Yes, that works fine.

> library(Biobase)
...
> library(arrayQualityMetrics)
Creating a generic function for ‘hist’ from package ‘graphics’ in package
‘affyPLM’
> library(affyPLM)
Loading required package: affy
Loading required package: gcrma
Loading required package: preprocessCore


So the affyPLM NAMESPACE file needs to declare the dependency;

importFrom(Biobase, "addVigs2WinMenu").

cheers,

Marcus


On Mon, Sep 3, 2012 at 5:05 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 09/02/2012 07:17 PM, Marcus Davy wrote:
>
>> This more informative error is from another fresh test
>>
>> ## Fresh Install of R-2.15.1
>>
>>> source("http://www.**bioconductor.org/biocLite.R<http://www.bioconductor.org/biocLite.R>
>>> ")
>>> biocLite("arrayQualityMetrics"**)
>>>
>> ...
>>
>>  library(arrayQualityMetrics)
>>>
>> Creating a generic function for ‘boxplot’ from package ‘graphics’ in
>> package ‘affyPLM’
>> Creating a generic function for ‘hist’ from package ‘graphics’ in package
>> ‘affyPLM’
>> Error : .onLoad failed in loadNamespace() for 'affyPLM', details:
>>    call: fun(libname, pkgname)
>>    error: could not find function "addVigs2WinMenu"
>> Error: package/namespace load failed for ‘arrayQualityMetrics’
>>
>
> affyPLM should importFrom(Biobase, addVigs2WinMenu). I think you can work
> around this by first loading Biobase
>
>   library(Biobase)
>   library(arrayQualityMetrics)
>
> Martin
>
>
>> Marcus
>>
>> On Mon, Sep 3, 2012 at 1:50 PM, Marcus Davy <mdavy86@gmail.com> wrote:
>>
>>  Hi,
>>> I have a script which works fine under R-2.14.1 on windows (and previous
>>> versions), but is throwing an error when loading the library on a fresh
>>> build with R-2.15.1. From a bioC thread recently about
>>> arrayQualityMetrics
>>> It looks like it is working on other platforms. The error looks like it
>>> is
>>> a namespace dependency issue with affyPLM and Biobase::addVigs2WinMenu.
>>>
>>> cheers,
>>>
>>> Marcus
>>>
>>>  library(arrayQualityMetrics)
>>>>
>>> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>>>    there is no package called ‘affyPLM’
>>> Error: package/namespace load failed for ‘arrayQualityMetrics’
>>>
>>>> sessionInfo()
>>>>
>>> R version 2.15.1 (2012-06-22)
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New
>>> Zealand.1252    LC_MONETARY=English_New Zealand.1252
>>> [4] LC_NUMERIC=C                         LC_TIME=English_New
>>> Zealand.1252
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] BiocInstaller_1.5.12 Biobase_2.17.7       BiocGenerics_0.3.1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affy_1.35.1           affyio_1.25.0         preprocessCore_1.19.0
>>> tools_2.15.1          zlibbioc_1.3.0
>>>
>>>
>>>
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>>
>>
>>
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>>
>
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