CRAN Package Check Results for Package polyRAD

Last updated on 2019-11-13 13:47:10 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 36.27 109.45 145.72 OK
r-devel-linux-x86_64-debian-gcc 1.1 25.15 82.16 107.31 OK
r-devel-linux-x86_64-fedora-clang 1.1 194.53 OK
r-devel-linux-x86_64-fedora-gcc 1.1 181.85 OK
r-devel-windows-ix86+x86_64 1.1 91.00 155.00 246.00 OK
r-patched-linux-x86_64 1.1 30.71 103.42 134.13 OK
r-patched-solaris-x86 1.1 235.50 OK
r-release-linux-x86_64 1.1 27.15 104.97 132.12 OK
r-release-windows-ix86+x86_64 1.1 87.00 150.00 237.00 OK
r-release-osx-x86_64 1.1 WARN
r-oldrel-windows-ix86+x86_64 1.1 58.00 200.00 258.00 OK
r-oldrel-osx-x86_64 1.1 WARN

Check Details

Version: 1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘polyRADtutorial.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.
    
    For example usage please run: vignette('qqman')
    
    Citation appreciated but not required:
    Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165 (2014).
    
    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,
     which.max, which.min
    
    Loading required package: GenomeInfoDb
    Loading required package: S4Vectors
    Warning: package 'S4Vectors' was built under R version 3.6.1
    Loading required package: stats4
    
    Attaching package: 'S4Vectors'
    
    The following object is masked from 'package:base':
    
     expand.grid
    
    Loading required package: IRanges
    Warning: package 'IRanges' was built under R version 3.6.1
    Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
     there is no package called 'GenomeInfoDbData'
    Quitting from lines 410-413 (polyRADtutorial.Rmd)
    Error: processing vignette 'polyRADtutorial.Rmd' failed with diagnostics:
    package 'GenomeInfoDb' could not be loaded
    --- failed re-building ‘polyRADtutorial.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘polyRADtutorial.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 1.1
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘Rsamtools’ ‘VariantAnnotation’ ‘GenomicFeatures’
Flavor: r-oldrel-osx-x86_64

Version: 1.1
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: ‘Rsamtools’, ‘BSgenome’, ‘GenomicFeatures’, ‘VariantAnnotation’
Flavor: r-oldrel-osx-x86_64

Version: 1.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    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.
    
    For example usage please run: vignette('qqman')
    
    Citation appreciated but not required:
    Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165 (2014).
    
    Quitting from lines 410-413 (polyRADtutorial.Rmd)
    Error: processing vignette 'polyRADtutorial.Rmd' failed with diagnostics:
    there is no package called 'VariantAnnotation'
    Execution halted
Flavor: r-oldrel-osx-x86_64