[Bioc-devel] Flagme creating vignettes ERROR

Riccardo Romoli riccardo.romoli at unifi.it
Sat Jul 4 12:26:25 CEST 2015


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:
>
> ----- Original Message -----
>> From: "Riccardo Romoli" <riccardo.romoli at unifi.it>
>> To: bioc-devel at r-project.org
>> Sent: Thursday, July 2, 2015 2:55:41 AM
>> Subject: [Bioc-devel] Flagme creating vignettes ERROR
>>
>> Hi, last night I received an automatic message regardless the flagme
>> package (I'm the co-author and the manteiner):
>>
>>     o ERROR for 'R CMD build' on zin2. See the details here:
>>   
>> http://bioconductor.org/checkResults/3.1/bioc-LATEST/flagme/zin2-buildsrc.html
>>
>> I followed the link above and I see the error:
>>
>> %----------------------------------------------------------------------------%
>> ##############################################################################
>> ##############################################################################
>> ###
>> ### Running command:
>> ###
>> ###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build
>> --keep-empty-dirs
>> --no-resave-data flagme
>> ###
>> ##############################################################################
>> ##############################################################################
>>
>>
>> * checking for file ‘flagme/DESCRIPTION’ ... OK
>> * preparing ‘flagme’:
>> * checking DESCRIPTION meta-information ... OK
>> * cleaning src
>> * installing the package to build vignettes
>> * creating vignettes ... ERROR
>>
>> ...
>>
>> Error: processing vignette 'flagme.Rnw' failed with diagnostics:
>>    chunk 3 (label = addXCMS)
>> Error in x$membership : $ operator not defined for this S4 class
>> Execution halted
>> %---------------------------------------------------------------------------------%
>>
>>
>> I downloaded the source of the package and I tried to build it. I get
>> no
>> errors.
>>
>>
>> %---------------------------------------------------------------------------------%
>> :~$ R CMD build --keep-empty-dirs --no-resave-data flagme
>>
>> * checking for file ‘flagme/DESCRIPTION’ ... OK
>> * preparing ‘flagme’:
>> * checking DESCRIPTION meta-information ... OK
>> * cleaning src
>> * installing the package to build vignettes
>> * creating vignettes ... OK
>> * cleaning src
>> * checking for LF line-endings in source and make files
>> * checking for empty or unneeded directories
>> * building ‘flagme_1.24.0.tar.gz’
>> %----------------------------------------------------------------------------------%
>>
>>
>> What should I do?
>>
> 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?
>
>> sessionInfo()
> 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:
>
>> ###################################################
>> ### code chunk number 3: addXCMS
>> ###################################################
>> pd.2 <- peaksDataset(cdfFiles[1:3], mz=seq(50,550), rtrange=c(7.5,8.5))
>   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
>
>> pd.2 <- addXCMSPeaks(cdfFiles[1:3], pd.2, peakPicking=c('mF'),
> +                      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’
>> traceback()
> 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
>
>
>> All the best, Riccardo
>>
>>
>> --
>> Riccardo Romoli, PhD
>> Mass Spectrometry Centre - CISM
>> University of Florence
>> Via Ugo Schiff 6, 50019 Sesto Fiorentino (FI), Italy
>> Phone: +39 055 4573783/2
>> email: riccardo.romoli at unifi.it
>> web site: www.cism.unifi.it
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>

-- 
Riccardo Romoli, PhD
Mass Spectrometry Centre - CISM
University of Florence
Via Ugo Schiff 6, 50019 Sesto Fiorentino (FI), Italy
Phone: +39 055 4573783/2
email: riccardo.romoli at unifi.it
web site: www.cism.unifi.it



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