- using R version 3.0.0 RC (2013-04-01 r62471)
- using platform: x86_64-w64-mingw32 (64-bit)
- using session charset: ISO8859-1
- checking for file 'HumMeth27QCReport/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'HumMeth27QCReport' version '1.2.14'
- 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
inst/.Rhistory
inst/doc/.Rhistory
inst/extdata/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
- checking for portable file names ... OK
- checking whether package 'HumMeth27QCReport' can be installed ... OK
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over 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
- 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 loading without being on the library search path ... WARNING
Loading required package: methylumi
Loading required package: Biobase
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, as.data.frame,
cbind, colnames, duplicated, eval, get, intersect, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: scales
Loading required package: reshape2
Loading required package: ggplot2
Error in loadNamespace(name) : there is no package called 'Rsamtools'
In addition: Warning messages:
1: In initDefaultClusterOptions(libname) : NAs introduced by coercion
2: replacing previous import 'image' when loading 'graphics'
Error: package 'methylumi' could not be loaded
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
- 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 sizes of PDF files under 'inst/doc' ... OK
- checking installed files from 'inst/doc' ... OK
- checking examples ... ERROR
Running examples in 'HumMeth27QCReport-Ex.R' failed
The error occurred in:
R version 3.0.0 RC (2013-04-01 r62471) -- "Masked Marvel"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> pkgname <- "HumMeth27QCReport"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('HumMeth27QCReport')
Loading required package: methylumi
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Warning in initDefaultClusterOptions(libname) :
NAs introduced by coercion
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, as.data.frame,
cbind, colnames, duplicated, eval, get, intersect, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: scales
Loading required package: reshape2
Loading required package: ggplot2
Warning: replacing previous import 'image' when loading 'graphics'
Error in loadNamespace(name) : there is no package called 'Rsamtools'
Error: package 'methylumi' could not be loaded
Execution halted