CRAN Package Check Results for Maintainer ‘Elisa Salviato <elisa.salviato.88 at gmail.com>’

Last updated on 2022-04-24 03:52:53 CEST.

Package	ERROR	WARN	NOTE	OK
simPATHy	2		3	7
SourceSet	2	2	8

Package simPATHy

Current CRAN status: ERROR: 2, NOTE: 3, OK: 7

Additional issues

noSuggests

Version: 0.6
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘clipper’
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-arm64, r-oldrel-macos-arm64

Version: 0.6
Check: package dependencies
Result: ERROR
    Package required but not available: ‘qpgraph’
    
    Packages suggested but not available for checking: 'clipper', 'topologyGSA'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64

Package SourceSet

Current CRAN status: ERROR: 2, WARN: 2, NOTE: 8

Version: 0.1.3
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'r2cytoscape'
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-release-linux-x86_64, r-release-macos-arm64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-windows-ix86+x86_64

Version: 0.1.3
Check: re-building of vignette outputs
Result: ERROR
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘SourceSet.Rmd’ using rmarkdown
    Loading required package: graph
    Loading required package: BiocGenerics
    
    Attaching package: 'BiocGenerics'
    
    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
    
    Identifing all possible orderings..
    Total run time: 2.6 secs
    Identifing all possible orderings..
    Total run time: 1.75 secs
    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: AnnotationDbi
    Loading required package: stats4
    Loading required package: IRanges
    Loading required package: S4Vectors
    
    Attaching package: 'S4Vectors'
    
    The following objects are masked from 'package:base':
    
     I, expand.grid, unname
    
    Loading required package: org.Hs.eg.db
    
    
    Quitting from lines 453-470 (SourceSet.Rmd)
    Error: processing vignette ‘SourceSet.Rmd’ failed with diagnostics:
    cannot download pathway data: are you using the latest graphite version?
    --- failed re-building ‘SourceSet.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘SourceSet.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.3
Check: re-building of vignette outputs
Result: ERROR
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘SourceSet.Rmd’ using rmarkdown
    Loading required package: graph
    Loading required package: BiocGenerics
    
    Attaching package: 'BiocGenerics'
    
    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
    
    Identifing all possible orderings..
    Total run time: 1.99 secs
    Identifing all possible orderings..
    Total run time: 1.21 secs
    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: AnnotationDbi
    Loading required package: stats4
    Loading required package: IRanges
    Loading required package: S4Vectors
    
    Attaching package: 'S4Vectors'
    
    The following objects are masked from 'package:base':
    
     I, expand.grid, unname
    
    Loading required package: org.Hs.eg.db
    
    
    Quitting from lines 453-470 (SourceSet.Rmd)
    Error: processing vignette ‘SourceSet.Rmd’ failed with diagnostics:
    cannot download pathway data: are you using the latest graphite version?
    --- failed re-building ‘SourceSet.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘SourceSet.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.1.3
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'r2cytoscape', 'hgu95av2.db', 'ALL', 'org.Hs.eg.db'
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 0.1.3
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘ALL’
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 0.1.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘SourceSet.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Loading required package: graph
    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.max, which.min
    
    Identifing all possible orderings..
    Total run time: 1.23 secs
    Identifing all possible orderings..
    Total run time: 0.61 secs
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Quitting from lines 346-347 (SourceSet.Rmd)
    Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
    invalid 'path' argument
    --- failed re-building ‘SourceSet.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘SourceSet.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64