CRAN Package Check Results for Package RNAseqQC

Last updated on 2023-02-03 04:50:40 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.4 41.65 542.74 584.39 OK
r-devel-linux-x86_64-debian-gcc 0.1.4 34.39 400.49 434.88 OK
r-devel-linux-x86_64-fedora-clang 0.1.4 661.83 NOTE
r-devel-linux-x86_64-fedora-gcc 0.1.4 697.47 OK
r-devel-windows-x86_64 0.1.4 55.00 613.00 668.00 NOTE
r-patched-linux-x86_64 0.1.4 39.44 536.93 576.37 OK
r-release-linux-x86_64 0.1.4 31.67 537.24 568.91 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 57.00 697.00 754.00 NOTE
r-oldrel-macos-arm64 0.1.4 119.00 ERROR
r-oldrel-macos-x86_64 0.1.4 190.00 ERROR
r-oldrel-windows-ix86+x86_64 0.1.4 92.00 414.00 506.00 ERROR

Check Details

Version: 0.1.4
Check: package dependencies
Result: NOTE
    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-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 in `map()`:
    ℹ In index: 1.
    Caused by error:
    ! 'colnames' is not an exported object from 'namespace:SummarizedExperiment'
    Backtrace:
     ▆
     1. ├─RNAseqQC::plot_library_complexity(dds)
     2. │ ├─... %>% ...
     3. │ └─purrr::map_dfr(...)
     4. │ └─purrr::map(.x, .f, ...)
     5. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
     6. │ ├─purrr:::with_indexed_errors(...)
     7. │ │ └─base::withCallingHandlers(...)
     8. │ ├─purrr:::call_with_cleanup(...)
     9. │ └─RNAseqQC (local) .f(.x[[i]], ...)
     10. │ └─tibble::tibble(...)
     11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
     12. │ └─rlang::eval_tidy(xs[[j]], mask)
     13. ├─ggplot2::ggplot(...)
     14. └─base::.handleSimpleError(...)
     15. └─purrr (local) h(simpleError(msg, call))
     16. └─cli::cli_abort(...)
     17. └─rlang::abort(...)
    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
    Quitting from lines 88-89 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    ℹ In index: 1.
    Caused by error:
    ! '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 in `map()`:
    i In index: 1.
    Caused by error:
    ! 'colnames' is not an exported object from 'namespace:SummarizedExperiment'
    Backtrace:
     x
     1. +-RNAseqQC::plot_library_complexity(dds)
     2. | +-... %>% ...
     3. | \-purrr::map_dfr(...)
     4. | \-purrr::map(.x, .f, ...)
     5. | \-purrr:::map_("list", .x, .f, ..., .progress = .progress)
     6. | +-purrr:::with_indexed_errors(...)
     7. | | \-base::withCallingHandlers(...)
     8. | +-purrr:::call_with_cleanup(...)
     9. | \-RNAseqQC (local) .f(.x[[i]], ...)
     10. | \-tibble::tibble(...)
     11. | \-tibble:::tibble_quos(xs, .rows, .name_repair)
     12. | \-rlang::eval_tidy(xs[[j]], mask)
     13. +-ggplot2::ggplot(...)
     14. \-base::.handleSimpleError(...)
     15. \-purrr (local) h(simpleError(msg, call))
     16. \-cli::cli_abort(...)
     17. \-rlang::abort(...)
    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
    Quitting from lines 88-89 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    i In index: 1.
    Caused by error:
    ! '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