ARGUMENT '1' __ignored__ R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # prerequisite in bash: sudo apt-get install libssl-dev > # source("https://bioconductor.org/biocLite.R") > # useDevel(TRUE) > # biocLite("git2r") > # biocLite("devtools") > # library(devtools) > # install_github("sneumann/xcms", ref = "xcms3") > library(BiocParallel) > mcp <- MulticoreParam() > mcp class: MulticoreParam bpisup: FALSE; bpnworkers: 4; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bptimeout: 2592000; bpprogressbar: FALSE bpRNGseed: bplogdir: NA bpresultdir: NA cluster type: FORK > register(mcp, default = TRUE) > library(xcms) Loading required package: mzR Loading required package: Rcpp Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: ProtGenerics Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > useOriginalCode(FALSE) [1] FALSE > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) 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] xcms_1.49.6 Biobase_2.33.3 ProtGenerics_1.5.1 [4] BiocGenerics_0.19.2 mzR_2.7.4 Rcpp_0.12.7 [7] BiocParallel_1.7.8 loaded via a namespace (and not attached): [1] RANN_2.5 lattice_0.20-33 codetools_0.2-14 [4] MASS_7.3-45 MassSpecWavelet_1.39.0 grid_3.3.1 [7] plyr_1.8.4 stats4_3.3.1 S4Vectors_0.11.13 [10] Matrix_1.2-7.1 splines_3.3.1 RColorBrewer_1.1-2 [13] survival_2.39-5 multtest_2.29.0 > data.path <- "/home/art/storage/renata/resin-2012/centroided" > # data.path <- "/home/art/storage/renata/resin-2012/small" > setwd(data.path) > myfiles <- list.files(path=".", pattern="*.mzML", recursive = TRUE) > format(Sys.time(), "%Y-%m-%d %X") [1] "2016-09-07 03:21:43 PM" > myset <- xcmsSet(files = myfiles, scanrange = c(1184,6046), + method="centWave", ppm=2.5, peakwidth=c(2.5,9), + mzdiff=-0.001, noise=1e5, snthresh=10 + ) Detecting mass traces at 2.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 12269 m/z ROI's. Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 4711 Peaks. Detecting mass traces at 2.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 12933 m/z ROI's. Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 7507 Peaks. Detecting mass traces at 2.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 15724 m/z ROI's. Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 5410 Peaks. Detecting mass traces at 2.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 13084 m/z ROI's. Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 5109 Peaks. Detecting mass traces at 2.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 11766 m/z ROI's. Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 3965 Peaks. Detecting mass traces at 2.5 ppm ... % finished: 0 10 20 30 40 50 60 70 80 90 100 10699 m/z ROI's. Detecting chromatographic peaks ... % finished: 0 10 20 30 40 50 60 70 80 90 100 3997 Peaks. Error: BiocParallel errors element index: 7, 8, 9, 10, 11, 12, ... first error: unable to find an inherited method for function ‘findPeaks.centWave’ for signature ‘"NULL"’ In addition: Warning message: stop worker failed: 'clear_cluster' receive data failed: reached elapsed time limit Execution halted