Laurent Gatto
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MSnbase |
| Branch: RELEASE_3_9 |
| Last Commit: 4d5899b |
| Last Changed Date: 2019-05-31 07:14:27 -0400 (Fri, 31 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:48:44 -0400 (Wed, 16 Oct 2019).
| Package 1055/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSnbase 2.10.1 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 | [ ERROR ] | OK |
| Package: MSnbase |
| Version: 2.10.1 |
| 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_2.10.1.tar.gz |
| StartedAt: 2019-10-16 04:53:23 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:15:55 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1351.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MSnbase.Rcheck |
| Warnings: NA |
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### 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_2.10.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MSnbase.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.10.1’
* 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 [aut, cre] ()
Johannes Rainer [aut, cre] ()
Sebastian Gibb [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 25.245 1.792 27.266
chromatogram-MSnExp-method 20.747 4.071 23.966
MSnSet-class 13.558 0.720 14.648
OnDiskMSnExp-class 11.731 0.420 12.224
quantify-methods 7.427 3.369 5.768
averageMSnSet 9.538 0.371 10.163
aggvar 9.700 0.159 10.165
estimateMzResolution 8.297 1.447 9.678
MSnSetList-class 5.766 0.111 5.879
plot-methods 5.266 0.296 5.569
missing-data 4.776 0.365 5.142
imageNA2 4.682 0.402 5.145
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
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
Error in x$.self$finalize() : attempt to apply non-function
...══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 2196 | SKIPPED: 9 | WARNINGS: 1058 | FAILED: 1 ]
1. Error: (unknown) (@test_MSmap.R#7)
Error: testthat unit tests failed
Execution halted
* 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: 1 ERROR, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/MSnbase.Rcheck/00check.log’
for details.
MSnbase.Rcheck/00install.out
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSnbase
###
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* 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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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
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.fail
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 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
This is MSnbase version 2.10.1
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$")
> extdata_mzXML_in_mem_ms2 <- readMSData(f, verbose = FALSE, centroided. = FALSE)
> extdata_mzXML_on_disk <- readMSData(f, centroided. = FALSE, mode = "onDisk")
> extdata_mzXML_on_disk_ms2 <- readMSData(f, msLevel = 2, centroided. = FALSE, mode = "onDisk")
>
> sf <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
> sciex <- readMSData(sf, mode = "onDisk")
>
> test_check("MSnbase")
Experiment data
Experimenter name: Laurent Gatto
Laboratory: Cambridge Centre for Proteomics (CCP)
Contact information: Laurent Gatto
Contact email: lg390@cam.ac.uk
Title: Example 'MSnExp' data set
URL:
PMIDs:
No abstract available.
Instrument :
Model: test (1)
Manufacturer:
Customisations:
Use 'msInfo(object)' for more MIAPE-MS information.
Experiment data
Experimenter name: Laurent Gatto
Laboratory: Cambridge Centre for Proteomics (CCP)
Contact information: Laurent Gatto
Contact email: lg390@cam.ac.uk
Title: Example 'MSnExp' data set
URL:
PMIDs:
No abstract available.
notes:
Note1:
First note
MIAPE-MS information:
1. General features:
Date stamp:
Contact: Laurent Gatto
Name: Laurent Gatto
Laboratory: Cambridge Centre for Proteomics (CCP)
Instument model: test
Manufacturer:
Customisations:
Software:
Version:
Switching:
Param file:
2. Ion source
Source:
Source details:
3. Post-source componentry
Analyzer:
Analyzer details:
Collision gas:
Pressure: bars
Energy:
Detector type:
Sensitivity:
── 1. Error: (unknown) (@test_MSmap.R#7) ──────────────────────────────────────
failed to load resource
name: AH49008
title: PXD000001: raw mass spectrometry data
reason: Recv failure: Connection reset by peer
1: ah[["AH49008"]] at testthat/test_MSmap.R:7
2: ah[["AH49008"]]
3: .local(x, i, j, ...)
4: .Hub_get1(x[idx], force = force, verbose = verbose)
5: tryCatch({
fls <- cache(getHub(class), force = force, verbose = verbose)
.get1(class)
}, error = function(err) {
stop("failed to load resource", "\n name: ", names(x), "\n title: ", x$title,
"\n reason: ", conditionMessage(err), call. = FALSE)
})
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: value[[3L]](cond)
9: stop("failed to load resource", "\n name: ", names(x), "\n title: ", x$title, "\n reason: ",
conditionMessage(err), call. = FALSE)
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x) : attempt to apply non-function
Object of class "MzTab".
Description: mzTab example file for reporting a summary report of
quantification data quantified on the protein level
Mode: Complete
Type: Quantification
Available data: Proteins PSMs
Instance of class 'MSnSetList' containig 3 objects.
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.25 Mb
- - - Spectra data - - -
MS level(s): 1 2
Number of spectra: 509
MSn retention times: 18:28 - 22:3 minutes
- - - Processing information - - -
Data loaded [Wed Oct 16 05:01:10 2019]
MSnbase version: 2.10.1
- - - Meta data - - -
phenoData
rowNames:
TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz
varLabels: sampleNames
varMetadata: labelDescription
Loaded from:
TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz
protocolData: none
featureData
featureNames: F1.S001 F1.S002 ... F1.S509 (509 total)
fvarLabels: fileIdx spIdx ... spectrum (33 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
......Error in x$.self$finalize() : attempt to apply non-function
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 Oct 16 05:08:36 2019
MSnbase version: 2.10.1
- - - Meta data - - -
phenoData
rowNames: dummyiTRAQ.mzXML
varLabels: sampleNames
varMetadata: labelDescription
Loaded from:
dummyiTRAQ.mzXML
protocolData: none
featureData
featureNames: F1.S1 F1.S2 ... F1.S5 (5 total)
fvarLabels: spectrum
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
MSn experiment data ("MSnExp")
Object size in memory: 0.21 Mb
- - - Spectra data - - -
MS level(s): 2
Number of spectra: 5
MSn retention times: 25:1 - 25:2 minutes
- - - Processing information - - -
Data loaded: Wed Oct 16 05:08:37 2019
MSnbase version: 2.10.1
- - - Meta data - - -
phenoData
rowNames: dummyiTRAQ.mzXML
varLabels: sampleNames
varMetadata: labelDescription
Loaded from:
dummyiTRAQ.mzXML
protocolData: none
featureData
featureNames: F1.S1 F1.S2 ... F1.S5 (5 total)
fvarLabels: spectrum
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Object of class "FeaturesOfInterest"
Created on Wed Oct 16 05:09:11 2019
Description:
small foi
3 features of interest:
P20353, P53501, Q7KU78
Traceable object of class "FeaturesOfInterest"
Created on Wed Oct 16 05:09:11 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
|
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
|
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$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
...══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 2196 | SKIPPED: 9 | WARNINGS: 1058 | FAILED: 1 ]
1. Error: (unknown) (@test_MSmap.R#7)
Error: testthat unit tests failed
Execution halted
MSnbase.Rcheck/MSnbase-Ex.timings
| name | user | system | elapsed | |
| Chromatogram-class | 0.065 | 0.005 | 0.069 | |
| Chromatograms-class | 0.295 | 0.007 | 0.302 | |
| FeatComp-class | 0.397 | 0.042 | 0.447 | |
| FeaturesOfInterest-class | 0.095 | 0.015 | 0.109 | |
| MSmap-class | 0.001 | 0.000 | 0.002 | |
| MSnExp-class | 0.706 | 0.014 | 0.723 | |
| MSnProcess-class | 0.002 | 0.000 | 0.002 | |
| MSnSet-class | 13.558 | 0.720 | 14.648 | |
| MSnSetList-class | 5.766 | 0.111 | 5.879 | |
| MzTab-class | 0.569 | 0.055 | 2.981 | |
| OnDiskMSnExp-class | 11.731 | 0.420 | 12.224 | |
| ProcessingStep-class | 0.007 | 0.000 | 0.007 | |
| ReporterIons-class | 0.012 | 0.000 | 0.013 | |
| Spectra | 0.113 | 0.009 | 0.122 | |
| TMT6 | 0.013 | 0.003 | 0.015 | |
| addIdentificationData-methods | 1.060 | 0.009 | 1.073 | |
| aggvar | 9.700 | 0.159 | 10.165 | |
| averageMSnSet | 9.538 | 0.371 | 10.163 | |
| bin-methods | 0.670 | 0.083 | 0.765 | |
| calculateFragments-methods | 1.898 | 0.046 | 2.068 | |
| chromatogram-MSnExp-method | 20.747 | 4.071 | 23.966 | |
| clean-methods | 0.360 | 0.103 | 0.463 | |
| combineFeatures | 2.769 | 0.494 | 3.272 | |
| combineSpectra | 0.314 | 0.046 | 0.360 | |
| combineSpectraMovingWindow | 3.851 | 0.549 | 4.415 | |
| commonFeatureNames | 0.481 | 0.021 | 0.503 | |
| compareSpectra-methods | 0.292 | 0.020 | 0.313 | |
| consensusSpectrum | 0.060 | 0.002 | 0.064 | |
| estimateMzResolution | 8.297 | 1.447 | 9.678 | |
| estimateMzScattering | 25.245 | 1.792 | 27.266 | |
| estimateNoise-method | 0.020 | 0.001 | 0.020 | |
| exprsToRatios-methods | 0.082 | 0.005 | 0.087 | |
| extractPrecSpectra-methods | 1.536 | 0.161 | 1.697 | |
| fData-utils | 0.574 | 0.019 | 0.611 | |
| factorsAsStrings | 0.023 | 0.003 | 0.026 | |
| featureCV | 0.039 | 0.003 | 0.042 | |
| fillUp | 0.009 | 0.002 | 0.011 | |
| formatRt | 0.001 | 0.001 | 0.002 | |
| get.amino.acids | 0.007 | 0.003 | 0.009 | |
| get.atomic.mass | 0.001 | 0.001 | 0.001 | |
| getVariableName | 0.006 | 0.000 | 0.006 | |
| hasSpectraOrChromatograms | 0.491 | 0.030 | 0.528 | |
| iPQF | 0.439 | 0.005 | 0.444 | |
| iTRAQ4 | 0.019 | 0.001 | 0.019 | |
| imageNA2 | 4.682 | 0.402 | 5.145 | |
| impute-methods | 0.941 | 0.037 | 0.997 | |
| isCentroidedFromFile | 3.876 | 0.401 | 4.217 | |
| itraqdata | 0.075 | 0.025 | 0.101 | |
| listOf | 0.003 | 0.000 | 0.003 | |
| makeCamelCase | 0.001 | 0.000 | 0.002 | |
| makeNaData | 1.615 | 0.034 | 1.649 | |
| meanMzInts | 0.070 | 0.006 | 0.077 | |
| missing-data | 4.776 | 0.365 | 5.142 | |
| mzRident2dfr | 0.040 | 0.002 | 0.041 | |
| nFeatures | 0.746 | 0.074 | 0.820 | |
| nQuants | 0.235 | 0.005 | 0.239 | |
| naplot | 0.095 | 0.009 | 0.103 | |
| navMS | 3.036 | 0.248 | 3.373 | |
| normToReference | 0.325 | 0.005 | 0.330 | |
| normalise-methods | 0.027 | 0.003 | 0.030 | |
| npcv | 0.008 | 0.000 | 0.008 | |
| pSet-class | 0.002 | 0.001 | 0.004 | |
| pickPeaks-method | 0.430 | 0.019 | 0.450 | |
| plot-methods | 5.266 | 0.296 | 5.569 | |
| plot2d-methods | 1.004 | 0.024 | 1.029 | |
| plotDensity-methods | 1.027 | 0.037 | 1.064 | |
| plotMzDelta-methods | 1.584 | 0.136 | 1.720 | |
| plotNA-methods | 0.868 | 0.006 | 0.875 | |
| plotSpectrumSpectrum-methods | 1.692 | 0.013 | 1.711 | |
| precSelection | 0.015 | 0.004 | 0.019 | |
| purityCorrect-methods | 0.038 | 0.007 | 0.047 | |
| quantify-methods | 7.427 | 3.369 | 5.768 | |
| readMSData | 2.194 | 0.014 | 2.208 | |
| readMSnSet | 0.125 | 0.006 | 0.135 | |
| readMgfData | 2.854 | 0.195 | 3.051 | |
| readMzIdData | 2.825 | 1.126 | 3.958 | |
| readMzTabData | 1.472 | 0.165 | 2.399 | |
| readMzTabData_v0.9 | 0.448 | 0.020 | 0.827 | |
| readSRMData | 1.948 | 0.049 | 1.998 | |
| reduce-data.frame-method | 0.032 | 0.001 | 0.033 | |
| removeNoId-methods | 1.636 | 0.090 | 1.727 | |
| removePeaks-methods | 1.118 | 0.050 | 1.171 | |
| removeReporters-methods | 1.320 | 0.059 | 1.380 | |
| selectFeatureData | 1.489 | 0.071 | 1.562 | |
| smooth-methods | 0.387 | 0.027 | 0.414 | |
| trimMz-methods | 0.186 | 0.018 | 0.204 | |
| writeMgfData-methods | 0.001 | 0.000 | 0.001 | |