CRAN Package Check Results for Package cRegulome

Last updated on 2021-04-18 00:47:36 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.2 7.70 215.42 223.12 NOTE
r-devel-linux-x86_64-debian-gcc 0.3.2 6.10 138.96 145.06 NOTE
r-devel-linux-x86_64-fedora-clang 0.3.2 254.23 NOTE
r-devel-linux-x86_64-fedora-gcc 0.3.2 239.64 NOTE
r-devel-windows-ix86+x86_64 0.3.2 19.00 134.00 153.00 WARN
r-devel-windows-x86_64-gcc10-UCRT 0.3.2 NOTE
r-patched-linux-x86_64 0.3.2 7.72 275.17 282.89 OK
r-patched-solaris-x86 0.3.2 409.20 OK
r-release-linux-x86_64 0.3.2 7.06 277.62 284.68 OK
r-release-macos-x86_64 0.3.2 WARN
r-release-windows-ix86+x86_64 0.3.2 28.00 160.00 188.00 WARN
r-oldrel-macos-x86_64 0.3.2 WARN
r-oldrel-windows-ix86+x86_64 0.3.2 11.00 133.00 144.00 WARN

Check Details

Version: 0.3.2
Check: LazyData
Result: NOTE
     'LazyData' is specified without a 'data' directory
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-devel-windows-ix86+x86_64, r-devel-windows-x86_64-gcc10-UCRT

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 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
    R.oo v1.24.0 (2020-08-26 16:11:58 UTC) 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 v2.10.1 (2020-08-26 22:50:31 UTC) 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.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 objects are masked from 'package:base':
    
     I, expand.grid, unname
    
    
    Attaching package: 'IRanges'
    
    The following object is masked from 'package:R.oo':
    
     trim
    
    The following object is masked from 'package:grDevices':
    
     windows
    
    
    
    clusterProfiler v3.99.1 For help: https://guangchuangyu.github.io/software/clusterProfiler
    
    If you use clusterProfiler in published research, please cite:
    Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
    
    Attaching package: 'clusterProfiler'
    
    The following object is masked from 'package:AnnotationDbi':
    
     select
    
    The following object is masked from 'package:IRanges':
    
     slice
    
    The following object is masked from 'package:S4Vectors':
    
     rename
    
    The following object is masked from 'package:igraph':
    
     simplify
    
    The following object is masked from 'package:stats':
    
     filter
    
    trying URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx'
    Warning in download.file("https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx", :
     InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
    Quitting from lines 44-55 (case_study.Rmd)
    Error: processing vignette 'case_study.Rmd' failed with diagnostics:
    cannot open URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx'
    --- 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-devel-windows-ix86+x86_64

Version: 0.3.2
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘clusterProfiler’
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 'clusterProfiler'
    --- 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-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
    Loading required package: R.oo
    Loading required package: R.methodsS3
    R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
    R.oo v1.24.0 (2020-08-26 16:11:58 UTC) 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 v2.10.1 (2020-08-26 22:50:31 UTC) 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.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
    
    The following object is masked from 'package:grDevices':
    
     windows
    
    
    
    clusterProfiler v3.18.1 For help: https://guangchuangyu.github.io/software/clusterProfiler
    
    If you use clusterProfiler in published research, please cite:
    Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
    
    Attaching package: 'clusterProfiler'
    
    The following object is masked from 'package:AnnotationDbi':
    
     select
    
    The following object is masked from 'package:IRanges':
    
     slice
    
    The following object is masked from 'package:S4Vectors':
    
     rename
    
    The following object is masked from 'package:igraph':
    
     simplify
    
    The following object is masked from 'package:stats':
    
     filter
    
    trying URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx'
    Warning in download.file("https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx", :
     InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
    Quitting from lines 44-55 (case_study.Rmd)
    Error: processing vignette 'case_study.Rmd' failed with diagnostics:
    cannot open URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx'
    --- 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-windows-ix86+x86_64

Version: 0.3.2
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'org.Hs.eg.db', 'clusterProfiler'
Flavor: 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
    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

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 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
    R.oo v1.24.0 (2020-08-26 16:11:58 UTC) 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 v2.10.1 (2020-08-26 22:50:31 UTC) 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
    
    The following object is masked from 'package:grDevices':
    
     windows
    
    
    
    Bioconductor version '3.10' is out-of-date; the current release version '3.12'
     is available with R version '4.0'; see https://bioconductor.org/install
    clusterProfiler v3.14.3 For help: https://guangchuangyu.github.io/software/clusterProfiler
    
    If you use clusterProfiler in published research, please cite:
    Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
    
    Attaching package: 'clusterProfiler'
    
    The following object is masked from 'package:igraph':
    
     simplify
    
    trying URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx'
    Warning in download.file("https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx", :
     InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
    Quitting from lines 44-55 (case_study.Rmd)
    Error: processing vignette 'case_study.Rmd' failed with diagnostics:
    cannot open URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx'
    --- 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-oldrel-windows-ix86+x86_64