CRAN Package Check Results for Package chicane

Last updated on 2021-10-20 23:50:04 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.7 13.05 538.32 551.37 WARN
r-devel-linux-x86_64-debian-gcc 0.1.7 8.70 460.94 469.64 WARN
r-devel-linux-x86_64-fedora-clang 0.1.7 644.14 WARN
r-devel-linux-x86_64-fedora-gcc 0.1.7 610.88 WARN
r-devel-windows-x86_64 0.1.7 18.00 696.00 714.00 NOTE
r-devel-windows-x86_64-gcc10-UCRT 0.1.7 NOTE
r-patched-linux-x86_64 0.1.7 11.48 500.18 511.66 WARN
r-patched-solaris-x86 0.1.7 431.70 NOTE
r-release-linux-x86_64 0.1.7 9.04 525.79 534.83 NOTE
r-release-macos-arm64 0.1.7 NOTE
r-release-macos-x86_64 0.1.7 NOTE
r-release-windows-ix86+x86_64 0.1.7 25.00 678.00 703.00 NOTE
r-oldrel-macos-x86_64 0.1.7 NOTE
r-oldrel-windows-ix86+x86_64 0.1.7 25.00 680.00 705.00 NOTE

Additional issues

M1mac

Check Details

Version: 0.1.7
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'countreg'
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-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-arm64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.1.7
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'Getting_Started.Rmd' using rmarkdown
    --- finished re-building 'Getting_Started.Rmd'
    
    --- re-building 'Visualising_Interactions.Rmd' using rmarkdown
    Loading required package: InteractionSet
    Loading required package: GenomicRanges
    Loading required package: stats4
    Loading required package: BiocGenerics
    
    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
    
    Loading required package: S4Vectors
    
    Attaching package: 'S4Vectors'
    
    The following objects are masked from 'package:data.table':
    
     first, second
    
    The following objects are masked from 'package:base':
    
     I, expand.grid, unname
    
    Loading required package: IRanges
    
    Attaching package: 'IRanges'
    
    The following object is masked from 'package:data.table':
    
     shift
    
    The following object is masked from 'package:nlme':
    
     collapse
    
    Loading required package: GenomeInfoDb
    Loading required package: SummarizedExperiment
    Loading required package: MatrixGenerics
    Loading required package: matrixStats
    
    Attaching package: 'MatrixGenerics'
    
    The following objects are masked from 'package:matrixStats':
    
     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
     colWeightedMeans, colWeightedMedians, colWeightedSds,
     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
     rowWeightedSds, rowWeightedVars
    
    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")'.
    
    
    Attaching package: 'Biobase'
    
    The following object is masked from 'package:MatrixGenerics':
    
     rowMedians
    
    The following objects are masked from 'package:matrixStats':
    
     anyMissing, rowMedians
    
    Loading required package: grid
    
    Attaching package: 'Gviz'
    
    The following object is masked from 'package:GenomicInteractions':
    
     availableDisplayPars
    
    Quitting from lines 41-111 (Visualising_Interactions.Rmd)
    Error: processing vignette 'Visualising_Interactions.Rmd' failed with diagnostics:
    There doesn't seem to be any chromosome length data available for genome 'hg38' at UCSC or the service is temporarily down.
    --- failed re-building 'Visualising_Interactions.Rmd'
    
    SUMMARY: processing the following file failed:
     'Visualising_Interactions.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 0.1.7
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     'knitr' 'rmarkdown'
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-gcc10-UCRT, r-patched-solaris-x86, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 0.1.7
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘Getting_Started.Rmd’ using rmarkdown
    --- finished re-building ‘Getting_Started.Rmd’
    
    --- re-building ‘Visualising_Interactions.Rmd’ using rmarkdown
    Loading required package: InteractionSet
    Loading required package: GenomicRanges
    Loading required package: stats4
    Loading required package: BiocGenerics
    
    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
    
    Loading required package: S4Vectors
    
    Attaching package: 'S4Vectors'
    
    The following objects are masked from 'package:data.table':
    
     first, second
    
    The following objects are masked from 'package:base':
    
     I, expand.grid, unname
    
    Loading required package: IRanges
    
    Attaching package: 'IRanges'
    
    The following object is masked from 'package:data.table':
    
     shift
    
    The following object is masked from 'package:nlme':
    
     collapse
    
    Loading required package: GenomeInfoDb
    Loading required package: SummarizedExperiment
    Loading required package: MatrixGenerics
    Loading required package: matrixStats
    
    Attaching package: 'MatrixGenerics'
    
    The following objects are masked from 'package:matrixStats':
    
     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
     colWeightedMeans, colWeightedMedians, colWeightedSds,
     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
     rowWeightedSds, rowWeightedVars
    
    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")'.
    
    
    Attaching package: 'Biobase'
    
    The following object is masked from 'package:MatrixGenerics':
    
     rowMedians
    
    The following objects are masked from 'package:matrixStats':
    
     anyMissing, rowMedians
    
    Loading required package: grid
    
    Attaching package: 'Gviz'
    
    The following object is masked from 'package:GenomicInteractions':
    
     availableDisplayPars
    
    Quitting from lines 41-111 (Visualising_Interactions.Rmd)
    Error: processing vignette 'Visualising_Interactions.Rmd' failed with diagnostics:
    There doesn't seem to be any chromosome length data available for genome 'hg38' at UCSC or the service is temporarily down.
    --- failed re-building ‘Visualising_Interactions.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘Visualising_Interactions.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.1.7
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'GenomicInteractions', 'countreg'
Flavors: r-devel-windows-x86_64-gcc10-UCRT, r-release-macos-x86_64, r-oldrel-macos-x86_64