Last updated on 2020-03-31 18:47:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.2 | 13.05 | 180.53 | 193.58 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.2 | 10.67 | 132.89 | 143.56 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.2 | 162.32 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.2 | 217.91 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 0.1.2 | 36.00 | 105.00 | 141.00 | ERROR | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.1.2 | 31.00 | 114.00 | 145.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.2 | 12.77 | 168.79 | 181.56 | OK | |
| r-patched-solaris-x86 | 0.1.2 | 232.90 | ERROR | |||
| r-release-linux-x86_64 | 0.1.2 | 11.35 | 165.02 | 176.37 | OK | |
| r-release-windows-ix86+x86_64 | 0.1.2 | 47.00 | 169.00 | 216.00 | ERROR | |
| r-release-osx-x86_64 | 0.1.2 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.1.2 | 31.00 | 153.00 | 184.00 | ERROR | |
| r-oldrel-osx-x86_64 | 0.1.2 | NOTE |
Version: 0.1.2
Check: installed package size
Result: NOTE
installed size is 7.0Mb
sub-directories of 1Mb or more:
doc 1.1Mb
extdata 4.9Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 0.1.2
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘MCMCpack’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.1.2
Check: examples
Result: ERROR
Running examples in ‘starmie-Ex.R’ failed
The error most likely occurred in:
> ### Name: bestK
> ### Title: Determine a suitable K value from multiple Structure runs
> ### Aliases: bestK
>
> ### ** Examples
>
> multi_K <- exampleStructure("multiple_runs")
> # Run the evanno method and display diagnostic plots.
> evanno_results <- bestK(multi_K, method = "evanno")
Creating diagnostic plots for structure runs.
> # Run the default structure method and display diagnostic plots
> structure_results <- bestK(multi_K, "structure")
Creating diagnostic plots for structure runs.
> # find 'best' K according to results
> deltaK <- evanno_results$variable == 'delta K'
> max_deltaK <- which(evanno_results$value == max(evanno_results$value[deltaK], na.rm = TRUE))
> evanno_results[max_deltaK, ]
K variable value sd
16 4 delta K 104.815 NA
> lK <- structure_results$variable == 'L(K)'
> max_Lk <- which(structure_results$value == max(structure_results$value[lK], na.rm = TRUE))
> structure_results[max_Lk,]
K variable value sd
5.1 5 L(K) -1410.7 2.687006
> # admixture example
> multi_K_admix <- exampleAdmixture()
> bestK(multi_K_admix)
Creating diagnositc plots for admixture runs
Error in value[[3L]](cond) :
The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(combineLogs(x)) or as.data.table(combineLogs(x)). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
Calls: bestK ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 0.1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘using-starmie-admixture.Rmd’ using rmarkdown
Warning in block_exec(params) :
Failed to tidy R code in chunk 'admix-read'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'admix-log'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'plotbar'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Quitting from lines 71-72 (using-starmie-admixture.Rmd)
Error: processing vignette 'using-starmie-admixture.Rmd' failed with diagnostics:
The melt generic in data.table has been passed a matrix, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(Q) or as.data.table(Q). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
--- failed re-building ‘using-starmie-admixture.Rmd’
--- re-building ‘using-starmie.Rmd’ using rmarkdown
Warning in block_exec(params) :
Failed to tidy R code in chunk 'parallel-structure'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'struct-example'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'qhat'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'plot-bar'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Quitting from lines 112-113 (using-starmie.Rmd)
Error: processing vignette 'using-starmie.Rmd' failed with diagnostics:
The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(Q_merge) or as.data.table(Q_merge). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
--- failed re-building ‘using-starmie.Rmd’
SUMMARY: processing the following files failed:
‘using-starmie-admixture.Rmd’ ‘using-starmie.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-release-windows-ix86+x86_64
Version: 0.1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘using-starmie-admixture.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in block_exec(params) :
Failed to tidy R code in chunk 'admix-read'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'admix-log'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'plotbar'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Quitting from lines 71-72 (using-starmie-admixture.Rmd)
Error: processing vignette 'using-starmie-admixture.Rmd' failed with diagnostics:
The melt generic in data.table has been passed a matrix, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(Q) or as.data.table(Q). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
--- failed re-building ‘using-starmie-admixture.Rmd’
--- re-building ‘using-starmie.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in block_exec(params) :
Failed to tidy R code in chunk 'parallel-structure'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'struct-example'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'qhat'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'plot-bar'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Quitting from lines 112-113 (using-starmie.Rmd)
Error: processing vignette 'using-starmie.Rmd' failed with diagnostics:
The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(Q_merge) or as.data.table(Q_merge). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
--- failed re-building ‘using-starmie.Rmd’
SUMMARY: processing the following files failed:
‘using-starmie-admixture.Rmd’ ‘using-starmie.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.1.2
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Warning in block_exec(params) :
Failed to tidy R code in chunk 'admix-read'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'admix-log'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'plotbar'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Quitting from lines 71-72 (using-starmie-admixture.Rmd)
Error: processing vignette 'using-starmie-admixture.Rmd' failed with diagnostics:
The melt generic in data.table has been passed a matrix, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(Q) or as.data.table(Q). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64