Hi,
I have two problems when I import ShortRead into my packages.
1. I get the following warning, when I load my package
Warning message:
"replacing previous import ‘show’ when loading ‘ShortRead’"
--> It looks to me like a conflict between BiocGenerics and
ShortRead. How can I get rid of this message?
2. I need a require(ShortRead) in my function even when I import
ShortRead entirely.
--> Put ShortRead to Depends would solve this issue, but this is
not a solution for me.
At the moment a have a require in the function and ShortRead in
the Suggests field to pass the checks. This is working, but is a
hack.
Greetings,
Anita
Here a mini package which shows the same behaviour:
*********
NAMESPACE
*********
import(methods)
import(BiocGenerics)
import(ShortRead)
export(funA, funB)
******
fun.R
******
funA <- function(){
message("Step A.1")
filters <- c(nFilter(2), dustyFilter(0.5))
message("Step A.2")
active(filters) <- TRUE
}
funB <- function(){
message("Step B.1")
require(ShortRead)
filters <- c(nFilter(2), dustyFilter(0.5))
message("Step B.2")
active(filters) <- TRUE
}
***********
DESCRIPTION
***********
Package: anRpackage
Type: Package
Title: What the package does (short line)
Version: 1.0
Date: 2012-11-16
Author: Who wrote it
Maintainer: Who to complain to <yourfa...@somewhere.net>
Depends: R (>= 2.15.0)
Imports: methods, BiocGenerics, ShortRead
Description: More about what it does (maybe more than one line)
License: What license is it under?
> library(anRpackage)
Warning message:
replacing previous import ‘show’ when loading ‘ShortRead’
> funA()
Step A.1
Error in asMethod(object) : could not find function "FilterRules"
> funB()
Step B.1
Loading required package: ShortRead
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following object(s) are masked from ‘package:stats’:
xtabs
The following object(s) are masked from ‘package:base’:
anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get,
intersect, lapply, Map, mapply, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce,
rep.int, rownames, sapply, setdiff,
table, tapply, union, unique
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
Loading required package: latticeExtra
Loading required package: RColorBrewer
Step B.2
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C
LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.16.2 latticeExtra_0.6-24 RColorBrewer_1.0-5
Rsamtools_1.10.2 lattice_0.20-6
[6] Biostrings_2.26.2 GenomicRanges_1.10.5 IRanges_1.16.4
BiocGenerics_0.4.0 anRpackage_1.0
loaded via a namespace (and not attached):
[1] Biobase_2.18.0 bitops_1.0-5 grid_2.15.1 hwriter_1.3
parallel_2.15.1 stats4_2.15.1 tools_2.15.1
[8] zlibbioc_1.4.0
--
Anita Lerch
Friedrich Miescher Institute
Maulbeerstrasse 66
WRO-1066.P22
4058 Basel
Phone: +41 (0)61 697 5172
Email: anita.le...@fmi.ch
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