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BioC 2.14: BUILD report for beadarray on zin2

This page was generated on 2014-10-08 08:47:57 -0700 (Wed, 08 Oct 2014).

Package 70/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.14.2
Mark Dunning
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/beadarray
Last Changed Rev: 94482 / Revision: 95116
Last Changed Date: 2014-09-24 08:45:13 -0700 (Wed, 24 Sep 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ ERROR ] skipped 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  ERROR  skipped  skipped 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: beadarray
Version: 2.14.2
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data beadarray
StartedAt: 2014-10-07 18:36:11 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 18:40:07 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 235.7 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data beadarray
###
##############################################################################
##############################################################################


* checking for file ‘beadarray/DESCRIPTION’ ... OK
* preparing ‘beadarray’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
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:stats':

    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, intersect,
    is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unlist

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: ggplot2
Welcome to beadarray version 2.14.2
beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
Loading required package: illuminaHumanv3.db
Loading required package: AnnotationDbi
Loading required package: GenomeInfoDb
Loading required package: org.Hs.eg.db
Loading required package: DBI


Annotating control probes using package illuminaHumanv3.db Version:1.22.1

Annotating control probes using package illuminaHumanv3.db Version:1.22.1

Warning: Removed 124 rows containing missing values (geom_point).
Warning: Removed 131 rows containing missing values (geom_point).
Warning: Removed 140 rows containing missing values (geom_point).
Warning: Removed 130 rows containing missing values (geom_point).
Warning: Removed 127 rows containing missing values (geom_point).
Warning: Removed 135 rows containing missing values (geom_point).
Warning: Removed 7 rows containing missing values (geom_point).
Warning: Removed 46 rows containing missing values (geom_point).
Warning: Removed 133 rows containing missing values (geom_point).
Warning: Removed 119 rows containing missing values (geom_point).
Warning: Removed 133 rows containing missing values (geom_point).
Warning: Removed 119 rows containing missing values (geom_point).
Warning: Removed 13 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 8 rows containing missing values (geom_point).
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Warning: Removed 15 rows containing missing values (geom_point).
Warning: Removed 7 rows containing missing values (geom_point).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 124 rows containing missing values (geom_point).
Warning: Removed 131 rows containing missing values (geom_point).
Warning: Removed 140 rows containing missing values (geom_point).
Warning: Removed 130 rows containing missing values (geom_point).
Warning: Removed 127 rows containing missing values (geom_point).
Warning: Removed 135 rows containing missing values (geom_point).
Warning: Removed 7 rows containing missing values (geom_point).
Warning: Removed 46 rows containing missing values (geom_point).
Warning: Removed 133 rows containing missing values (geom_point).
Warning: Removed 119 rows containing missing values (geom_point).
Warning: Removed 133 rows containing missing values (geom_point).
Warning: Removed 119 rows containing missing values (geom_point).
Warning: Removed 118 rows containing missing values (geom_point).
Warning: Removed 131 rows containing missing values (geom_point).
Warning: Removed 138 rows containing missing values (geom_point).
Warning: Removed 125 rows containing missing values (geom_point).
Warning: Removed 127 rows containing missing values (geom_point).
Warning: Removed 133 rows containing missing values (geom_point).
Warning: Removed 7 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 42 rows containing missing values (geom_point).
Warning: Removed 126 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 112 rows containing missing values (geom_point).
Warning: Removed 117 rows containing missing values (geom_point).
Warning: Removed 114 rows containing missing values (geom_point).
illuminaHumanv3PFAM is deprecated because up to date IPI IDs are no longer available.
Please use select() if you need access to PFAM or PROSITE accessions. 

illuminaHumanv3PROSITE is deprecated because up to date IPI IDs are no longer available.
Please use select() if you need access to PFAM or PROSITE accessions. 

Loading required package: gridExtra
Loading required package: grid
Warning: Removed 118 rows containing missing values (geom_point).
Warning: Removed 131 rows containing missing values (geom_point).
Warning: Removed 138 rows containing missing values (geom_point).
Warning: Removed 125 rows containing missing values (geom_point).
Warning: Removed 127 rows containing missing values (geom_point).
Warning: Removed 133 rows containing missing values (geom_point).
Warning: Removed 7 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 42 rows containing missing values (geom_point).
Warning: Removed 126 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 112 rows containing missing values (geom_point).
Warning: Removed 117 rows containing missing values (geom_point).
Warning: Removed 114 rows containing missing values (geom_point).
No sample factor specified. Comparing to reference array
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
geom_smooth: method="auto" and size of largest group is >=1000, so using gam with formula: y ˜ s(x, bs = "cs"). Use 'method = x' to change the smoothing method.
Warning: Removed 1 rows containing missing values (stat_smooth).
Warning: Removed 1 rows containing non-finite values (stat_boxplot).
Warning: Removed 1462 rows containing missing values (geom_point).
Warning: Removed 75 rows containing missing values (geom_point).
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Warning: Removed 41 rows containing missing values (geom_point).
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Warning: Removed 821 rows containing missing values (geom_point).
Warning: Removed 307 rows containing missing values (geom_point).
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Calculating array weights
Array weights
Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:nlme':

    collapse

Quitting from lines 402-403 (beadsummary.rnw) 
Error: processing vignette 'beadsummary.rnw' failed with diagnostics:
could not find function "plotGrandLinear"
Execution halted