Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1337/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSnbase 2.33.2 (landing page) Laurent Gatto
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the MSnbase package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: MSnbase |
Version: 2.33.2 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MSnbase_2.33.2.tar.gz |
StartedAt: 2024-12-24 00:09:14 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 00:26:42 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 1047.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSnbase.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MSnbase_2.33.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MSnbase.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘MSnbase/DESCRIPTION’ ... OK * this is package ‘MSnbase’ version ‘2.33.2’ * 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 13.3.0-6ubuntu2~24.04) 13.3.0’ * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 5.5Mb sub-directories of 1Mb or more: R 1.9Mb data 1.7Mb * 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] (ORCID: <https://orcid.org/0000-0002-1520-2268>) Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre] (ORCID: <https://orcid.org/0000-0002-6977-7147>) Sebastian Gibb <mail@sebastiangibb.de> [aut, cre] (ORCID: <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 code 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 whether startup messages can be suppressed ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: Chromatogram-class.Rd: closest FeaturesOfInterest-class.Rd: Versioned-class MIAPE-class.Rd: MIAME-class, MIAxE-class, Versioned-class MSnExp-class.Rd: AnnotatedDataFrame-class, phenoData, eSet-class, featureData, experimentData, protocolData, Versions-class, VersionedBiobase-class, Versioned-class, isolationWindow MSnProcess-class.Rd: Versioned-class MSnSet-class.Rd: eSet-class, ExpressionSet-class, AnnotatedDataFrame-class, AssayData-class, exprs, assayData, phenoData, featureData, experimentData, protocolData, Versions-class, VersionedBiobase-class, Versioned-class, impute, meanSdPlot, ma.plot, mva.pairs MSnSetList-class.Rd: AnnotatedDataFrame-class MSpectra.Rd: mcols, DataFrame, SimpleList OnDiskMSnExp-class.Rd: AnnotatedDataFrame-class, phenoData, featureData, experimentData, eSet-class, protocolData, Versions-class, VersionedBiobase-class, Versioned-class ProcessingStep-class.Rd: Versioned-class ReporterIons-class.Rd: Versioned-class Spectrum-class.Rd: Versioned-class Spectrum1-class.Rd: Versioned-class Spectrum2-class.Rd: Versioned-class combineFeatures.Rd: impute combineSpectra.Rd: bpparam extractSpectraData.Rd: DataFrame normToReference.Rd: exprs normalise-methods.Rd: vsn2 pSet-class.Rd: eSet-class, AnnotatedDataFrame-class, phenoData, featureData, experimentData, protocolData, Versions-class, VersionedBiobase-class, Versioned-class plotMzDelta-methods.Rd: geom_histogram readMSData.Rd: AnnotatedDataFrame-class readMSnSet.Rd: readExpressionSet, read.AnnotatedDataFrame, read.MIAME readMgfData.Rd: AnnotatedDataFrame-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed chromatogram-MSnExp-method 12.852 1.003 13.857 OnDiskMSnExp-class 8.230 0.254 8.499 estimateMzResolution 5.624 0.276 5.886 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/MSnbase.Rcheck/00check.log’ for details.
MSnbase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MSnbase ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘MSnbase’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -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-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -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++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -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; | ^~~ utils.c: 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++17 -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-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 ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra” in method for ‘coerce’ with signature ‘"Spectra","MSpectra"’: no definition for class “Spectra” 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 ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra” in method for ‘coerce’ with signature ‘"Spectra","MSpectra"’: no definition for class “Spectra” 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
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 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 2.33.2 Visit https://lgatto.github.io/MSnbase/ to get started. Consider switching to the 'R for Mass Spectrometry' packages - see https://RforMassSpectrometry.org for details. 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 Dec 24 00:16:02 2024] MSnbase version: 2.33.2 - - - 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 Dec 24 00:20:19 2024 MSnbase version: 2.33.2 - - - 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 Dec 24 00:20:20 2024 MSnbase version: 2.33.2 - - - 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)' Object of class "FeaturesOfInterest" Created on Tue Dec 24 00:20:37 2024 Description: small foi 3 features of interest: P20353, P53501, Q7KU78 Traceable object of class "FeaturesOfInterest" Created on Tue Dec 24 00:20:37 2024 Description: my description 10 features of interest: P20353, P53501 ... Q9VCK0, Q9VIU7 A collection of 1 features of interest. A collection of 10 features of interest. MSpectra with 3 spectra and 1 metadata column(s): msLevel rtime peaksCount | id 1 2 NA 3 | 1 2 2 1.23245 4 | 2 3 1 1.23245 5 | 3 MSpectra with 3 spectra and 1 metadata column(s): msLevel rtime peaksCount | id <integer> <numeric> <integer> | <integer> 1 2 NA 3 | 1 2 2 1.23245 4 | 2 3 1 1.23245 5 | 3 MSpectra with 3 spectra and 1 metadata column(s): msLevel rtime peaksCount | id <integer> <numeric> <integer> | <integer> 1 2 NA 3 | 1 2 2 1.23245 4 | 2 3 1 1.23245 5 | 3 reading dummyiTRAQ.mzid... DONE! [ FAIL 0 | WARN 1092 | SKIP 12 | PASS 2371 ] ══ Skipped tests (12) ══════════════════════════════════════════════════════════ • empty test (12): 'test_MzTab.R:108:1', 'test_MzTab.R:123:1', 'test_OnDiskMSnExp2.R:132:1', 'test_fdata-selection.R:71:1', 'test_functions-Chromatogram.R:39:1', 'test_functions-MSpectra.R:72:1', 'test_functions-plotting.R:1:1', 'test_io.R:3:1', 'test_methods-MChromatograms.R:155:1', 'test_readMSData2.R:51:1', 'test_readMSData2.R:63:1', 'test_readMSData2.R:80:1' [ FAIL 0 | WARN 1092 | SKIP 12 | PASS 2371 ] Warning message: In for (i in seq_along(extends)) { : closing unused connection 4 (/tmp/RtmpysJZZU/file19b676479dce82) > > proc.time() user system elapsed 462.068 40.116 491.364
MSnbase.Rcheck/MSnbase-Ex.timings
name | user | system | elapsed | |
Chromatogram-class | 0.082 | 0.005 | 0.087 | |
FeatComp-class | 0.204 | 0.007 | 0.214 | |
FeaturesOfInterest-class | 0.045 | 0.004 | 0.047 | |
MChromatograms-class | 0.140 | 0.005 | 0.147 | |
MSmap-class | 0.001 | 0.000 | 0.001 | |
MSnExp-class | 1.047 | 0.084 | 1.134 | |
MSnProcess-class | 0.001 | 0.000 | 0.001 | |
MSnSet-class | 3.746 | 0.119 | 3.864 | |
MSnSetList-class | 0.901 | 0.014 | 0.916 | |
MSpectra | 0.071 | 0.013 | 0.085 | |
MzTab-class | 1.143 | 0.030 | 3.115 | |
OnDiskMSnExp-class | 8.230 | 0.254 | 8.499 | |
ProcessingStep-class | 0.001 | 0.001 | 0.002 | |
ReporterIons-class | 0.009 | 0.001 | 0.010 | |
TMT6 | 0.006 | 0.002 | 0.007 | |
addIdentificationData-methods | 0.954 | 0.002 | 0.957 | |
aggvar | 3.733 | 0.029 | 3.763 | |
averageMSnSet | 4.397 | 0.247 | 4.652 | |
bin-methods | 1.707 | 0.218 | 1.926 | |
calculateFragments-methods | 1.378 | 0.247 | 1.625 | |
chromatogram-MSnExp-method | 12.852 | 1.003 | 13.857 | |
clean-methods | 0.110 | 0.001 | 0.111 | |
combineFeatures | 0.921 | 0.012 | 0.933 | |
combineSpectra | 4.292 | 0.203 | 4.495 | |
combineSpectraMovingWindow | 2.525 | 0.154 | 2.679 | |
commonFeatureNames | 0.230 | 0.004 | 0.234 | |
compareSpectra-methods | 0.151 | 0.006 | 0.157 | |
consensusSpectrum | 0.025 | 0.002 | 0.027 | |
estimateMzResolution | 5.624 | 0.276 | 5.886 | |
estimateMzScattering | 1.496 | 0.055 | 1.551 | |
estimateNoise-method | 0.008 | 0.000 | 0.009 | |
extractPrecSpectra-methods | 1.227 | 0.001 | 1.228 | |
extractSpectraData | 2.715 | 0.227 | 2.946 | |
fData-utils | 0.311 | 0.008 | 0.320 | |
factorsAsStrings | 0.010 | 0.001 | 0.011 | |
featureCV | 0.029 | 0.002 | 0.031 | |
fillUp | 0.004 | 0.000 | 0.004 | |
formatRt | 0.001 | 0.000 | 0.001 | |
getVariableName | 0.003 | 0.000 | 0.004 | |
hasSpectraOrChromatograms | 0.322 | 0.041 | 0.367 | |
iPQF | 0.214 | 0.003 | 0.217 | |
iTRAQ4 | 0.009 | 0.002 | 0.010 | |
imageNA2 | 2.629 | 0.035 | 2.665 | |
impute | 0.906 | 0.010 | 0.916 | |
isCentroidedFromFile | 2.617 | 0.160 | 2.771 | |
itraqdata | 0.034 | 0.001 | 0.035 | |
listOf | 0.001 | 0.000 | 0.001 | |
makeCamelCase | 0 | 0 | 0 | |
makeNaData | 0.316 | 0.004 | 0.320 | |
meanMzInts | 0.041 | 0.002 | 0.043 | |
missing-data | 2.498 | 0.034 | 2.532 | |
mzRident2dfr | 0.027 | 0.001 | 0.027 | |
nFeatures | 0.585 | 0.007 | 0.592 | |
nQuants | 0.099 | 0.001 | 0.100 | |
naplot | 0.059 | 0.001 | 0.059 | |
navMS | 3.173 | 0.043 | 3.270 | |
normToReference | 0.142 | 0.002 | 0.145 | |
normalise-methods | 0.011 | 0.001 | 0.012 | |
npcv | 0.004 | 0.000 | 0.004 | |
pSet-class | 0.002 | 0.000 | 0.002 | |
pickPeaks-method | 0.272 | 0.003 | 0.275 | |
plot-methods | 4.126 | 0.026 | 4.152 | |
plot2d-methods | 0.429 | 0.015 | 0.444 | |
plotDensity-methods | 0.589 | 0.010 | 0.599 | |
plotMzDelta-methods | 0.650 | 0.021 | 0.671 | |
plotNA-methods | 0.356 | 0.000 | 0.356 | |
plotSpectrumSpectrum-methods | 1.555 | 0.047 | 1.602 | |
precSelection | 0.006 | 0.002 | 0.008 | |
purityCorrect-methods | 0.015 | 0.002 | 0.017 | |
quantify-methods | 2.756 | 0.062 | 2.818 | |
readMSData | 2.570 | 0.058 | 2.627 | |
readMSnSet | 0.068 | 0.003 | 0.072 | |
readMgfData | 1.343 | 0.024 | 1.367 | |
readMzIdData | 0.598 | 0.704 | 1.303 | |
readMzTabData | 0.903 | 0.016 | 0.981 | |
readMzTabData_v0.9 | 0.193 | 0.004 | 0.472 | |
readSRMData | 1.092 | 0.070 | 1.163 | |
reduce-data.frame-method | 0.011 | 0.002 | 0.013 | |
removeNoId-methods | 1.554 | 0.019 | 1.574 | |
removePeaks-methods | 0.465 | 0.016 | 0.479 | |
removeReporters-methods | 0.465 | 0.018 | 0.483 | |
selectFeatureData | 1.410 | 0.029 | 1.439 | |
smooth-methods | 0.172 | 0.001 | 0.173 | |
trimMz-methods | 0.127 | 0.000 | 0.127 | |
writeMgfData-methods | 1.363 | 0.020 | 1.383 | |