• using R version 2.15.0 (2012-03-30)
• using platform: x86_64-pc-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'RobLoxBioC/DESCRIPTION' ... OK
• this is package 'RobLoxBioC' version '0.8.2'
• package encoding: latin1
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking whether package 'RobLoxBioC' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• loading checks for arch 'i386'
  ** checking whether the package can be loaded ... OK
  ** checking whether the package can be loaded with stated dependencies ... OK
  ** checking whether the package can be unloaded cleanly ... OK
  ** checking whether the namespace can be loaded with stated dependencies ... OK
  ** checking whether the namespace can be unloaded cleanly ... OK
• loading checks for arch 'x64'
  ** checking whether the package can be loaded ... OK
  ** checking whether the package can be loaded with stated dependencies ... OK
  ** checking whether the package can be unloaded cleanly ... OK
  ** checking whether the namespace can be loaded with stated dependencies ... OK
  ** checking whether the namespace can be unloaded cleanly ... OK
• checking for unstated dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking R/sysdata.rda ... OK
• checking examples ...
  ** running examples for arch 'i386' ... OK
  ** checking differences from 'RobLoxBioC-Ex_i386.Rout' to 'RobLoxBioC-Ex.Rout.save' ...
  3c3
  < Attaching package: 'BiocGenerics'
  ---
  > Welcome to Bioconductor
  5c5,7
  < The following object(s) are masked from 'package:stats':
  ---
  > Vignettes contain introductory material. To view, type
  > 'browseVignettes()'. To cite Bioconductor, see
  > 'citation("Biobase")' and for packages 'citation("pkgname")'.
  7d8
  < xtabs
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  < The following object(s) are masked from 'package:base':
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  > Attaching package: 'reshape'
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  < Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
  < colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
  < order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
  < rownames, sapply, setdiff, table, tapply, union, unique
  ---
  > The following object(s) are masked from 'package:plyr':
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  < Welcome to Bioconductor
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  > rename, round_any
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  < Vignettes contain introductory material; view with
  < 'browseVignettes()'. To cite Bioconductor, see
  < 'citation("Biobase")', and for packages 'citation("pkgname")'.
  <
  < Find out what's changed in ggplot2 with
  < news(Version == "0.9.1", package = "ggplot2")
  < Welcome to beadarray version 2.6.0
  ---
  > Welcome to beadarray version 2.4.1
  26c18,25
  < :startupmsg> Utilities for start-up messages (version 0.7.2)
  ---
  >
  > Attaching package: 'beadarray'
  >
  > The following object(s) are masked from 'package:plyr':
  >
  > summarize
  >
  > :startupmsg> Utilities for start-up messages (version 0.7.3)
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  < :SweaveListingUtils> 0.5.5)
  ---
  > :SweaveListingUtils> 0.5.4)
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  < :distr> 2.3.3)
  ---
  > :distr> 2.3.4)
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  < :distrEx> Extensions of package distr (version 2.3.1)
  ---
  > :distrEx> Extensions of package distr (version 2.3.2)
  126c125
  < :distrMod> (version 2.3.1)
  ---
  > :distrMod> (version 2.3.3)
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  < [1] 0.1642185 0.1567706 0.1571387 0.1609188 0.1617499 0.1607157 0.1382646
  < [8] 0.1471997 0.1693088 0.1836652 0.1787724 0.1601283 0.1728984 0.1519412
  ---
  > [1] 0.1755693 0.1567648 0.1571403 0.1609188 0.1617499 0.1607157 0.1382646
  > [8] 0.1471997 0.1693088 0.1836652 0.1787724 0.1601283 0.1729001 0.1519412
  354c353
  < 6.20 0.22 6.43
  ---
  > 5.597 0.044 5.660
  364c363
  < > concentrations <- as.numeric(colnames(SpikeIn))
  ---
  > > concentrations <- as.numeric(sampleNames(SpikeIn))
  OK
  ** running examples for arch 'x64' ... OK
  ** checking differences from 'RobLoxBioC-Ex_x64.Rout' to 'RobLoxBioC-Ex.Rout.save' ...
  3c3
  < Attaching package: 'BiocGenerics'
  ---
  > Welcome to Bioconductor
  5c5,7
  < The following object(s) are masked from 'package:stats':
  ---
  > Vignettes contain introductory material. To view, type
  > 'browseVignettes()'. To cite Bioconductor, see
  > 'citation("Biobase")' and for packages 'citation("pkgname")'.
  7d8
  < xtabs
  9c10
  < The following object(s) are masked from 'package:base':
  ---
  > Attaching package: 'reshape'
  11,14c12
  < Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
  < colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
  < order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
  < rownames, sapply, setdiff, table, tapply, union, unique
  ---
  > The following object(s) are masked from 'package:plyr':
  16c14
  < Welcome to Bioconductor
  ---
  > rename, round_any
  18,22c16
  < Vignettes contain introductory material; view with
  < 'browseVignettes()'. To cite Bioconductor, see
  < 'citation("Biobase")', and for packages 'citation("pkgname")'.
  <
  < Welcome to beadarray version 2.6.0
  ---
  > Welcome to beadarray version 2.4.1
  24c18,25
  < :startupmsg> Utilities for start-up messages (version 0.7.2)
  ---
  >
  > Attaching package: 'beadarray'
  >
  > The following object(s) are masked from 'package:plyr':
  >
  > summarize
  >
  > :startupmsg> Utilities for start-up messages (version 0.7.3)
  31c32
  < :SweaveListingUtils> 0.5.5)
  ---
  > :SweaveListingUtils> 0.5.4)
  57c58
  < :distr> 2.3.3)
  ---
  > :distr> 2.3.4)
  96c97
  < :distrEx> Extensions of package distr (version 2.3.1)
  ---
  > :distrEx> Extensions of package distr (version 2.3.2)
  124c125
  < :distrMod> (version 2.3.1)
  ---
  > :distrMod> (version 2.3.3)
  352c353
  < 7.65 0.29 7.95
  ---
  > 5.597 0.044 5.660
  362c363
  < > concentrations <- as.numeric(colnames(SpikeIn))
  ---
  > > concentrations <- as.numeric(sampleNames(SpikeIn))
  OK
• checking PDF version of manual ... OK