CRAN Package Check Results for Package cRegulome

Last updated on 2018-06-19 06:48:04 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.1 3.23 66.01 69.24 OK
r-devel-linux-x86_64-debian-gcc 0.1.1 2.37 58.50 60.87 OK
r-devel-linux-x86_64-fedora-clang 0.1.1 89.80 NOTE
r-devel-linux-x86_64-fedora-gcc 0.1.1 87.44 NOTE
r-devel-windows-ix86+x86_64 0.1.1 11.00 134.00 145.00 WARN
r-patched-linux-x86_64 0.1.1 2.99 66.18 69.17 OK
r-patched-solaris-x86 0.1.1 115.50 NOTE
r-release-linux-x86_64 0.1.1 2.78 66.05 68.83 OK
r-release-windows-ix86+x86_64 0.1.1 6.00 89.00 95.00 WARN
r-release-osx-x86_64 0.1.1 ERROR
r-oldrel-windows-ix86+x86_64 0.1.1 7.00 118.00 125.00 OK
r-oldrel-osx-x86_64 0.1.1 ERROR

Check Details

Version: 0.1.1
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘AnnotationDbi’ ‘clusterProfiler’ ‘org.Hs.eg.db’
     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

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: R.oo
    Loading required package: R.methodsS3
    R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
    R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.
    
    Attaching package: 'R.oo'
    
    The following objects are masked from 'package:methods':
    
     getClasses, getMethods
    
    The following objects are masked from 'package:base':
    
     attach, detach, gc, load, save
    
    R.utils v2.6.0 (2017-11-04) 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, colMeans, colSums, colnames,
     dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
     intersect, is.unsorted, lapply, lengths, mapply, match, mget,
     order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
     rowMeans, rowSums, 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
    
    
    
    clusterProfiler v3.7.1 For help: https://guangchuangyu.github.io/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'
    Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheetapplication/zip' length 11004 bytes (10 KB)
    ==================================================
    downloaded 10 KB
    
    trying URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s003.xls'
    Content type 'application/vnd.ms-office' length 58880 bytes (57 KB)
    ==================================================
    downloaded 57 KB
    
    Joining, by = c("tf", "feature")
    Joining, by = c("mirna_base", "feature")
    Picking joint bandwidth of 0.0412
    Picking joint bandwidth of 0.0496
    Joining, by = c("tf", "feature")
    Joining, by = c("mirna_base", "feature")
    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns
    Quitting from lines 240-254 (case_study.Rmd)
    Error: processing vignette 'case_study.Rmd' failed with diagnostics:
    No enrichment found in any of gene cluster, please check your input...
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: R.oo
    Loading required package: R.methodsS3
    R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
    R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.
    
    Attaching package: 'R.oo'
    
    The following objects are masked from 'package:methods':
    
     getClasses, getMethods
    
    The following objects are masked from 'package:base':
    
     attach, detach, gc, load, save
    
    R.utils v2.6.0 (2017-11-04) 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, 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, colMeans, colSums, colnames,
     dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
     intersect, is.unsorted, lapply, lengths, mapply, match, mget,
     order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
     rowMeans, rowSums, 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
    
    
    
    clusterProfiler v3.7.1 For help: https://guangchuangyu.github.io/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'
    Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheetapplication/zip' length 11004 bytes (10 KB)
    ==================================================
    downloaded 10 KB
    
    trying URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s003.xls'
    Content type 'application/vnd.ms-office' length 58880 bytes (57 KB)
    ==================================================
    downloaded 57 KB
    
    Joining, by = c("tf", "feature")
    Joining, by = c("mirna_base", "feature")
    Picking joint bandwidth of 0.0412
    Picking joint bandwidth of 0.0496
    Joining, by = c("tf", "feature")
    Joining, by = c("mirna_base", "feature")
    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns
    'select()' returned 1:1 mapping between keys and columns
    Quitting from lines 240-254 (case_study.Rmd)
    Error: processing vignette 'case_study.Rmd' failed with diagnostics:
    No enrichment found in any of gene cluster, please check your input...
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 0.1.1
Check: package dependencies
Result: ERROR
    Package required but not available: ‘clusterProfiler’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64

Version: 0.1.1
Check: package dependencies
Result: ERROR
    Package required but not available: ‘org.Hs.eg.db’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-oldrel-osx-x86_64