[Bioc-devel] Flagme creating vignettes ERROR
Dan Tenenbaum
dtenenba at fredhutch.org
Thu Jul 2 20:58:15 CEST 2015
----- 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
>
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