############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data proFIA ### ############################################################################## ############################################################################## * checking for file ‘proFIA/DESCRIPTION’ ... OK * preparing ‘proFIA’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘proFIA-vignette.Rmd’ using rmarkdown Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min 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")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.22.0 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.18.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma 1 directories have been found : mzML 6 files found in directories mzML Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Beginning band detection for C100A Create profile matrix with method 'bin' and step 1 ... OK Beginning band detection for C100B Create profile matrix with method 'bin' and step 1 ... OK Beginning band detection for C10A Create profile matrix with method 'bin' and step 1 ... OK Beginning band detection for C10B Create profile matrix with method 'bin' and step 1 ... OK Beginning band detection for C1A Create profile matrix with method 'bin' and step 1 ... OK Beginning band detection for C1B Create profile matrix with method 'bin' and step 1 ... OK processing: /home/biocbuild/bbs-3.15-bioc/R/library/plasFIA/mzML/C100A.mzML A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default Beginning band detection for C100A 5 chromatograms have been used for peak shape determination. Band filtering: 0 10 20 30 40 50 60 70 80 90 100 Signal filtering finished. 583 signals detected with an injection between: 17.0-85.2 Create profile matrix with method 'bin' and step 1 ... OK processing: /home/biocbuild/bbs-3.15-bioc/R/library/plasFIA/mzML/C100B.mzML A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default Beginning band detection for C100B 4 chromatograms have been used for peak shape determination. Band filtering: 0 10 20 30 40 50 60 70 80 90 100 Signal filtering finished. 589 signals detected with an injection between: 17.0-85.5 Create profile matrix with method 'bin' and step 1 ... OK processing: /home/biocbuild/bbs-3.15-bioc/R/library/plasFIA/mzML/C10A.mzML A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default Beginning band detection for C10A 2 chromatograms have been used for peak shape determination. Band filtering: 0 10 20 30 40 50 60 70 80 90 100 Signal filtering finished. 621 signals detected with an injection between: 17.0-74.7 Create profile matrix with method 'bin' and step 1 ... OK processing: /home/biocbuild/bbs-3.15-bioc/R/library/plasFIA/mzML/C10B.mzML A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default Beginning band detection for C10B 1 chromatograms have been used for peak shape determination. Band filtering: 0 10 20 30 40 50 60 70 80 90 100 Signal filtering finished. 587 signals detected with an injection between: 14.9-77.9 Create profile matrix with method 'bin' and step 1 ... OK processing: /home/biocbuild/bbs-3.15-bioc/R/library/plasFIA/mzML/C1A.mzML A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default Beginning band detection for C1A 3 chromatograms have been used for peak shape determination. Band filtering: 0 10 20 30 40 50 60 70 80 90 100 Signal filtering finished. 510 signals detected with an injection between: 14.9-85.3 Create profile matrix with method 'bin' and step 1 ... OK processing: /home/biocbuild/bbs-3.15-bioc/R/library/plasFIA/mzML/C1B.mzML A noise model is provided but no threshold was specified, the threshold is therefore set to 0.01 by default Beginning band detection for C1B 4 chromatograms have been used for peak shape determination. Band filtering: 0 10 20 30 40 50 60 70 80 90 100 Signal filtering finished. 521 signals detected with an injection between: 17.0-89.5 processus finished 6 samples treated 3411 peaks found. A mass interval of 0.0307m/z will be used for the density estimation. 0 :0 10 :66 20 :164 30 :243 40 :342 40 :445 50 :540 60 :620 70 :681 80 :722 90 :769 Quitting from lines 214-215 (proFIA-vignette.Rmd) Error: processing vignette 'proFIA-vignette.Rmd' failed with diagnostics: unused argument (plotL = FALSE) --- failed re-building ‘proFIA-vignette.Rmd’ SUMMARY: processing the following file failed: ‘proFIA-vignette.Rmd’ Error: Vignette re-building failed. Execution halted