mzR Error for XCMS

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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: mzR
Error : objects ‘annotation’, ‘annotation<-’ are not exported by 'namespace:BiocGenerics'
Error: package ‘mzR’ could not be loaded

ALSO, HOW CAN I GET CORRECT SET OF XCMS AND RELATED PACKAGES FOR R 2.15.2.

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#rpack

The help to biocLite is the definite reference:
http://stuff.mit.edu/afs/athena/softwar ... cLite.html

The "annotation" error hints at an outdated BioCGenerics package,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 R
if incompatible mixes of mzR and Rcpp were used. If that happens to you,
please report back.

Yours,
Steffen

Re: mzR Error for XCMS

Reply #2 – December 03, 2012, 10:13:17 PM

Thanks for reply,

Packages I a using are
BioCGenerics_0.2.0
Biobase_2.19.1
Rcpp_0.10.1
mzR_1.4.1

Is this combination is fine or need more updates?
I tried several times changing R 2.15.0, 2.15.2 and 2.16.0
Getting same error-
> library(mzR)
Loading required package: Rcpp
Error : objects ‘annotation’, ‘annotation<-’ are not exported by 'namespace:BiocGenerics'
Error: package/namespace load failed for ‘mzR’

Please help me out.

Prasad

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

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..

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

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’:

xtabs

The 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 mzR
negative length vectors are not allowed
Error: package or namespace load failed for ‘mzR’
>

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

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

Re: mzR Error for XCMS

Reply #9 – December 05, 2012, 06:03:16 AM

Hi, I just posted sessionInfo().
Please help.

Prasad....

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 Gatto
Subject:    Re: mzR installation
Date:    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 if
appropriate.

I have observed this very same error message yesterday and have
triggered a rebuild on the Bioc servers (release and devel) this
morning. 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

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...

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 itself
I can't see why it should be a 32/64 bit problem, and I still
have 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

Re: mzR Error for XCMS

Reply #13 – December 07, 2012, 03:28:47 AM

Thanks Steffen.

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.