Last updated on 2023-08-18 14:51:19 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.83 | 11.09 | 69.45 | 80.54 | NOTE | --no-examples --no-tests --no-vignettes |
| r-devel-linux-x86_64-debian-gcc | 0.83 | 7.79 | 51.93 | 59.72 | NOTE | --no-examples --no-tests --no-vignettes |
| r-devel-windows-x86_64 | 0.83 | 11.00 | 58.00 | 69.00 | NOTE | --install=fake |
| r-patched-linux-x86_64 | 0.83 | 6.87 | 67.32 | 74.19 | OK | --no-examples --no-tests --no-vignettes |
| r-release-linux-x86_64 | 0.83 | 6.15 | 67.00 | 73.15 | OK | --no-examples --no-tests --no-vignettes |
| r-release-macos-arm64 | 0.83 | 83.00 | ERROR | |||
| r-release-macos-x86_64 | 0.83 | 138.00 | ERROR | |||
| r-release-windows-x86_64 | 0.83 | 13.00 | 62.00 | 75.00 | OK | --install=fake |
| r-oldrel-macos-arm64 | 0.83 | 70.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 0.83 | 118.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.83 | 13.00 | 62.00 | 75.00 | OK | --install=fake |
Version: 0.83
Flags: --no-examples --no-tests --no-vignettes
Check: Rd metadata
Result: NOTE
Invalid package aliases in Rd file ‘caRpools.Rd’:
‘CRISPR-AnalyzeR-package’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.83
Flags: --no-examples --no-tests --no-vignettes
Check: Rd contents
Result: NOTE
Auto-generated content requiring editing in Rd object ‘caRpools’:
\references: ‘~~ Literature or other references for background information ~~’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.83
Flags: --install=fake
Check: Rd metadata
Result: NOTE
Invalid package aliases in Rd file 'caRpools.Rd':
'CRISPR-AnalyzeR-package'
Flavor: r-devel-windows-x86_64
Version: 0.83
Flags: --install=fake
Check: Rd contents
Result: NOTE
Auto-generated content requiring editing in Rd object 'caRpools':
\references: '~~ Literature or other references for background information ~~'
Flavor: r-devel-windows-x86_64
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-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
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
Flavor: r-release-macos-arm64
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")
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘tibble’
Calls: stat.DESeq ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-release-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
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
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
Flavor: r-release-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
Quitting from lines 940-945 [geneinfo-replace] (CaRpools.Rmd)
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
Service Unavailable (HTTP 503).
--- failed re-building ‘CaRpools.Rmd’
SUMMARY: processing the following file failed:
‘CaRpools.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.83
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘CaRpools.Rmd’ using rmarkdown
sh: mageck: command not found
Quitting from lines 1956-1959 [HT-method-MAGeCK] (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
Flavor: r-oldrel-macos-x86_64