[Bioc-devel] Problems with imported ShortRead pkg

[Anita Lerch]

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 <yourfault at 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.lerch at fmi.ch