mzR Error for XCMS December 03, 2012, 02:23:50 AM Dear all,Please help for this.Although I have installed and unpacked mzR folder for R 2.15.2 version. I am getting this error continuously.Loading required package: mzRError : objects ‘annotation’, ‘annotation<-’ are not exported by 'namespace:BiocGenerics'Error: package ‘mzR’ could not be loadedALSO, HOW CAN I GET CORRECT SET OF XCMS AND RELATED PACKAGES FOR R 2.15.2. Quote Selected
Re: mzR Error for XCMS Reply #1 – December 03, 2012, 02:13:19 PM Hi,please don't hijack other threads, for easier navigation this thread is perfectly fine.Here's a quick help how to update:http://nebc.nerc.ac.uk/tools/bioinforma ... ctor#rpackThe help to biocLite is the definite reference:http://stuff.mit.edu/afs/athena/softwar ... cLite.htmlThe "annotation" error hints at an outdated BioCGenerics package,and/or BioBase etc. Please update your BioC packages. In recent days, there has also been a problem with a crash of Rif incompatible mixes of mzR and Rcpp were used. If that happens to you,please report back.Yours,Steffen Quote Selected
Re: mzR Error for XCMS Reply #2 – December 03, 2012, 10:13:17 PM Thanks for reply,Packages I a using are BioCGenerics_0.2.0Biobase_2.19.1Rcpp_0.10.1mzR_1.4.1Is this combination is fine or need more updates?I tried several times changing R 2.15.0, 2.15.2 and 2.16.0Getting same error-> library(mzR)Loading required package: RcppError : objects ‘annotation’, ‘annotation<-’ are not exported by 'namespace:BiocGenerics'Error: package/namespace load failed for ‘mzR’Please help me out.Prasad Quote Selected
Re: mzR Error for XCMS Reply #3 – December 04, 2012, 01:47:38 AM Hi,to me it seems you need to update to at least BiocGenerics_0.4.0.Steffen Quote Selected
Re: mzR Error for XCMS Reply #4 – December 04, 2012, 02:40:43 AM Thanks,I dowloaded and installed package BiocGenerics_0.4.0.zip and tried on R-2.16 (devel),but with same error.> utils:::menuInstallLocal()package ‘BiocGenerics’ successfully unpacked and MD5 sums checked> library(mzR)Error : objects ‘annotation’, ‘annotation<-’ are not exported by 'namespace:BiocGenerics'Error: package or namespace load failed for ‘mzR’Please guide further.Prasad.. Quote Selected
Re: mzR Error for XCMS Reply #5 – December 04, 2012, 10:02:52 AM Since I can't reproduce this, I am poking a bit in the dark.Let's back off and isolate the problem:1) Can you library(methods) I expect yes.2) Can you library(BiocGenerics) Possibly.3) Can you library(Biobase) Maybe not ?I expect the problem at 3), which then hints at a broken BioC base installation. In that case, try to update all BioC related packes.Yours,Steffen Quote Selected
Re: mzR Error for XCMS Reply #6 – December 05, 2012, 01:52:12 AM Hi,I tried your 3 suggetions but still getting error which is different from previous. Here is my script for your review.Thanks.> library(methods)> library(BiocGenerics)Attaching package: ‘BiocGenerics’The following object is masked from ‘package:stats’: xtabsThe following objects 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> library(BiocGenerics)> library(Biobase)Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.> library(Biobase)> library(Rcpp)> library(mzR)Error : .onLoad failed in loadNamespace() for 'mzR', details: call: value[[3L]](cond) error: failed to load module Ramp from package mzRnegative length vectors are not allowedError: package or namespace load failed for ‘mzR’> Quote Selected
Re: mzR Error for XCMS Reply #7 – December 05, 2012, 05:51:43 AM So, can I have sessionInfo() for the last situation ?Yours,Steffen Quote Selected
Re: mzR Error for XCMS Reply #8 – December 05, 2012, 05:54:16 AM R Under development (unstable) (2012-12-01 r61188)Platform: i386-w64-mingw32/i386 (32-bit)locale:[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252[4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages:[1] parallel stats graphics grDevices utils datasets methods base other attached packages:[1] Biobase_2.19.1 BiocGenerics_0.5.1 Rcpp_0.10.1 loaded via a namespace (and not attached):[1] tools_2.16.0 Quote Selected
Re: mzR Error for XCMS Reply #9 – December 05, 2012, 06:03:16 AM Hi, I just posted sessionInfo().Please help.Prasad.... Quote Selected
Re: mzR Error for XCMS Reply #10 – December 05, 2012, 07:53:24 AM Hi, I can forward a message from another mzR developer:From: Laurent GattoSubject: Re: mzR installationDate: Wed, 5 Dec 2012 13:43:25 +0000 (12/05/2012 02:43:25 PM)Don't have a user account on that forum; thank you for forwarding ifappropriate.I have observed this very same error message yesterday and havetriggered a rebuild on the Bioc servers (release and devel) thismorning. There has been a Rcpp 0.10.1 release recently very recently,so it might be related to that - the message looks vaguely similar to[1]. Will hopefully resolve automagically tomorrow.Laurent[1] http://stackoverflow.com/questions/1118 ... r/11212115 Quote Selected
Re: mzR Error for XCMS Reply #11 – December 06, 2012, 11:10:47 PM Dear,I switched to 64 bit PC with same versions of Bioc and R.Surprisingly mzR error gone and it works fine now.But still couldn't understand whats wrong with 32bit PC, still trying to solve and any clues?Prasad... Quote Selected
Re: mzR Error for XCMS Reply #12 – December 07, 2012, 01:02:25 AM Hi Prasad,great to see your problem fixed. From the error message itselfI can't see why it should be a 32/64 bit problem, and I stillhave the feeling that some combination of the underlying package versions caused the problem. So maybe it was the clean 64bit install that finally fixed your issue.Yours,Steffen Quote Selected
Re: mzR Error for XCMS Reply #14 – December 07, 2012, 05:11:33 AM I used new binary packages of mzR, version 1.5.4 (devel) and worked fine with 32 bit system. But my R is getting crashed.So, I switched to 64 bit PC and it works. But my 32 bit system still get crashed for R with this.Anyway thanks I am working with 64 bit system and its fine.Thanks a lot. Quote Selected