Help Error could not find function xcmsSet
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Entering edit mode
grateshak • 0
@grateshak-10586
Last seen 5.0 years ago

Hi, I am using bioconductor packages in R. I keep getting this error: 

Error: could not find function "xcmsSet" 

This is what I ran. 

# load required libraries
library(xcms)
library(CAMERA)

# set nslaves for the number of available cores of your machine
# Follow xcms vignette to understand data structure
# http://www.bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcmsPreprocess.pdf

nslaves <- 4

xset <- xcmsSet(
         "C:/", method='centWave', ppm=2, peakwidth=c(10,50),
        snthresh=3, prefilter=c(3,100), integrate=1, mzdiff=-0.00005,
           verbose.columns=TRUE,fitgauss=FALSE, nSlaves=nslaves
        )

# negative mode
xset2 <- xcmsSet(
         "C:/", method='centWave', ppm=2, peakwidth=c(10,50),
          snthresh=3, prefilter=c(3,100), integrate=1, mzdiff=-0.00005,
          verbose.columns=TRUE,fitgauss=FALSE, nSlaves=nslaves
         )

xcms is there in my win-library and all other bioconductor package neccesary. I also checked for xcmsSet in the unitTest folder of the xcms package. it is there as runit.xcmsSet.R.

I tried to load the library (xcms) alone. I get this error on mzR package:

> library(xcms)
Loading required package: mzR
Loading required package: Rcpp
Error : .onLoad failed in loadNamespace() for 'mzR', details:
  call: value[[3L]](cond)
  error: failed to load module Ramp from package mzR
invalid assignment for reference class field ‘class_pointer’, should be from class “externalptr” or a subclass (was class “character”)
In addition: Warning messages:
1: package ‘Rcpp’ was built under R version 3.0.3 
2: In fun(libname, pkgname) :
   mzR has been built against a different Rcpp version
 than is installed on your system. This might lead to errors
 when loading mzR. If you encounter such issues, please send
 a report, including the output of sessionInfo() to the Bioc
 mailing list -- http://www.bioconductor.org/help/mailing-list.
Error: package ‘mzR’ could not be loaded 

I also see the packages Rcpp and mzR in my library. I have downloaded the latest zip ofr this package. No result.Pls Help

xcms metabolomics mzr rcpp ramp • 1.3k views
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Entering edit mode
Johannes Rainer ★ 1.9k
@johannes-rainer-6987
Last seen 4 days ago
Italy

Could you please provide some more information on the R you are using? the output of sessionInfo() would e.g. be useful. There is definitely a problem with the mzR package...
 

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Thanks Johannes. I run R 3.0.1 now, when I started getting the error, I installed latest R 3.2.5 and I got same errors. so I simply removed the new version, believing versions were not the problem. When I shifted version, I copied every file within win-library to ensure my packages were still there. Anyway, sessionInfo()

Error: could not find function "xcmsSet"
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252   
[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C                  
[5] LC_TIME=English_India.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] Biobase_2.30.0      BiocGenerics_0.16.1

 I also tried the latest mzR and latest Rcpp al to no avail. I have also used earlier versions of Rcpp, then it will say Rcpp; could not be found by mzR': 

> library(xcms)
Loading required package: mzR
Error: package ‘Rcpp’ required by ‘mzR’ could not be found
In addition: Warning message:
package ‘mzR’ was built under R version 3.2.3 .

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Entering edit mode
grateshak • 0
@grateshak-10586
Last seen 5.0 years ago

Thanks Johannes. I run R 3.0.1 now, when I started getting the error, I installed latest R 3.2.5 and I got same errors. so I simply removed the new version, believing versions were not the problem. When I shifted version, I copied every file within win-library to ensure my packages were still there. Anyway, sessionInfo()

Error: could not find function "xcmsSet"
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252   
[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C                  
[5] LC_TIME=English_India.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] Biobase_2.30.0      BiocGenerics_0.16.1

 I also tried the latest mzR and latest Rcpp al to no avail. I have also used earlier versions of Rcpp, then it will say Rcpp; could not be found by mzR': 

> library(xcms)
Loading required package: mzR
Error: package ‘Rcpp’ required by ‘mzR’ could not be found
In addition: Warning message:
package ‘mzR’ was built under R version 3.2.3 .

 

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Entering edit mode

you should never do this, always install the "correct" Bioconductor package versions for the R version you've got installed; you should not install Bioconductor packages manually by downloading the zip file, always install them with the biocLite call!

I suggest you to start your R and install Bioconductor again:

source("https://bioconductor.org/biocLite.R")
biocLite()
## Eventually, if it's not updating xcms etc install them again
biocLite(c("mzR", "xcms"))

check the corresponding page on bioconductor: http://www.bioconductor.org/install/

this should fix your problem

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Entering edit mode

Thanks again, Johannes. Sure, that is how I initially installed all packages before I encountered the problem. Yes, I did use the code as u wrote above, with biocLite installation and all.

It gave me the error I mentioned 'could not find xcmsSet and later mzR could not be loaded. 

It was those error that led me to all the installation of  latest zip file.

Thanks

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Entering edit mode

I am beginning to think again that some syntax in my R version is still the problem

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