[BioC] XCMS / mzR / Rcpp dependency issue

[Dan Tenenbaum]

On Thu, Jun 28, 2012 at 3:16 AM, Laurent Gatto <laurent.gatto at gmail.com> wrote:
> Dear Uwe,
>
> Something is happening with mzR and Rcpp 0.9.12 on Windows - see [1] and [2].
> As a temporary fix, you can downgrade to Rcpp 0.9.10 [3] and proceed normally.
>

This problem is fixed in the latest release and devel versions of mzR,
available now via biocLite().

mzR just needed a version bump to trigger a fresh build to propagate.

Dan


> Best wishes,
>
> Laurent
>
> [1] http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2012-June/thread.html#3940
> [2] https://stat.ethz.ch/pipermail/bioconductor/2012-June/thread.html#46503
> [3] http://cran.us.r-project.org/bin/windows/contrib/2.13/Rcpp_0.9.10.zip
>
>
> On 28 June 2012 10:47, Uwe Schmitt <uschmitt at mineway.de> wrote:
>> Hi,
>>
>> I have some problems to install xcms for R 2.5.1 on Windows 7, 64 bit.
>> I follow the installation instructions and enter:
>>
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("xcms", dep=T)
>>
>> this loads some packages and gives me a warning:
>> installed directory not writable, cannot update packages 'boot', 'class',
>> 'KernSmooth', 'MASS', 'nnet', 'rpart', 'spatial'
>>
>> If I want to check if xmcs is installed I get:
>>
>>> require("xcms")
>>
>> Lade nötiges Paket: xcms
>> Lade nötiges Paket: mzR
>> Lade nötiges Paket: Rcpp
>> Error : .onLoad failed in loadNamespace() for 'mzR', details:
>> call: value[[3L]](cond)
>> error: failed to load module Ramp from package mzR
>> konnte Funktion "errorOccured" nicht finden
>> Failed with error: ‘Paket ‘mzR’ konnte nicht geladen werden’
>>
>> I try to translate the messages to english:
>>
>> load required packet: xcms
>> load required packet: mzR
>> load required packet: Rcpp
>> Error : .onLoad failed in loadNamespace() for 'mzR', details:
>> call: value[[3L]](cond)
>> error: failed to load module Ramp from package mzR
>> could not find function "errorOccured"
>> Failed with error: ‘Paket ‘mzR’ could not be loaded'
>>
>> Any hints what is going wrong ? I installed xcms on an older machine six
>> months ago and I had no problems at all.
>>
>> Kind Regards,
>>
>> Uwe
>>
>>
>> --
>> Dr. rer. nat. Uwe Schmitt
>> Leitung F/E Mathematik
>>
>> mineway GmbH
>> Gebäude 4
>> Im Helmerswald 2
>> 66121 Saarbrücken
>>
>> Telefon: +49 (0)681 8390 5334
>> Telefax: +49 (0)681 830 4376
>>
>> uschmitt at mineway.de
>> www.mineway.de
>>
>> Geschäftsführung: Dr.-Ing. Mathias Bauer
>> Amtsgericht Saarbrücken HRB 12339
>>
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