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BioC 3.2: BUILD report for GenoView on oaxaca

This page was generated on 2016-04-23 10:28:12 -0700 (Sat, 23 Apr 2016).

Package 430/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoView 1.4.0
Sharon Lee
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GenoView
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded [ ERROR ] skipped  skipped 

Summary

Package: GenoView
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GenoView
StartedAt: 2016-04-22 20:27:57 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 20:28:54 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 56.4 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GenoView
###
##############################################################################
##############################################################################


* 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, as.vector, 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, unlist, unsplit

Loading required package: S4Vectors
Loading required package: stats4
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