CRAN Package Check Results for Package genoPlotR

Last updated on 2020-12-03 04:47:12 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.8.9 6.73 50.34 57.07 ERROR
r-devel-linux-x86_64-debian-gcc 0.8.9 6.43 41.38 47.81 ERROR
r-devel-linux-x86_64-fedora-clang 0.8.9 74.53 ERROR
r-devel-linux-x86_64-fedora-gcc 0.8.9 65.89 ERROR
r-devel-windows-ix86+x86_64 0.8.9 12.00 63.00 75.00 ERROR
r-patched-linux-x86_64 0.8.9 6.33 79.72 86.05 OK
r-patched-solaris-x86 0.8.9 135.20 OK
r-release-linux-x86_64 0.8.9 5.75 82.13 87.88 OK
r-release-macos-x86_64 0.8.9 OK
r-release-windows-ix86+x86_64 0.8.9 13.00 109.00 122.00 OK
r-oldrel-macos-x86_64 0.8.9 OK
r-oldrel-windows-ix86+x86_64 0.8.9 9.00 106.00 115.00 OK

Check Details

Version: 0.8.9
Check: examples
Result: ERROR
    Running examples in 'genoPlotR-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: annotation
    > ### Title: Annotation class and class functions
    > ### Aliases: annotation as.annotation is.annotation
    > ### Keywords: data
    >
    > ### ** Examples
    >
    > ## loading data
    > data(three_genes)
    >
    > ## Calculating middle positions
    > mid_pos <- middle(dna_segs[[1]])
    >
    > # Create first annotation
    > annot1 <- annotation(x1=mid_pos, text=dna_segs[[1]]$name)
    > plot_gene_map(dna_segs=dna_segs, comparisons=comparisons, annotations=annot1)
    >
    > ## Exploring options
    > annot2 <- annotation(x1=c(mid_pos[1], dna_segs[[1]]$end[2]),
    + x2=c(NA, dna_segs[[1]]$end[3]),
    + text=c(dna_segs[[1]]$name[1], "region1"),
    + rot=c(30, 0), col=c("grey", "black"))
    > plot_gene_map(dna_segs=dna_segs, comparisons=comparisons,
    + annotations=annot2, annotation_height=1.3)
    >
    > ## Annotations on all the segments
    > annots <- lapply(dna_segs, function(x){
    + mid <- middle(x)
    + annot <- annotation(x1=mid, text=x$name, rot=30)
    + })
    > plot_gene_map(dna_segs=dna_segs, comparisons=comparisons,
    + annotations=annots, annotation_height=1.8, annotation_cex=1)
    >
    > ##
    > ## Using a bigger dataset from a 4-genome comparison
    > ##
    > data(barto)
    > ## Adding a tree
    > tree <- newick2phylog("(BB:2.5,(BG:1.8,(BH:1,BQ:0.8):1.9):3);")
    > ## Showing several subsegments
    > xlims2 <- list(c(1445000, 1415000, 1380000, 1412000),
    + c( 10000, 45000, 50000, 83000, 90000, 120000),
    + c( 15000, 36000, 90000, 120000, 74000, 98000),
    + c( 5000, 82000))
    > ## Adding annotations for all genomes, allow segments to be placed out
    > ## of the longest segment
    > annots <- lapply(barto$dna_segs, function(x){
    + mid <- middle(x)
    + annot <- annotation(x1=mid, text=x$name, rot=30)
    + # removing gene names starting with "B" and keeping 1 in 4
    + idx <- grep("^[^B]", annot$text, perl=TRUE)
    + annot[idx[idx %% 4 == 0],]
    + })
    > plot_gene_map(barto$dna_segs, barto$comparisons, tree=tree,
    + annotations=annots,
    + xlims=xlims2,
    + limit_to_longest_dna_seg=FALSE,
    + dna_seg_scale=TRUE)
    Error in valid.viewport(x, y, width, height, just, gp, clip, mask, xscale, :
     invalid 'xscale' in viewport
    Calls: plot_gene_map -> pushViewport -> viewport -> valid.viewport
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.8.9
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'genoPlotR.Rnw' using Sweave
    Loading required package: ade4
    Loading required package: grid
    
    Error: processing vignette 'genoPlotR.Rnw' failed with diagnostics:
     chunk 3 (label = quick_plot)
    Error in valid.viewport(x, y, width, height, just, gp, clip, mask, xscale, :
     invalid 'xscale' in viewport
    
    --- failed re-building 'genoPlotR.Rnw'
    
    SUMMARY: processing the following file failed:
     'genoPlotR.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.8.9
Check: examples
Result: ERROR
    Running examples in ‘genoPlotR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: annotation
    > ### Title: Annotation class and class functions
    > ### Aliases: annotation as.annotation is.annotation
    > ### Keywords: data
    >
    > ### ** Examples
    >
    > ## loading data
    > data(three_genes)
    >
    > ## Calculating middle positions
    > mid_pos <- middle(dna_segs[[1]])
    >
    > # Create first annotation
    > annot1 <- annotation(x1=mid_pos, text=dna_segs[[1]]$name)
    > plot_gene_map(dna_segs=dna_segs, comparisons=comparisons, annotations=annot1)
    >
    > ## Exploring options
    > annot2 <- annotation(x1=c(mid_pos[1], dna_segs[[1]]$end[2]),
    + x2=c(NA, dna_segs[[1]]$end[3]),
    + text=c(dna_segs[[1]]$name[1], "region1"),
    + rot=c(30, 0), col=c("grey", "black"))
    > plot_gene_map(dna_segs=dna_segs, comparisons=comparisons,
    + annotations=annot2, annotation_height=1.3)
    >
    > ## Annotations on all the segments
    > annots <- lapply(dna_segs, function(x){
    + mid <- middle(x)
    + annot <- annotation(x1=mid, text=x$name, rot=30)
    + })
    > plot_gene_map(dna_segs=dna_segs, comparisons=comparisons,
    + annotations=annots, annotation_height=1.8, annotation_cex=1)
    >
    > ##
    > ## Using a bigger dataset from a 4-genome comparison
    > ##
    > data(barto)
    > ## Adding a tree
    > tree <- newick2phylog("(BB:2.5,(BG:1.8,(BH:1,BQ:0.8):1.9):3);")
    > ## Showing several subsegments
    > xlims2 <- list(c(1445000, 1415000, 1380000, 1412000),
    + c( 10000, 45000, 50000, 83000, 90000, 120000),
    + c( 15000, 36000, 90000, 120000, 74000, 98000),
    + c( 5000, 82000))
    > ## Adding annotations for all genomes, allow segments to be placed out
    > ## of the longest segment
    > annots <- lapply(barto$dna_segs, function(x){
    + mid <- middle(x)
    + annot <- annotation(x1=mid, text=x$name, rot=30)
    + # removing gene names starting with "B" and keeping 1 in 4
    + idx <- grep("^[^B]", annot$text, perl=TRUE)
    + annot[idx[idx %% 4 == 0],]
    + })
    > plot_gene_map(barto$dna_segs, barto$comparisons, tree=tree,
    + annotations=annots,
    + xlims=xlims2,
    + limit_to_longest_dna_seg=FALSE,
    + dna_seg_scale=TRUE)
    Error in valid.viewport(x, y, width, height, just, gp, clip, mask, xscale, :
     invalid 'xscale' in viewport
    Calls: plot_gene_map -> pushViewport -> viewport -> valid.viewport
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 0.8.9
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘genoPlotR.Rnw’ using Sweave
    Loading required package: ade4
    Loading required package: grid
    
    Error: processing vignette 'genoPlotR.Rnw' failed with diagnostics:
     chunk 3 (label = quick_plot)
    Error in valid.viewport(x, y, width, height, just, gp, clip, mask, xscale, :
     invalid 'xscale' in viewport
    
    --- failed re-building ‘genoPlotR.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘genoPlotR.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64