CentWave error

Topic: CentWave error (Read 20355 times) previous topic - next topic

Re: CentWave error

Reply #30 – October 12, 2012, 01:55:57 PM

That did it,
Thanks Ralf

not quite. I actually must have been installing the latest stable version. I am still getting the same error when I install the devel verion:

Loading required package: mzR
Loading required package: Rcpp
Error in eval(expr, envir, enclos) :
could not find function ".getNamespace"
In addition: Warning message:
package ‘xcms’ was built under R version 2.16.0
Error : unable to load R code in package ‘xcms’
Error: package/namespace load failed for ‘xcms’

I am on 64 bit windows, FWIW.

Re: CentWave error

Reply #31 – October 13, 2012, 12:42:52 PM

Hi,

can you load the individual dependencies,
esp. library(mzR) ?

Yours,
Steffen

Re: CentWave error

Reply #32 – October 16, 2012, 01:35:20 PM

> library(Rcpp)
> library(mzR)
> library(xcms)
Error in eval(expr, envir, enclos) :
could not find function ".getNamespace"
In addition: Warning message:
package ‘xcms’ was built under R version 2.16.0
Error : unable to load R code in package ‘xcms’
Error: package/namespace load failed for ‘xcms’
>

Same issue. This is a new R session. Doesn't sound like Jan had this problem, so it is either user error or platform dependent.

Re: CentWave error

Reply #33 – October 17, 2012, 09:11:23 AM

any chance I need R 2.16.0? I am running the latest stable version 2.15.1.

Re: CentWave error

Reply #34 – October 18, 2012, 04:50:00 PM

Found this online:

"Beginning on October 2, 2012, with the release of Bioconductor 2.11, the way to use the development (devel) version of Bioconductor (2.12) is to install R-devel (R-2.16). Packages can then be installed normally; for example, this will install the devel version of IRanges and its dependencies:"

So I went and downloaded devel R, which is necessary for devel Bioconducor, and apparently one or the other is necessary for devel xcms, becuase now I seem to have the right version installed:

trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/2.16/xcms_1.35.1.zip'
Content type 'application/zip' length 1871951 bytes (1.8 Mb)
opened URL
downloaded 1.8 Mb

package ‘xcms’ successfully unpacked and MD5 sums checked

> library(xcms)
Loading required package: mzR
Loading required package: Rcpp
>

Re: CentWave error

Reply #35 – October 18, 2012, 05:01:50 PM

and the new 'conversion' tool is working great. Everything has to be devel versions! Thanks again,
Corey

Re: CentWave error

Reply #36 – October 19, 2012, 05:00:28 AM

Hi,

glad you have it solved, sometimes the version and devel stuff
can be frustrating. Hope it helps someone else when googl'ing
their problem.

Yours,
Steffen

Re: CentWave error

Reply #37 – October 19, 2012, 09:01:22 AM

I had two files that generate this error with new write.mxXML function.
The two files are two functions (MS and MSe) derived from the same waters raw file, that was converted to two independent cdf files:

Error in if (is.unsorted(peaks[, "mz"])) { :
missing value where TRUE/FALSE needed

Re: CentWave error

Reply #38 – October 19, 2012, 12:04:52 PM

That means that some scans are either empty or contain only NA's for some reason ?
Can you send me one of those files ?