Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:16 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the MSnbase package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSnbase.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1266/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSnbase 2.25.1 (landing page) Laurent Gatto
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: MSnbase |
Version: 2.25.1 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MSnbase_2.25.1.tar.gz |
StartedAt: 2023-02-07 09:11:11 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 09:32:05 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 1253.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: MSnbase.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MSnbase_2.25.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘MSnbase/DESCRIPTION’ ... OK * this is package ‘MSnbase’ version ‘2.25.1’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MSnbase’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: R 1.8Mb data 1.9Mb libs 1.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Laurent Gatto <laurent.gatto@uclouvain.be> [aut, cre] (<https://orcid.org/0000-0002-1520-2268>) Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre] (<https://orcid.org/0000-0002-6977-7147>) Sebastian Gibb <mail@sebastiangibb.de> [aut, cre] (<https://orcid.org/0000-0001-7406-4443>) * 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 dependencies in R code ... NOTE ':::' calls which should be '::': ‘S4Vectors:::makeClassinfoRowForCompactPrinting’ ‘S4Vectors:::makePrettyMatrixForCompactPrinting’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘Biobase:::.showAnnotatedDataFrame’ ‘MALDIquant:::.estimateNoise’ ‘MALDIquant:::.localMaxima’ ‘MALDIquant:::.movingAverage’ ‘MALDIquant:::.savitzkyGolay’ ‘mzR:::.hasChromatograms’ ‘mzR:::.hasSpectra’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘MSnbase-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: isCentroidedFromFile > ### Title: Get mode from mzML data file > ### Aliases: isCentroidedFromFile > > ### ** Examples > > library("msdata") > f <- proteomics(full.names = TRUE, + pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz") > x <- readMSData(f, mode = "onDisk") Killed * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: MSnbase version: 2.25.1 - - - Meta data - - - phenoData rowNames: dummyiTRAQ.mzXML varLabels: sampleNames varMetadata: labelDescription Loaded from: dummyiTRAQ.mzXML protocolData: none featureData featureNames: F1.S1 F1.S2 ... F1.S5 (5 total) fvarLabels: spectrum fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘v01-MSnbase-demo.Rmd’ using ‘UTF-8’... OK ‘v02-MSnbase-io.Rmd’ using ‘UTF-8’... OK ‘v03-MSnbase-centroiding.Rmd’ using ‘UTF-8’... OK ‘v04-benchmarking.Rmd’ using ‘UTF-8’... OK ‘v05-MSnbase-development.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘v01-MSnbase-demo.Rmd’ using rmarkdown Killed --- re-building ‘v02-MSnbase-io.Rmd’ using rmarkdown --- finished re-building ‘v02-MSnbase-io.Rmd’ --- re-building ‘v03-MSnbase-centroiding.Rmd’ using rmarkdown The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck/vign_test/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/serine-plot-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck/vign_test/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/serine-spectrum24-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck/vign_test/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/simple-pickPeaks-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck/vign_test/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/proline-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck/vign_test/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/smoothSG-pp-serine-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck/vign_test/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/smoothSG-pp-proline-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck/vign_test/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/proline-rtsmooth-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck/vign_test/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/refineMz-serine-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck/vign_test/MSnbase/vignettes/v03-MSnbase-centroiding_files/figure-html/refineMz-proline-1.png" but not available. --- finished re-building ‘v03-MSnbase-centroiding.Rmd’ --- re-building ‘v04-benchmarking.Rmd’ using rmarkdown The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck/vign_test/MSnbase/vignettes/v04-benchmarking_files/figure-html/plot1-1.png" but not available. --- finished re-building ‘v04-benchmarking.Rmd’ --- re-building ‘v05-MSnbase-development.Rmd’ using rmarkdown --- finished re-building ‘v05-MSnbase-development.Rmd’ SUMMARY: processing the following file failed: ‘v01-MSnbase-demo.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/MSnbase.Rcheck/00check.log’ for details.
MSnbase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MSnbase ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘MSnbase’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Spectrum1_class.c -o Spectrum1_class.o Spectrum1_class.c:8:13: warning: ‘_new_Spectrum1’ defined but not used [-Wunused-function] 8 | static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt, | ^~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Spectrum2_class.c -o Spectrum2_class.o Spectrum2_class.c:9:13: warning: ‘_new_Spectrum2’ defined but not used [-Wunused-function] 9 | static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt, | ^~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o utils.c: In function ‘compar_double_dd_for_stable_asc_order’: utils.c:92:15: warning: unused variable ‘ret’ [-Wunused-variable] 92 | int i1, i2, ret; | ^~~ utils.c: In function ‘compar_double_dd_for_stable_desc_order’: utils.c:107:15: warning: unused variable ‘ret’ [-Wunused-variable] 107 | int i1, i2, ret; | ^~~ utils.c: In function ‘compar_double_asc_order’: utils.c:123:18: warning: unused variable ‘ret’ [-Wunused-variable] 123 | double d1, d2, ret; | ^~~ utils.c: In function ‘compar_double_desc_order’: utils.c:133:18: warning: unused variable ‘ret’ [-Wunused-variable] 133 | double d1, d2, ret; | ^~~ At top level: utils.c:131:12: warning: ‘compar_double_desc_order’ defined but not used [-Wunused-function] 131 | static int compar_double_desc_order(const void *p1, const void *p2) | ^~~~~~~~~~~~~~~~~~~~~~~~ utils.c:121:12: warning: ‘compar_double_asc_order’ defined but not used [-Wunused-function] 121 | static int compar_double_asc_order(const void *p1, const void *p2) | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-MSnbase/00new/MSnbase/libs ** R ** data *** moving datasets to lazyload DB Creating a new generic function for ‘trimws’ in package ‘MSnbase’ in method for ‘coerce’ with signature ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra” in method for ‘plotMzDelta’ with signature ‘"mzRramp"’: no definition for class “mzRramp” ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘trimws’ in package ‘MSnbase’ in method for ‘coerce’ with signature ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment” in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra” in method for ‘plotMzDelta’ with signature ‘"mzRramp"’: no definition for class “mzRramp” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSnbase)
MSnbase.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. 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. > # setting R_TESTS to empty string because of > # https://github.com/hadley/testthat/issues/144 > # revert this when that issue in R is fixed. > Sys.setenv("R_TESTS" = "") > library("testthat") > library("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: 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 2.25.1 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws > setMSnbaseVerbose(FALSE) > ## register(SerialParam()) ## see issue 205 > > ## Erwinia > f <- msdata::proteomics(full.names = TRUE, + pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz") > tmt_erwinia_in_mem_ms1 <- readMSData(f, msLevel = 1) > tmt_erwinia_in_mem_ms2 <- readMSData(f, msLevel = 2) > tmt_erwinia_on_disk <- readMSData(f, mode = "onDisk") > tmt_erwinia_on_disk_ms1 <- readMSData(f, msLevel = 1, mode = "onDisk") > tmt_erwinia_on_disk_ms2 <- readMSData(f, msLevel = 2, mode = "onDisk") > ## subset by rt > tmt_im_ms1_sub <- filterRt(tmt_erwinia_in_mem_ms1, c(1200, 1250)) > tmt_im_ms2_sub <- filterRt(tmt_erwinia_in_mem_ms2, c(1200, 1250)) > tmt_od_sub <- filterRt(tmt_erwinia_on_disk, c(1200, 1250)) > tmt_od_ms1_sub <- filterRt(tmt_erwinia_on_disk_ms1, c(1200, 1250)) > tmt_od_ms2_sub <- filterRt(tmt_erwinia_on_disk_ms2, c(1200, 1250)) > > ## microtofq > f <- c(system.file("microtofq/MM14.mzML", package = "msdata"), + system.file("microtofq/MM8.mzML", package = "msdata")) > microtofq_in_mem_ms1 <- readMSData(f, msLevel = 1) > microtofq_on_disk_ms1 <- readMSData(f, msLevel = 1, mode = "onDisk") > microtofq_on_disk <- readMSData(f, mode = "onDisk") > > ## extdata mzML > f <- dir(system.file(package = "MSnbase", dir = "extdata"), + full.name = TRUE, pattern = "mzXML$") > extdata_mzXML_in_mem_ms2 <- readMSData(f, verbose = FALSE, centroided. = FALSE) > extdata_mzXML_on_disk <- readMSData(f, centroided. = FALSE, mode = "onDisk") > extdata_mzXML_on_disk_ms2 <- readMSData(f, msLevel = 2, centroided. = FALSE, mode = "onDisk") > > sf <- dir(system.file("sciex", package = "msdata"), full.names = TRUE) > sciex <- readMSData(sf, mode = "onDisk") > > test_check("MSnbase") Experiment data Experimenter name: Laurent Gatto Laboratory: Cambridge Centre for Proteomics (CCP) Contact information: Laurent Gatto Contact email: lg390@cam.ac.uk Title: Example 'MSnExp' data set URL: PMIDs: No abstract available. Instrument : Model: test (1) Manufacturer: Customisations: Use 'msInfo(object)' for more MIAPE-MS information. Experiment data Experimenter name: Laurent Gatto Laboratory: Cambridge Centre for Proteomics (CCP) Contact information: Laurent Gatto Contact email: lg390@cam.ac.uk Title: Example 'MSnExp' data set URL: PMIDs: No abstract available. notes: Note1: First note MIAPE-MS information: 1. General features: Date stamp: Contact: Laurent Gatto Name: Laurent Gatto Laboratory: Cambridge Centre for Proteomics (CCP) Instument model: test Manufacturer: Customisations: Software: Version: Switching: Param file: 2. Ion source Source: Source details: 3. Post-source componentry Analyzer: Analyzer details: Collision gas: Pressure: bars Energy: Detector type: Sensitivity: Object of class "MSmap" Map [75, 401] [1] Retention time: 30:01 - 34:58 [2] M/Z: 521 - 523 (res 0.005) Object of class "MSmap" Map [401, 75] [1] M/Z: 521 - 523 (res 0.005) [2] Retention time: 30:01 - 34:58 Object of class "MzTab". Description: mzTab example file for reporting a summary report of quantification data quantified on the protein level Mode: Complete Type: Quantification Available data: Proteins PSMs Object of class "MzTab". Description: Mode: Type: Available data: SmallMolecules Object of class "MzTab". Description: Mode: Type: Available data: SmallMolecules Instance of class 'MSnSetList' containig 3 objects. MSn experiment data ("OnDiskMSnExp") Object size in memory: 0.26 Mb - - - Spectra data - - - MS level(s): 1 2 Number of spectra: 509 MSn retention times: 18:28 - 22:03 minutes - - - Processing information - - - Data loaded [Tue Feb 7 09:16:45 2023] MSnbase version: 2.25.1 - - - Meta data - - - phenoData rowNames: TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz varLabels: sampleNames varMetadata: labelDescription Loaded from: TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz protocolData: none featureData featureNames: F1.S001 F1.S002 ... F1.S509 (509 total) fvarLabels: fileIdx spIdx ... spectrum (35 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Object of class "ReporterIons" TMT10HCD: '10-plex TMT HCD' with 10 reporter ions - [126] 126.1277 +/- 0.002 (#8DD3C7) - [127N] 127.1248 +/- 0.002 (#FFFFB3) - [127C] 127.1311 +/- 0.002 (#BEBADA) - [128N] 128.1281 +/- 0.002 (#FB8072) - [128C] 128.1344 +/- 0.002 (#80B1D3) - [129N] 129.1315 +/- 0.002 (#FDB462) - [129C] 129.1378 +/- 0.002 (#B3DE69) - [130N] 130.1348 +/- 0.002 (#FCCDE5) - [130C] 130.1411 +/- 0.002 (#D9D9D9) - [131] 131.1382 +/- 0.002 (#BC80BD) Object of class "Spectrum1" Retention time: 0:00 MSn level: 1 Total ion count: 684 Polarity: 1 MSn experiment data ("MSnExp") Object size in memory: 0.18 Mb - - - Spectra data - - - MS level(s): 2 Number of spectra: 5 MSn retention times: 25:01 - 25:02 minutes - - - Processing information - - - Data loaded: Tue Feb 7 09:28:44 2023 MSnbase version: 2.25.1 - - - Meta data - - - phenoData rowNames: dummyiTRAQ.mzXML varLabels: sampleNames varMetadata: labelDescription Loaded from: dummyiTRAQ.mzXML protocolData: none featureData featureNames: F1.S1 F1.S2 ... F1.S5 (5 total) fvarLabels: spectrum fvarMetadata: labelDescription experimentData: use 'experimentData(object)' MSn experiment data ("MSnExp") Object size in memory: 0.2 Mb - - - Spectra data - - - MS level(s): 2 Number of spectra: 5 MSn retention times: 25:01 - 25:02 minutes - - - Processing information - - - Data loaded: Tue Feb 7 09:28:44 2023 MSnbase version: 2.25.1 - - - Meta data - - - phenoData rowNames: dummyiTRAQ.mzXML varLabels: sampleNames varMetadata: labelDescription Loaded from: dummyiTRAQ.mzXML protocolData: none featureData featureNames: F1.S1 F1.S2 ... F1.S5 (5 total) fvarLabels: spectrum fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Killed
MSnbase.Rcheck/MSnbase-Ex.timings
name | user | system | elapsed | |
Chromatogram-class | 0.105 | 0.004 | 0.109 | |
FeatComp-class | 0.241 | 0.008 | 0.514 | |
FeaturesOfInterest-class | 0.057 | 0.004 | 0.093 | |
MChromatograms-class | 0.169 | 0.000 | 0.169 | |
MSmap-class | 0.001 | 0.000 | 0.000 | |
MSnExp-class | 0.629 | 0.000 | 0.643 | |
MSnProcess-class | 0.001 | 0.000 | 0.001 | |
MSnSet-class | 10.026 | 0.161 | 11.814 | |
MSnSetList-class | 3.093 | 0.092 | 3.538 | |
MSpectra | 0.108 | 0.004 | 0.112 | |
MzTab-class | 1.961 | 0.035 | 15.515 | |
OnDiskMSnExp-class | 9.550 | 0.904 | 16.878 | |
ProcessingStep-class | 0.002 | 0.000 | 0.003 | |
ReporterIons-class | 0.013 | 0.000 | 0.021 | |
TMT6 | 0.008 | 0.000 | 0.007 | |
addIdentificationData-methods | 0.966 | 0.012 | 1.682 | |
aggvar | 5.513 | 0.030 | 6.186 | |
averageMSnSet | 7.638 | 0.167 | 11.405 | |
bin-methods | 0.357 | 0.000 | 0.430 | |
calculateFragments-methods | 1.284 | 0.129 | 2.325 | |
chromatogram-MSnExp-method | 14.592 | 0.293 | 15.466 | |
clean-methods | 0.174 | 0.000 | 0.199 | |
combineFeatures | 1.284 | 0.004 | 1.290 | |
combineSpectra | 4.897 | 0.048 | 5.074 | |
combineSpectraMovingWindow | 3.349 | 0.020 | 3.384 | |
commonFeatureNames | 0.346 | 0.004 | 0.354 | |
compareSpectra-methods | 0.239 | 0.000 | 0.240 | |
consensusSpectrum | 0.039 | 0.000 | 0.040 | |
estimateMzResolution | 5.460 | 0.235 | 5.729 | |
estimateMzScattering | 1.648 | 0.008 | 1.656 | |
estimateNoise-method | 0.011 | 0.001 | 0.012 | |
extractPrecSpectra-methods | 1.184 | 0.008 | 1.215 | |
extractSpectraData | 2.366 | 0.192 | 2.788 | |
fData-utils | 0.404 | 0.008 | 0.422 | |
factorsAsStrings | 0.010 | 0.004 | 0.015 | |
featureCV | 0.025 | 0.000 | 0.025 | |
fillUp | 0.004 | 0.000 | 0.003 | |
formatRt | 0 | 0 | 0 | |
get.amino.acids | 0.000 | 0.004 | 0.003 | |
get.atomic.mass | 0 | 0 | 0 | |
getVariableName | 0.004 | 0.000 | 0.003 | |
hasSpectraOrChromatograms | 0.384 | 0.016 | 0.411 | |
iPQF | 0.332 | 0.004 | 0.339 | |
iTRAQ4 | 0.013 | 0.000 | 0.013 | |
imageNA2 | 3.943 | 0.032 | 4.057 | |
impute | 1.777 | 0.056 | 2.038 | |