Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:06:16 -0400 (Wed, 15 Apr 2020).
Package 1101/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
MSnbase 2.12.0 Laurent Gatto
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | TIMEOUT | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: MSnbase |
Version: 2.12.0 |
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MSnbase_2.12.0.tar.gz |
StartedAt: 2020-04-15 00:57:56 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 01:12:27 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 871.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSnbase.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MSnbase_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/MSnbase.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSnbase/DESCRIPTION’ ... OK * this is package ‘MSnbase’ version ‘2.12.0’ * 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 * checking installed package size ... NOTE installed size is 6.1Mb 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] * 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 Unexported objects imported by ':::' calls: ‘Biobase:::.showAnnotatedDataFrame’ ‘MALDIquant:::.estimateNoise’ ‘MALDIquant:::.localMaxima’ ‘MALDIquant:::.movingAverage’ ‘MALDIquant:::.savitzkyGolay’ ‘S4Vectors:::makeClassinfoRowForCompactPrinting’ ‘S4Vectors:::makePrettyMatrixForCompactPrinting’ ‘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 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 or elapsed time > 5s user system elapsed estimateMzScattering 22.092 0.048 22.180 chromatogram-MSnExp-method 10.288 1.040 11.166 MSnSet-class 9.796 0.224 10.041 OnDiskMSnExp-class 8.212 0.104 8.742 averageMSnSet 6.580 0.032 6.812 estimateMzResolution 6.060 0.228 6.290 combineSpectra 4.704 0.140 5.264 MzTab-class 1.328 0.060 5.595 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.10-bioc/meat/MSnbase.Rcheck/00check.log’ for details.
MSnbase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MSnbase ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘MSnbase’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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] static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt, ^~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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] static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt, ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-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] 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] int i1, i2, ret; ^~~ utils.c: In function ‘compar_double_asc_order’: utils.c:123:18: warning: unused variable ‘ret’ [-Wunused-variable] double d1, d2, ret; ^~~ utils.c: In function ‘compar_double_desc_order’: utils.c:133:18: warning: unused variable ‘ret’ [-Wunused-variable] double d1, d2, ret; ^~~ At top level: utils.c:131:12: warning: ‘compar_double_desc_order’ defined but not used [-Wunused-function] 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] static int compar_double_asc_order(const void *p1, const void *p2) ^~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-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-3.10-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.10-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” ** 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” ** 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 version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 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. 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: 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, 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, 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:base': expand.grid Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.12.0 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: 30:1 - 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: 30:1 - 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 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 - 22:3 minutes - - - Processing information - - - Data loaded [Wed Apr 15 01:03:09 2020] MSnbase version: 2.12.0 - - - 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: 0:0 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: 25:1 - 25:2 minutes - - - Processing information - - - Data loaded: Wed Apr 15 01:07:55 2020 MSnbase version: 2.12.0 - - - 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: 0.21 Mb - - - Spectra data - - - MS level(s): 2 Number of spectra: 5 MSn retention times: 25:1 - 25:2 minutes - - - Processing information - - - Data loaded: Wed Apr 15 01:07:56 2020 MSnbase version: 2.12.0 - - - 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 Wed Apr 15 01:08:20 2020 Description: small foi 3 features of interest: P20353, P53501, Q7KU78 Traceable object of class "FeaturesOfInterest" Created on Wed Apr 15 01:08:20 2020 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. Spectra 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 Spectra 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 Spectra 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! Iterations of EM: 1...2...3...4...5...6...7...8...9...10...11... [1] 0.07947339 Error in x$.self$finalize() : attempt to apply non-function ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 2239 | SKIPPED: 9 | WARNINGS: 1082 | FAILED: 0 ] > > proc.time() user system elapsed 545.104 15.696 562.349
MSnbase.Rcheck/MSnbase-Ex.timings
name | user | system | elapsed | |
Chromatogram-class | 0.036 | 0.004 | 0.037 | |
Chromatograms-class | 0.160 | 0.004 | 0.167 | |
FeatComp-class | 0.240 | 0.012 | 0.319 | |
FeaturesOfInterest-class | 0.076 | 0.000 | 0.073 | |
MSmap-class | 0 | 0 | 0 | |
MSnExp-class | 0.600 | 0.004 | 0.605 | |
MSnProcess-class | 0.000 | 0.000 | 0.001 | |
MSnSet-class | 9.796 | 0.224 | 10.041 | |
MSnSetList-class | 3.496 | 0.052 | 3.563 | |
MzTab-class | 1.328 | 0.060 | 5.595 | |
OnDiskMSnExp-class | 8.212 | 0.104 | 8.742 | |
ProcessingStep-class | 0.004 | 0.000 | 0.005 | |
ReporterIons-class | 0.012 | 0.000 | 0.011 | |
Spectra | 0.116 | 0.000 | 0.117 | |
TMT6 | 0.008 | 0.000 | 0.010 | |
addIdentificationData-methods | 0.924 | 0.000 | 1.008 | |
aggvar | 4.836 | 0.020 | 4.941 | |
averageMSnSet | 6.580 | 0.032 | 6.812 | |
bin-methods | 0.308 | 0.040 | 0.352 | |
calculateFragments-methods | 1.180 | 0.016 | 1.196 | |
chromatogram-MSnExp-method | 10.288 | 1.040 | 11.166 | |
clean-methods | 0.148 | 0.016 | 0.163 | |
combineFeatures | 1.464 | 0.100 | 1.567 | |
combineSpectra | 4.704 | 0.140 | 5.264 | |
combineSpectraMovingWindow | 2.540 | 0.008 | 2.549 | |
commonFeatureNames | 0.400 | 0.004 | 0.405 | |
compareSpectra-methods | 0.208 | 0.000 | 0.208 | |
consensusSpectrum | 0.032 | 0.000 | 0.033 | |
estimateMzResolution | 6.060 | 0.228 | 6.290 | |
estimateMzScattering | 22.092 | 0.048 | 22.180 | |
estimateNoise-method | 0.008 | 0.000 | 0.009 | |
exprsToRatios-methods | 0.064 | 0.000 | 0.066 | |
extractPrecSpectra-methods | 1.136 | 0.000 | 1.140 | |
fData-utils | 0.528 | 0.004 | 0.647 | |
factorsAsStrings | 0.012 | 0.004 | 0.012 | |
featureCV | 0.02 | 0.00 | 0.02 | |
fillUp | 0.008 | 0.000 | 0.006 | |
formatRt | 0.000 | 0.000 | 0.001 | |
get.amino.acids | 0.004 | 0.000 | 0.005 | |
get.atomic.mass | 0.000 | 0.000 | 0.001 | |
getVariableName | 0.008 | 0.000 | 0.005 | |
hasSpectraOrChromatograms | 0.504 | 0.028 | 0.617 | |
iPQF | 0.380 | 0.000 | 0.379 | |
iTRAQ4 | 0.012 | 0.000 | 0.012 | |
imageNA2 | 2.980 | 0.008 | 3.012 | |
impute-methods | 0.552 | 0.004 | 0.577 | |
isCentroidedFromFile | 2.772 | 0.056 | 2.829 | |
itraqdata | 0.068 | 0.004 | 0.072 | |
listOf | 0.004 | 0.000 | 0.003 | |
makeCamelCase | 0.000 | 0.000 | 0.001 | |
makeNaData | 0.744 | 0.000 | 0.742 | |
meanMzInts | 0.036 | 0.000 | 0.034 | |
missing-data | 2.492 | 0.004 | 2.500 | |
mzRident2dfr | 0.032 | 0.000 | 0.031 | |
nFeatures | 0.548 | 0.016 | 0.567 | |
nQuants | 0.176 | 0.000 | 0.178 | |
naplot | 0.108 | 0.000 | 0.109 | |
navMS | 2.492 | 0.024 | 3.257 | |
normToReference | 0.260 | 0.000 | 0.263 | |
normalise-methods | 0.020 | 0.000 | 0.019 | |
npcv | 0.008 | 0.000 | 0.006 | |
pSet-class | 0.000 | 0.000 | 0.001 | |
pickPeaks-method | 0.436 | 0.000 | 0.438 | |
plot-methods | 3.824 | 0.012 | 3.846 | |
plot2d-methods | 0.656 | 0.000 | 0.657 | |
plotDensity-methods | 0.940 | 0.000 | 0.942 | |
plotMzDelta-methods | 1.672 | 0.004 | 1.679 | |
plotNA-methods | 0.444 | 0.004 | 0.448 | |
plotSpectrumSpectrum-methods | 1.352 | 0.000 | 1.350 | |
precSelection | 0.004 | 0.000 | 0.006 | |
purityCorrect-methods | 0.020 | 0.000 | 0.029 | |
quantify-methods | 3.348 | 0.756 | 2.518 | |
readMSData | 2.124 | 0.004 | 2.131 | |
readMSnSet | 0.112 | 0.004 | 0.157 | |
readMgfData | 2.240 | 0.028 | 2.288 | |
readMzIdData | 1.372 | 0.236 | 1.706 | |
readMzTabData | 1.328 | 0.012 | 1.965 | |
readMzTabData_v0.9 | 0.340 | 0.008 | 0.834 | |
readSRMData | 1.728 | 0.024 | 1.763 | |
reduce-data.frame-method | 0.016 | 0.000 | 0.017 | |
removeNoId-methods | 1.176 | 0.000 | 1.179 | |
removePeaks-methods | 0.724 | 0.008 | 0.749 | |
removeReporters-methods | 0.696 | 0.000 | 0.705 | |
selectFeatureData | 1.228 | 0.008 | 1.248 | |
smooth-methods | 0.308 | 0.000 | 0.307 | |
trimMz-methods | 0.268 | 0.004 | 0.271 | |
writeMgfData-methods | 0 | 0 | 0 | |