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[Bioc-devel] Flagme creating vignettes ERROR

3 messages · Dan Tenenbaum, Riccardo Romoli

Original
Dan Tenenbaum
# 
----- Original Message -----
Are you using R-3.2.1 when you try and build it?
Does your sessionInfo() (package versions) look more or less like this when you Stangle and source your vignette?
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] flagme_1.24.0       CAMERA_1.24.0       igraph_1.0.1       
 [4] xcms_1.44.0         Biobase_2.28.0      ProtGenerics_1.0.0 
 [7] BiocGenerics_0.14.0 mzR_2.2.1           Rcpp_0.11.6        
[10] gcspikelite_1.6.0  

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2  plyr_1.8.3          bitops_1.0-6       
 [4] tools_3.2.1         rpart_4.1-10        digest_0.6.8       
 [7] gtable_0.1.2        lattice_0.20-31     graph_1.46.0       
[10] SparseM_1.6         proto_0.3-10        gridExtra_0.9.1    
[13] stringr_1.0.0       cluster_2.0.2       caTools_1.17.1     
[16] gtools_3.5.0        stats4_3.2.1        grid_3.2.1         
[19] nnet_7.3-10         RBGL_1.44.0         survival_2.38-2    
[22] foreign_0.8-64      gdata_2.16.1        latticeExtra_0.6-26
[25] Formula_1.2-1       ggplot2_1.0.1       reshape2_1.4.1     
[28] magrittr_1.5        Hmisc_3.16-0        scales_0.2.5       
[31] gplots_2.17.0       codetools_0.2-11    splines_3.2.1      
[34] MASS_7.3-41         colorspace_1.2-6    KernSmooth_2.23-15 
[37] stringi_0.5-5       acepack_1.3-3.3     munsell_0.4.2
Try updating (with biocLite()) so all your packages are the most recent version and then see if you can reproduce the issue. 

Incidentally, here is the traceback from sourcing the stangled vignette:
Reading  /home/biocbuild/bbs-3.1-bioc/R/library/gcspikelite/data/0709_468.CDF 
 Reading  /home/biocbuild/bbs-3.1-bioc/R/library/gcspikelite/data/0709_474.CDF 
 Reading  /home/biocbuild/bbs-3.1-bioc/R/library/gcspikelite/data/0709_475.CDF
+                      snthresh=3, fwhm=4, step=1, steps=2, mzdiff=0.5)

Start grouping after retention time.
Created 34 pseudospectra.
Error in x$membership : $ operator not defined for this S4 class
In addition: Warning message:
replacing previous import by ?igraph::groups? when loading ?CAMERA?
14: groups.default(object at xcmsSet)
13: groups(object at xcmsSet)
12: nrow(groups(object at xcmsSet))
11: findIsotopes(xa, maxcharge = maxcharge, maxiso = maxiso, ppm = ppm, 
        mzabs = mzabs, intval = intval, minfrac = minfrac)
10: findIsotopes(xa, maxcharge = maxcharge, maxiso = maxiso, ppm = ppm, 
        mzabs = mzabs, intval = intval, minfrac = minfrac)
9: annotate(s, perfwhm = 0.6, max_peaks = 500, quick = TRUE)
8: annotate(s, perfwhm = 0.6, max_peaks = 500, quick = TRUE)
7: FUN(X[[i]], ...)
6: lapply(cdfFiles, function(x, y) {
       f <- which(cdfFiles %in% x)
       xr <- xcmsRaw(x)
       rtrange <- c(min(object at rawrt[[f]]), max(object at rawrt[[f]])) * 
           60
       scanRange <- c(max(1, which(xr at scantime > rtrange[1])[1], 
           na.rm = TRUE), min(length(xr at scantime), which(xr at scantime > 
           rtrange[2])[1] - 1, na.rm = TRUE))
       if (peakPicking == "cwt") {
           s <- xcmsSet(x, method = "centWave", prefilter = c(3, 
               100), scanrange = scanRange, integrate = 1, mzdiff = -0.001, 
               fitgauss = TRUE, ...)
       }
       if (peakPicking == "mF") {
           s <- xcmsSet(x, method = "matchedFilter", scanrange = scanRange, 
               max = 500, ...)
       }
       a <- annotate(s, perfwhm = 0.6, max_peaks = 500, quick = TRUE)
       return(a)
   }, y = peakPicking)
5: addXCMSPeaks(cdfFiles[1:3], pd.2, peakPicking = c("mF"), snthresh = 3, 
       fwhm = 4, step = 1, steps = 2, mzdiff = 0.5) at flagme.R#27
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("flagme.R", echo = TRUE, max = Inf)
Dan
1 day later
Riccardo Romoli
# 
Hi, as Dan suggested after the update I get the same error as in Zin2... 
so I tried to isolate the error and it seems to be correlated wit the 
CAMERA package. Searching in the repos 
(http://bioconductor.org/checkResults/release/bioc-LATEST/CAMERA/zin2-checksrc.html) 
I found that the 'CAMERA guys' get the same error:

 > xsa <- annotate(xs) Start grouping after retention time. Created 14 
pseudospectra. Error in x$membership : $ operator not defined for this 
S4 class

What should I do now?

All the Best, Riccardo
On 02/07/15 20:58, Dan Tenenbaum wrote:

  
    

      
      
    

  


  


      

    

    
2 days later

    

      
      

        


  

        

      Riccardo Romoli
    

    

      
      #
    

  


  

      
Hi, as Dan suggested after the update I get the same error as in Zin2... 
so I tried to isolate the error and it seems to be correlated wit the 
CAMERA package. Searching in the repos 
(http://bioconductor.org/checkResults/release/bioc-LATEST/CAMERA/zin2-checksrc.html) 
I found that the 'CAMERA guys' get the same error:

 > xsa <- annotate(xs) Start grouping after retention time. Created 14 
pseudospectra. Error in x$membership : $ operator not defined for this 
S4 class

What should I do now?

All the Best, Riccardo

        
On 02/07/15 20:58, Dan Tenenbaum wrote: