Laurent Gatto
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/MSnbase |
| Branch: RELEASE_3_10 |
| Last Commit: c9e328c |
| Last Changed Date: 2019-10-29 13:08:19 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
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 |
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###
### 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
###
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* 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
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###
### 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 | |