Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:00:17 -0400 (Tue, 09 Apr 2019).
Package 1037/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
MSnbase 2.9.3 Laurent Gatto
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: MSnbase |
Version: 2.9.3 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSnbase_2.9.3.tar.gz |
StartedAt: 2019-04-09 03:48:35 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 04:10:20 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 1305.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSnbase.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSnbase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSnbase_2.9.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MSnbase.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSnbase/DESCRIPTION’ ... OK * this is package ‘MSnbase’ version ‘2.9.3’ * 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 5.2Mb sub-directories of 1Mb or more: R 1.8Mb data 1.9Mb * 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 <[email protected]> [aut, cre] (<https://orcid.org/0000-0002-1520-2268>) Johannes Rainer <[email protected]> [aut, cre] Sebastian Gibb <[email protected]> [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 ... NOTE Found the following apparent S3 methods exported but not registered: as.data.frame.MSnExp as.data.frame.MSnSet as.data.frame.Spectrum as.data.frame.mzRident as.matrix.FoICollection droplevels.MSnSet is.na.MSnSet t.MSnSet See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * 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 25.618 1.880 27.500 chromatogram-MSnExp-method 14.158 3.077 15.862 MSnSet-class 12.293 0.705 13.003 OnDiskMSnExp-class 12.274 0.504 13.141 quantify-methods 6.451 3.272 4.875 aggvar 8.992 0.190 9.597 estimateMzResolution 7.051 1.296 8.257 averageMSnSet 7.544 0.277 7.945 MSnSetList-class 6.242 0.299 6.542 imageNA2 4.739 0.396 5.137 plot-methods 4.883 0.247 5.135 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/MSnbase.Rcheck/00check.log’ for details.
MSnbase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSnbase ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘MSnbase’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Spectrum1_class.c -o Spectrum1_class.o Spectrum1_class.c:8:13: warning: unused function '_new_Spectrum1' [-Wunused-function] static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt, ^ 1 warning generated. clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Spectrum2_class.c -o Spectrum2_class.o Spectrum2_class.c:9:13: warning: unused function '_new_Spectrum2' [-Wunused-function] static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt, ^ 1 warning generated. clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable] int i1, i2, ret; ^ utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable] int i1, i2, ret; ^ utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable] double d1, d2, ret; ^ utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable] double d1, d2, ret; ^ utils.c:121:12: warning: unused function 'compar_double_asc_order' [-Wunused-function] static int compar_double_asc_order(const void *p1, const void *p2) ^ utils.c:131:12: warning: unused function 'compar_double_desc_order' [-Wunused-function] static int compar_double_desc_order(const void *p1, const void *p2) ^ 6 warnings generated. clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-MSnbase/00new/MSnbase/libs ** R ** data *** moving datasets to lazyload DB Registered S3 methods overwritten by 'ggplot2': method from [.quosures rlang c.quosures rlang print.quosures rlang Creating a new generic function for ‘smooth’ in package ‘MSnbase’ 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 ‘smooth’ in package ‘MSnbase’ 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, 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, rowMeans, rowSums, 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 This is MSnbase version 2.9.3 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:stats': smooth 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: [email protected] 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: [email protected] 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: 0.24 Mb - - - Spectra data - - - MS level(s): 1 2 Number of spectra: 509 MSn retention times: 18:28 - 22:3 minutes - - - Processing information - - - Data loaded [Tue Apr 9 03:55:47 2019] MSnbase version: 2.9.3 - - - 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 (30 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: Tue Apr 9 04:03:08 2019 MSnbase version: 2.9.3 - - - 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: Tue Apr 9 04:03:08 2019 MSnbase version: 2.9.3 - - - 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 Apr 9 04:03:44 2019 Description: small foi 3 features of interest: P20353, P53501, Q7KU78 Traceable object of class "FeaturesOfInterest" Created on Tue Apr 9 04:03:44 2019 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 ......══ testthat results ═══════════════════════════════════════════════════════════ OK: 3248 SKIPPED: 9 FAILED: 0 > > proc.time() user system elapsed 777.671 114.286 879.655
MSnbase.Rcheck/MSnbase-Ex.timings
name | user | system | elapsed | |
Chromatogram-class | 0.057 | 0.003 | 0.061 | |
Chromatograms-class | 0.382 | 0.007 | 0.390 | |
FeatComp-class | 0.374 | 0.038 | 0.417 | |
FeaturesOfInterest-class | 0.087 | 0.013 | 0.101 | |
MSmap-class | 0.001 | 0.001 | 0.002 | |
MSnExp-class | 0.726 | 0.013 | 0.740 | |
MSnProcess-class | 0.003 | 0.001 | 0.004 | |
MSnSet-class | 12.293 | 0.705 | 13.003 | |
MSnSetList-class | 6.242 | 0.299 | 6.542 | |
MzTab-class | 0.490 | 0.063 | 4.981 | |
NAnnotatedDataFrame-class | 0.026 | 0.001 | 0.027 | |
OnDiskMSnExp-class | 12.274 | 0.504 | 13.141 | |
ProcessingStep-class | 0.01 | 0.00 | 0.01 | |
ReporterIons-class | 0.017 | 0.001 | 0.018 | |
Spectra | 0.098 | 0.006 | 0.104 | |
TMT6 | 0.012 | 0.003 | 0.014 | |
addIdentificationData-methods | 1.048 | 0.009 | 1.057 | |
aggvar | 8.992 | 0.190 | 9.597 | |
averageMSnSet | 7.544 | 0.277 | 7.945 | |
bin-methods | 0.567 | 0.026 | 0.594 | |
calculateFragments-methods | 1.373 | 0.027 | 1.401 | |
chromatogram-MSnExp-method | 14.158 | 3.077 | 15.862 | |
clean-methods | 0.322 | 0.074 | 0.396 | |
combineFeatures | 2.442 | 0.403 | 2.845 | |
combineSpectra | 0.210 | 0.022 | 0.232 | |
combineSpectraMovingWindow | 3.656 | 0.540 | 4.236 | |
commonFeatureNames | 0.462 | 0.014 | 0.476 | |
compareSpectra-methods | 0.236 | 0.022 | 0.259 | |
consensusSpectrum | 0.038 | 0.001 | 0.039 | |
estimateMzResolution | 7.051 | 1.296 | 8.257 | |
estimateMzScattering | 25.618 | 1.880 | 27.500 | |
estimateNoise-method | 0.018 | 0.000 | 0.018 | |
exprsToRatios-methods | 0.081 | 0.004 | 0.085 | |
extractPrecSpectra-methods | 1.303 | 0.043 | 1.346 | |
fData-utils | 0.453 | 0.016 | 0.471 | |
factorsAsStrings | 0.022 | 0.004 | 0.027 | |
featureCV | 0.028 | 0.003 | 0.031 | |
fillUp | 0.008 | 0.001 | 0.009 | |
formatRt | 0.001 | 0.001 | 0.001 | |
get.amino.acids | 0.007 | 0.002 | 0.009 | |
get.atomic.mass | 0.001 | 0.001 | 0.001 | |
getVariableName | 0.006 | 0.000 | 0.006 | |
hasSpectraOrChromatograms | 0.478 | 0.029 | 0.513 | |
iPQF | 0.469 | 0.005 | 0.474 | |
iTRAQ4 | 0.015 | 0.001 | 0.017 | |
imageNA2 | 4.739 | 0.396 | 5.137 | |
impute-methods | 0.881 | 0.037 | 0.939 | |
isCentroidedFromFile | 3.787 | 0.314 | 4.036 | |
itraqdata | 0.065 | 0.020 | 0.086 | |
listOf | 0.002 | 0.000 | 0.003 | |
makeCamelCase | 0.001 | 0.000 | 0.002 | |
makeNaData | 1.806 | 0.050 | 1.856 | |
meanMzInts | 0.065 | 0.003 | 0.068 | |
missing-data | 4.568 | 0.269 | 4.839 | |
mzRident2dfr | 0.061 | 0.003 | 0.064 | |
nFeatures | 0.795 | 0.113 | 0.908 | |
nQuants | 0.238 | 0.004 | 0.243 | |
naplot | 0.076 | 0.006 | 0.082 | |
navMS | 2.887 | 0.201 | 3.126 | |
normToReference | 0.233 | 0.004 | 0.237 | |
normalise-methods | 0.017 | 0.003 | 0.019 | |
npcv | 0.005 | 0.000 | 0.005 | |
pSet-class | 0.001 | 0.000 | 0.002 | |
pickPeaks-method | 0.477 | 0.029 | 0.507 | |
plot-methods | 4.883 | 0.247 | 5.135 | |
plot2d-methods | 0.973 | 0.026 | 1.001 | |
plotDensity-methods | 1.278 | 0.027 | 1.306 | |
plotMzDelta-methods | 1.186 | 0.129 | 1.315 | |
plotNA-methods | 0.735 | 0.005 | 0.741 | |
plotSpectrumSpectrum-methods | 1.754 | 0.056 | 1.810 | |
precSelection | 0.014 | 0.002 | 0.016 | |
purityCorrect-methods | 0.029 | 0.005 | 0.035 | |
quantify-methods | 6.451 | 3.272 | 4.875 | |
readMSData | 2.065 | 0.012 | 2.077 | |
readMSnSet | 0.130 | 0.005 | 0.139 | |
readMgfData | 2.643 | 0.187 | 2.831 | |
readMzIdData | 2.527 | 1.015 | 3.545 | |
readMzTabData | 1.395 | 0.073 | 2.102 | |
readMzTabData_v0.9 | 0.185 | 0.006 | 0.612 | |
readSRMData | 1.940 | 0.048 | 1.988 | |
reduce-data.frame-method | 0.026 | 0.002 | 0.028 | |
removeNoId-methods | 1.388 | 0.036 | 1.424 | |
removePeaks-methods | 0.919 | 0.047 | 0.966 | |
removeReporters-methods | 0.999 | 0.060 | 1.059 | |
selectFeatureData | 1.576 | 0.120 | 1.696 | |
smooth-methods | 0.382 | 0.038 | 0.419 | |
trimMz-methods | 0.213 | 0.025 | 0.237 | |
writeMgfData-methods | 0.001 | 0.001 | 0.001 | |