Question: XCMS / mzR / Rcpp dependency issue
0
gravatar for Uwe Schmitt
7.5 years ago by
Uwe Schmitt30
Uwe Schmitt30 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 n?tiges Paket: xcms Lade n?tiges Paket: mzR Lade n?tiges 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 Geb?ude 4 Im Helmerswald 2 66121 Saarbr?cken Telefon: +49 (0)681 8390 5334 Telefax: +49 (0)681 830 4376 uschmitt at mineway.de www.mineway.de Gesch?ftsf?hrung: Dr.-Ing. Mathias Bauer Amtsgericht Saarbr?cken HRB 12339
xcms • 1.6k views
ADD COMMENTlink modified 7.5 years ago by Laurent Gatto1.2k • written 7.5 years ago by Uwe Schmitt30
Answer: XCMS / mzR / Rcpp dependency issue
0
gravatar for Laurent Gatto
7.5 years ago by
Laurent Gatto1.2k
Belgium
Laurent Gatto1.2k 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. 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 n?tiges Paket: xcms > Lade n?tiges Paket: mzR > Lade n?tiges 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 > Geb?ude 4 > Im Helmerswald 2 > 66121 Saarbr?cken > > Telefon: +49 (0)681 8390 5334 > Telefax: +49 (0)681 830 4376 > > uschmitt at mineway.de > www.mineway.de > > Gesch?ftsf?hrung: Dr.-Ing. Mathias Bauer > Amtsgericht Saarbr?cken HRB 12339 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.5 years ago by Laurent Gatto1.2k
Thanks for your help, downgrading Rcpp fixed the problem. Kind Regards, Uwe. Am 28.06.2012 12:16, schrieb Laurent Gatto: > 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. > > 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.htm l#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 n?tiges Paket: xcms >> Lade n?tiges Paket: mzR >> Lade n?tiges 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 >> Geb?ude 4 >> Im Helmerswald 2 >> 66121 Saarbr?cken >> >> Telefon: +49 (0)681 8390 5334 >> Telefax: +49 (0)681 830 4376 >> >> uschmitt at mineway.de >> www.mineway.de >> >> Gesch?ftsf?hrung: Dr.-Ing. Mathias Bauer >> Amtsgericht Saarbr?cken HRB 12339 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dr. rer. nat. Uwe Schmitt Leitung F/E Mathematik mineway GmbH Geb?ude 4 Im Helmerswald 2 66121 Saarbr?cken Telefon: +49 (0)681 8390 5334 Telefax: +49 (0)681 830 4376 uschmitt at mineway.de www.mineway.de Gesch?ftsf?hrung: Dr.-Ing. Mathias Bauer Amtsgericht Saarbr?cken HRB 12339
ADD REPLYlink written 7.5 years ago by Uwe Schmitt30
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.htm l#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 n?tiges Paket: xcms >> Lade n?tiges Paket: mzR >> Lade n?tiges 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 >> Geb?ude 4 >> Im Helmerswald 2 >> 66121 Saarbr?cken >> >> Telefon: +49 (0)681 8390 5334 >> Telefax: +49 (0)681 830 4376 >> >> uschmitt at mineway.de >> www.mineway.de >> >> Gesch?ftsf?hrung: Dr.-Ing. Mathias Bauer >> Amtsgericht Saarbr?cken HRB 12339 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.4 years ago by Dan Tenenbaum8.2k
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