Last updated on 2022-09-11 12:56:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.83 | 8.24 | 65.87 | 74.11 | OK | --no-examples --no-tests --no-vignettes |
| r-devel-linux-x86_64-debian-gcc | 0.83 | 5.74 | 49.74 | 55.48 | OK | --no-examples --no-tests --no-vignettes |
| r-devel-windows-x86_64 | 0.83 | 46.00 | 64.00 | 110.00 | OK | --install=fake |
| r-patched-linux-x86_64 | 0.83 | 6.46 | 65.22 | 71.68 | OK | --no-examples --no-tests --no-vignettes |
| r-release-linux-x86_64 | 0.83 | 6.13 | 65.41 | 71.54 | OK | --no-examples --no-tests --no-vignettes |
| r-release-macos-arm64 | 0.83 | 128.00 | ERROR | |||
| r-release-macos-x86_64 | 0.83 | 142.00 | ERROR | |||
| r-release-windows-x86_64 | 0.83 | 58.00 | 64.00 | 122.00 | OK | --install=fake |
| r-oldrel-macos-arm64 | 0.83 | 135.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 0.83 | 123.00 | ERROR | |||
| r-oldrel-windows-ix86+x86_64 | 0.83 | 17.00 | 71.00 | 88.00 | OK | --install=fake |
Version: 0.83
Check: examples
Result: ERROR
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:
> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ### Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
>
> ### ** Examples
>
> data(caRpools)
>
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+ treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+ normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+ control.picks=NULL)
>
>
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+ treated.list = list(TREAT1,TREAT2), namecolumn=1,
+ fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+ sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+ fitType="parametric")
converting counts to integer mode
Warning in DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
>
> data.mageck = stat.mageck(untreated.list = list(CONTROL1, CONTROL2),
+ treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+ norm.fun="median", extractpattern=expression("^(.+?)(_.+)"),
+ mageckfolder=NULL, sort.criteria="neg", adjust.method="fdr", filename = "TEST" , fdr.pval = 0.05)
sh: mageck: command not found
Warning in system(mageckstring) : error in running command
Warning in file(file, "rt") :
cannot open file 'TEST.gene_summary.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: stat.mageck -> load.file -> read.table -> file
Execution halted
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.83
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘CaRpools.Rmd’ using rmarkdown
converting counts to integer mode
Warning in DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
sh: mageck: command not found
Quitting from lines 1956-1959 (CaRpools.Rmd)
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘CaRpools.Rmd’
SUMMARY: processing the following file failed:
‘CaRpools.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-release-macos-arm64, r-release-macos-x86_64
Version: 0.83
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘CaRpools.Rmd’ using rmarkdown
converting counts to integer mode
Warning in DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
sh: mageck: command not found
Quitting from lines 1956-1959 (CaRpools.Rmd)
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘CaRpools.Rmd’
SUMMARY: processing the following file failed:
‘CaRpools.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64