CRAN Package Check Results for Package cRegulome

Last updated on 2022-09-30 00:49:12 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.2 8.64 227.77 236.41 NOTE
r-devel-linux-x86_64-debian-gcc 0.3.2 6.65 142.86 149.51 NOTE
r-devel-linux-x86_64-fedora-clang 0.3.2 294.28 NOTE
r-devel-linux-x86_64-fedora-gcc 0.3.2 283.88 NOTE
r-devel-windows-x86_64 0.3.2 33.00 220.00 253.00 ERROR
r-patched-linux-x86_64 0.3.2 14.00 194.58 208.58 NOTE
r-release-linux-x86_64 0.3.2 6.85 195.71 202.56 NOTE
r-release-macos-arm64 0.3.2 77.00 NOTE
r-release-macos-x86_64 0.3.2 157.00 NOTE
r-release-windows-x86_64 0.3.2 33.00 218.00 251.00 ERROR
r-oldrel-macos-arm64 0.3.2 133.00 NOTE
r-oldrel-macos-x86_64 0.3.2 140.00 NOTE
r-oldrel-windows-ix86+x86_64 0.3.2 21.00 146.00 167.00 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-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.3.2
Check: re-building of vignette outputs
Result: ERROR
    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 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
    R.oo v1.25.0 (2022-06-12 02:20:02 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 v2.12.0 (2022-06-28 03:20:05 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, 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
    
    Attaching package: 'BiocGenerics'
    
    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 v4.3.4 For help: https://yulab-smu.top/biomedical-knowledge-mining-book/
    
    If you use clusterProfiler in published research, please cite:
    T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141
    
    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'
    Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' 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
    
    Picking joint bandwidth of 0.0412
    Picking joint bandwidth of 0.0496
    '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
    Warning in utils::download.file(url, quiet = TRUE, method = method, ...) :
     URL 'https://rest.kegg.jp/link/hsa/pathway': status was 'Failure when receiving data from the peer'
    Quitting from lines 240-254 (case_study.Rmd)
    Error: processing vignette 'case_study.Rmd' failed with diagnostics:
    Failed to download KEGG data. Wrong 'species' or the network is unreachable. The 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'
    --- 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
Flavors: r-devel-windows-x86_64, r-release-windows-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 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
    R.oo v1.25.0 (2022-06-12 02:20:02 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 v2.12.0 (2022-06-28 03:20:05 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, 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
    
    Attaching package: 'BiocGenerics'
    
    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 v4.2.2 For help: https://yulab-smu.top/biomedical-knowledge-mining-book/
    
    If you use clusterProfiler in published research, please cite:
    T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141
    
    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-oldrel-windows-ix86+x86_64