CRAN Package Check Results for Package cRegulome

Last updated on 2020-07-12 14:47:33 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.2 7.13 197.33 204.46 OK
r-devel-linux-x86_64-debian-gcc 0.3.2 5.92 127.81 133.73 OK
r-devel-linux-x86_64-fedora-clang 0.3.2 224.52 OK
r-devel-linux-x86_64-fedora-gcc 0.3.2 216.77 OK
r-devel-windows-ix86+x86_64 0.3.2 22.00 241.00 263.00 OK
r-patched-linux-x86_64 0.3.2 7.34 273.71 281.05 OK
r-patched-solaris-x86 0.3.2 387.90 OK
r-release-linux-x86_64 0.3.2 6.86 272.16 279.02 OK
r-release-macos-x86_64 0.3.2 WARN
r-release-windows-ix86+x86_64 0.3.2 32.00 364.00 396.00 OK
r-oldrel-macos-x86_64 0.3.2 WARN
r-oldrel-windows-ix86+x86_64 0.3.2 21.00 291.00 312.00 OK

Check Details

Version: 0.3.2
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'org.Hs.eg.db', 'clusterProfiler'
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 0.3.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘case_study.Rmd’ using rmarkdown
    Loading required package: R.oo
    Loading required package: R.methodsS3
    R.methodsS3 v1.8.0 (2020-02-14 07:10:20 UTC) successfully loaded. See ?R.methodsS3 for help.
    R.oo v1.23.0 successfully loaded. See ?R.oo for help.
    
    Attaching package: 'R.oo'
    
    The following object is masked from 'package:R.methodsS3':
    
     throw
    
    The following objects are masked from 'package:methods':
    
     getClasses, getMethods
    
    The following objects are masked from 'package:base':
    
     attach, detach, load, save
    
    R.utils v2.9.2 successfully loaded. See ?R.utils for help.
    
    Attaching package: 'R.utils'
    
    The following object is masked from 'package:utils':
    
     timestamp
    
    The following objects are masked from 'package:base':
    
     cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
     warnings
    
    
    Attaching package: 'igraph'
    
    The following object is masked from 'package:R.oo':
    
     hierarchy
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: stats4
    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:igraph':
    
     normalize, path, union
    
    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: Biobase
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
    Loading required package: IRanges
    Loading required package: S4Vectors
    
    Attaching package: 'S4Vectors'
    
    The following object is masked from 'package:base':
    
     expand.grid
    
    
    Attaching package: 'IRanges'
    
    The following object is masked from 'package:R.oo':
    
     trim
    
    Quitting from lines 32-41 (case_study.Rmd)
    Error: processing vignette 'case_study.Rmd' failed with diagnostics:
    there is no package called 'org.Hs.eg.db'
    --- failed re-building ‘case_study.Rmd’
    
    --- re-building ‘using_cRegulome.Rmd’ using rmarkdown
    Picking joint bandwidth of 0.0445
    --- finished re-building ‘using_cRegulome.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘case_study.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-macos-x86_64

Version: 0.3.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘case_study.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.
    Loading required package: R.oo
    Loading required package: R.methodsS3
    R.methodsS3 v1.8.0 (2020-02-14 07:10:20 UTC) successfully loaded. See ?R.methodsS3 for help.
    R.oo v1.23.0 successfully loaded. See ?R.oo for help.
    
    Attaching package: 'R.oo'
    
    The following object is masked from 'package:R.methodsS3':
    
     throw
    
    The following objects are masked from 'package:methods':
    
     getClasses, getMethods
    
    The following objects are masked from 'package:base':
    
     attach, detach, load, save
    
    R.utils v2.9.2 successfully loaded. See ?R.utils for help.
    
    Attaching package: 'R.utils'
    
    The following object is masked from 'package:utils':
    
     timestamp
    
    The following objects are masked from 'package:base':
    
     cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
     warnings
    
    
    Attaching package: 'igraph'
    
    The following object is masked from 'package:R.oo':
    
     hierarchy
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: stats4
    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:igraph':
    
     normalize, path, union
    
    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: Biobase
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
    Loading required package: IRanges
    Loading required package: S4Vectors
    
    Attaching package: 'S4Vectors'
    
    The following object is masked from 'package:base':
    
     expand.grid
    
    
    Attaching package: 'IRanges'
    
    The following object is masked from 'package:R.oo':
    
     trim
    
    Quitting from lines 32-41 (case_study.Rmd)
    Error: processing vignette 'case_study.Rmd' failed with diagnostics:
    there is no package called 'org.Hs.eg.db'
    --- failed re-building ‘case_study.Rmd’
    
    --- re-building ‘using_cRegulome.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.
    Picking joint bandwidth of 0.0445
    --- finished re-building ‘using_cRegulome.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘case_study.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64