[Bioc-devel] Problems with imported ShortRead pkg

Hahne, Florian florian.hahne at novartis.com
Fri Nov 16 14:59:53 CET 2012

Oh wait, correction. Not your fault. I thought you call FilterRules
directly. So ShortRead is using it internally in methods-SRFilter.R and
never imports it from IRanges. Looks like a simple fix in there.

On 11/16/12 12:40 PM, "Anita Lerch" <anita.lerch at fmi.ch> wrote:

>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 Œshow¹ when loading ŒShortRead¹"
>   --> 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.
>Here a mini package which shows the same behaviour:
>export(funA, funB)
>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
>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 Œshow¹ when loading ŒShortRead¹
>> 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: ŒBiocGenerics¹
>The following object(s) are masked from Œpackage:stats¹:
>    xtabs
>The following object(s) are masked from Œpackage:base¹:
>    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)
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>            LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=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
>4058 Basel
>Phone: +41 (0)61 697 5172
>Email: anita.lerch at fmi.ch

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