Last updated on 2020-08-07 01:50:26 CEST.
| Package | WARN | NOTE | OK |
|---|---|---|---|
| polyRAD | 1 | 6 | 5 |
| polysat | 7 | 5 |
Current CRAN status: WARN: 1, NOTE: 6, OK: 5
Version: 1.2
Check: installed package size
Result: NOTE
installed size is 8.3Mb
sub-directories of 1Mb or more:
extdata 3.7Mb
libs 3.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.2
Check: Rd cross-references
Result: NOTE
Undeclared package ‘BSgenome’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘isolocus_sorting.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘isolocus_sorting.Rmd’
--- re-building ‘polyRADtutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Allele frequencies for mapping population not found. Estimating.
Genotype likelihoods not found. Estimating.
Generating sampling permutations for allele depth.
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
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
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 437-440 (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-oldrel-macos-x86_64
Current CRAN status: NOTE: 7, OK: 5
Version: 1.7-4
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
'SPAGfreqExample2.txt' 'SpagInputExample.txt' 'SpagOutExample.txt'
'SpagTemp.txt' 'TetrasatExample.txt' 'atetraexample.txt'
'atetratest.txt' 'exampleGMoutput.txt' 'forPOPDIST.txt'
'genodiveExample.txt' 'readGMtest.txt' 'strtemp.txt' 'structtest.txt'
'testGenoDive2.txt' 'testGenoDive3.txt' 'testPOPDIST.txt'
'tetrasattest.txt'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64