* using log directory 'd:/Rcompile/CRANpkg/local/2.15/RobLoxBioC.Rcheck'
* 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
9c10
< The following object(s) are masked from 'package:base':
---
> 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':
16c14
< Welcome to Bioconductor
---
>     rename, round_any
18,24c16
<     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)
33c32
< :SweaveListingUtils>  0.5.5)
---
> :SweaveListingUtils>  0.5.4)
59c58
< :distr>  2.3.3)
---
> :distr>  2.3.4)
98c97
< :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)
232,233c231,232
<  [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