CRAN Package Check Results for Package DEVis

Last updated on 2019-01-11 06:46:46 CET.

Check Details

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘DEVis_vignette.Rmd’ using rmarkdown
    Loading required package: DESeq2
    Loading required package: S4Vectors
    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: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, 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
    
    
    Attaching package: 'S4Vectors'
    
    The following object is masked from 'package:base':
    
     expand.grid
    
    Loading required package: IRanges
    Loading required package: GenomicRanges
    Loading required package: GenomeInfoDb
    Loading required package: SummarizedExperiment
    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: DelayedArray
    Loading required package: matrixStats
    
    Attaching package: 'matrixStats'
    
    The following objects are masked from 'package:Biobase':
    
     anyMissing, rowMedians
    
    Loading required package: BiocParallel
    
    Attaching package: 'DelayedArray'
    
    The following objects are masked from 'package:matrixStats':
    
     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
    
    The following objects are masked from 'package:base':
    
     aperm, apply
    
    factor levels were dropped which had no samples
    factor levels were dropped which had no samples
    using pre-existing size factors
    estimating dispersions
    gene-wise dispersion estimates
    mean-dispersion relationship
    final dispersion estimates
    fitting model and testing
    ! LaTeX Error: Option clash for package xcolor.
    
    Error: processing vignette 'DEVis_vignette.Rmd' failed with diagnostics:
    Failed to compile DEVis_vignette.tex. See DEVis_vignette.log for more info.
    --- failed re-building ‘DEVis_vignette.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘DEVis_vignette.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: DESeq2
    Loading required package: S4Vectors
    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: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
    
    
    Attaching package: 'S4Vectors'
    
    The following object is masked from 'package:base':
    
     expand.grid
    
    Loading required package: IRanges
    Loading required package: GenomicRanges
    Loading required package: GenomeInfoDb
    Loading required package: SummarizedExperiment
    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: DelayedArray
    Loading required package: matrixStats
    
    Attaching package: 'matrixStats'
    
    The following objects are masked from 'package:Biobase':
    
     anyMissing, rowMedians
    
    Loading required package: BiocParallel
    
    Attaching package: 'DelayedArray'
    
    The following objects are masked from 'package:matrixStats':
    
     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
    
    The following objects are masked from 'package:base':
    
     aperm, apply
    
    factor levels were dropped which had no samples
    factor levels were dropped which had no samples
    using pre-existing size factors
    estimating dispersions
    gene-wise dispersion estimates
    mean-dispersion relationship
    final dispersion estimates
    fitting model and testing
    ! LaTeX Error: Option clash for package xcolor.
    
    Error: processing vignette ‘DEVis_vignette.Rmd’ failed with diagnostics:
    Failed to compile DEVis_vignette.tex. See DEVis_vignette.log for more info.
    Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
Flavor: r-release-windows-ix86+x86_64