GenoView 1.6.0
Sharon Lee
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/GenoView | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | [ ERROR ] | skipped | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | ERROR | skipped | skipped | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GenoView
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* checking for file ‘GenoView/DESCRIPTION’ ... OK
* preparing ‘GenoView’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: GenoView
Loading required package: gridExtra
Loading required package: GenomicRanges
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 object is masked from ‘package:gridExtra’:
combine
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
Warning: Package 'GenoView' is deprecated and will be removed from Bioconductor
version 3.3
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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: biovizBase
Loading required package: grid
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Error: processing vignette 'GenoView.Rnw' failed with diagnostics:
chunk 8 (label = ml1lab)
Error in gtable_table(d, name = "core", fg_fun = theme$core$fg_fun, bg_fun = theme$core$bg_fun, :
unused arguments (gpar.coretext = list(fontsize = 10), gpar.coltext = list(fontsize = 12), show.rownames = FALSE, equal.height = FALSE, padding.h = 2, padding.v = 2, h.even.alpha = 0.15, h.odd.alpha = 0.35, v.even.alpha = 0.5, v.odd.alpha = 0.5, show.hlines = FALSE, show.vlines = FALSE, show.box = TRUE, separator = "black", gpar.corefill = list(fill = "grey80", col = "black"), gpar.colfill = list(fill = "white", col = "black"))
Execution halted