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 |
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