############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:msPurity.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings msPurity_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/msPurity.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘msPurity/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘msPurity’ version ‘1.28.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘msPurity’ can be installed ... OK * checking installed package size ... NOTE installed size is 19.6Mb sub-directories of 1Mb or more: extdata 18.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘Rcpp’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE addGenericMS1LookupResults: no visible global function definition for ‘count.fields’ addMetFragResults: no visible global function definition for ‘count.fields’ addSiriusResults: no visible global function definition for ‘count.fields’ assessPuritySingle: no visible binding for global variable ‘parallel’ combineAnnotations: no visible binding for global variable ‘compoundDbname’ createDatabase: no visible global function definition for ‘featureValues’ create_database : getxcmsSetObject: no visible global function definition for ‘sampclass<-’ dimsPredictPuritySingleMz: no visible binding for global variable ‘mtchi’ dimsPredictPuritySingleMz: no visible binding for global variable ‘alli’ dimsPredictPuritySingleMz: no visible binding for global variable ‘mtch’ filterPrecursors: no visible binding for global variable ‘l_speakmetaFiltered’ filterSMeta: no visible binding for global variable ‘accession’ filterSMeta: no visible binding for global variable ‘inPurity’ filterSMeta: no visible global function definition for ‘lower’ filterSMeta: no visible binding for global variable ‘polarity’ filterSMeta: no visible binding for global variable ‘instrument_type’ filterSMeta: no visible binding for global variable ‘instrument’ filterSMeta: no visible binding for global variable ‘name.y’ filterSMeta: no visible binding for global variable ‘retention_time’ filterSMeta: no visible binding for global variable ‘grpid’ filterSMeta: no visible binding for global variable ‘pid’ filterSMeta: no visible binding for global variable ‘spectrum_type’ flag_remove: no visible global function definition for ‘PeakDensityParam’ flag_remove: no visible global function definition for ‘chromPeaks<-’ flag_remove: no visible global function definition for ‘chromPeaks’ getScanPeaksSqlite: no visible binding for global variable ‘pid’ getScanPeaksSqlite: no visible binding for global variable ‘library_spectra_meta_id’ getScanPeaksSqlite: no visible binding for global variable ‘pass_flag’ getScanPeaksSqlite: no visible binding for global variable ‘type’ getScanPeaksSqlite: no visible binding for global variable ‘spectraType’ getScanPeaksSqlite: no visible binding for global variable ‘ra’ getSmeta: no visible binding for global variable ‘pid’ get_topn: no visible binding for global variable ‘topn’ matchi: no visible global function definition for ‘match_factor’ plotPurity: no visible binding for global variable ‘idx’ plotPurity: no visible binding for global variable ‘purity’ plotPurity: no visible binding for global variable ‘variable’ purityA: no visible binding for global variable ‘i’ queryVlibrary: no visible binding for global variable ‘precursor_mz’ queryVlibrary: no visible binding for global variable ‘retention_time’ queryVlibrarySingle: no visible binding for global variable ‘pid’ queryVlibrarySingle: no visible binding for global variable ‘library_spectra_meta_id’ sum_calc_peaklist: no visible global function definition for ‘phenoData’ averageSpectra,purityD: no visible binding for global variable ‘i’ subtract,purityD: no visible binding for global variable ‘i’ Undefined global functions or variables: PeakDensityParam accession alli chromPeaks chromPeaks<- compoundDbname count.fields featureValues grpid i idx inPurity instrument instrument_type l_speakmetaFiltered library_spectra_meta_id lower match_factor mtch mtchi name.y parallel pass_flag phenoData pid polarity precursor_mz purity ra retention_time sampclass<- spectraType spectrum_type topn type variable Consider adding importFrom("utils", "count.fields") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘msPurity-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: createDatabase > ### Title: Create database > ### Aliases: createDatabase > > ### ** Examples > > library(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, aperm, 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: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches 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 2.28.0 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 4.0.0 Attaching package: ‘xcms’ The following object is masked from ‘package:stats’: sigma > library(MSnbase) > library(magrittr) Attaching package: ‘magrittr’ The following object is masked from ‘package:msPurity’: subtract > #====== XCMS ================================= > ## Read in MS data > msmsPths <- list.files(system.file("extdata", "lcms", "mzML", + package="msPurityData"), full.names = TRUE, pattern = "MSMS") > ms_data = readMSData(msmsPths, mode = 'onDisk', msLevel. = 1) > > ## Find peaks in each file > cwp <- CentWaveParam(snthresh = 5, noise = 100, ppm = 10, peakwidth = c(3, 30)) > xcmsObj <- xcms::findChromPeaks(ms_data, param = cwp) Detecting mass traces at 10 ppm ... OK Detecting chromatographic peaks in 16425 regions of interest ... OK: 9114 found. Detecting mass traces at 10 ppm ... OK Detecting chromatographic peaks in 16399 regions of interest ... OK: 9185 found. > > ## Optionally adjust retention time > xcmsObj <- adjustRtime(xcmsObj , param = ObiwarpParam(binSize = 0.6)) Sample number 1 used as center sample. Aligning LCMSMS_2.mzML against LCMSMS_1.mzML ... OK Applying retention time adjustment to the identified chromatographic peaks ... OK > > ## Group features across samples > pdp <- PeakDensityParam(sampleGroups = c(1, 1), minFraction = 0, bw = 30) > xcmsObj <- groupChromPeaks(xcmsObj , param = pdp) > > #====== msPurity ============================ > pa <- purityA(msmsPths) > pa <- frag4feature(pa = pa, xcmsObj = xcmsObj) * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 1716124 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: [1] "#########################################################################" [1] "## Checking averageAllFragSpectra (with filter) (xcms v2 functions) ##" [1] "#########################################################################" [1] "\n" [1] "########################################################" [1] "## Checking createMSP functions (xcms v2 functions) ##" [1] "########################################################" [1] "\n" [1] "########################################################" [1] "## checking flag and remove (lc-ms) ##" [1] "########################################################" [1] "\n" [1] "#######################################################" [1] "## Checking database (new schema) ##" [1] "#######################################################" * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 4 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/msPurity.Rcheck/00check.log’ for details.