The following object is masked from 'package:grDevices':
    
     windows
    
    Loading required package: GenomicRanges
    Loading required package: GenomeInfoDb
    Loading required package: SummarizedExperiment
    Loading required package: MatrixGenerics
    Loading required package: matrixStats
    
    Attaching package: 'MatrixGenerics'
    
    The following objects are masked from 'package:matrixStats':
    
     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
     colWeightedMeans, colWeightedMedians, colWeightedSds,
     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
     rowWeightedSds, rowWeightedVars
    
    Loading required package: Biobase
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
    
    Attaching package: 'Biobase'
    
    The following object is masked from 'package:MatrixGenerics':
    
     rowMedians
    
    The following objects are masked from 'package:matrixStats':
    
     anyMissing, rowMedians
    
    Loading required package: GenomicFeatures
    Loading required package: AnnotationDbi
    Loading required package: AnnotationFilter
    
    Attaching package: 'ensembldb'
    
    The following object is masked from 'package:stats':
    
     filter
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:ensembldb':
    
     filter, select
    
    The following object is masked from 'package:AnnotationDbi':
    
     select
    
    The following object is masked from 'package:Biobase':
    
     combine
    
    The following object is masked from 'package:matrixStats':
    
     count
    
    The following objects are masked from 'package:GenomicRanges':
    
     intersect, setdiff, union
    
    The following object is masked from 'package:GenomeInfoDb':
    
     intersect
    
    The following objects are masked from 'package:IRanges':
    
     collapse, desc, intersect, setdiff, slice, union
    
    The following objects are masked from 'package:S4Vectors':
    
     first, intersect, rename, setdiff, setequal, union
    
    The following objects are masked from 'package:BiocGenerics':
    
     combine, intersect, setdiff, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
    Attaching package: 'purrr'
    
    The following object is masked from 'package:GenomicRanges':
    
     reduce
    
    The following object is masked from 'package:IRanges':
    
     reduce
    
    
    Attaching package: 'tidyr'
    
    The following object is masked from 'package:S4Vectors':
    
     expand
    
    
    Attaching package: 'magrittr'
    
    The following object is masked from 'package:tidyr':
    
     extract
    
    The following object is masked from 'package:purrr':
    
     set_names
    
    The following object is masked from 'package:AnnotationFilter':
    
     not
    
    Quitting from lines 88-89 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    'colnames' is not an exported object from 'namespace:SummarizedExperiment'
    --- failed re-building 'introduction.Rmd'
    
    SUMMARY: processing the following file failed:
     'introduction.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64