| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:45 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the xcms package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/xcms.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 2183/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| xcms 3.99.2 (landing page) Steffen Neumann
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: xcms |
| Version: 3.99.2 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:xcms.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings xcms_3.99.2.tar.gz |
| StartedAt: 2023-06-06 09:30:44 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 10:00:52 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 1807.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: xcms.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:xcms.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings xcms_3.99.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/xcms.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘3.99.2’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘xcms’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 8.2Mb
sub-directories of 1Mb or more:
R 3.4Mb
libs 2.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
GPL (>= 2) + file LICENSE
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘MALDIquant:::.localMaxima’ ‘MSnbase:::.MSnExpReqFvarLabels’
‘MSnbase:::.plotXIC’ ‘MSnbase:::.vertical_sub_layout’
‘MSnbase:::formatFileSpectrumNames’ ‘Spectra:::.concatenate_spectra’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.copy_env’ ‘.get_closest_index’ ‘.validChromPeaksMatrix’ ‘MSW.cwt’
‘MSW.getLocalMaximumCWT’ ‘MSW.getRidge’ ‘descendMin’ ‘descendMinTol’
‘estimateChromNoise’ ‘getLocalNoiseEstimate’ ‘na.flatfill’
‘patternVsRowScore’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.xcmsFragments.plotTree: no visible global function definition for
‘edgemode<-’
.xcmsFragments.plotTree: no visible global function definition for
‘addEdge’
buildAnalysisSummary: no visible global function definition for
‘newXMLNode’
buildAssayList : <anonymous>: no visible global function definition for
‘newXMLNode’
buildAssayList: no visible global function definition for ‘newXMLNode’
buildAuditCollection: no visible global function definition for
‘newXMLNode’
buildCVlist: no visible global function definition for ‘newXMLNode’
buildCVlist: no visible global function definition for ‘addChildren’
buildCvParams : <anonymous>: no visible global function definition for
‘newXMLNode’
buildDataProcessingList: no visible global function definition for
‘newXMLNode’
buildFeatureList : <anonymous>: no visible global function definition
for ‘newXMLNode’
buildInputFiles : <anonymous>: no visible global function definition
for ‘newXMLNode’
buildInputFiles: no visible global function definition for ‘newXMLNode’
buildMzq: no visible global function definition for ‘xmlTree’
buildSmallMoleculeList : <anonymous>: no visible global function
definition for ‘newXMLNode’
buildSmallMoleculeList: no visible global function definition for
‘newXMLNode’
buildSoftwareList: no visible global function definition for
‘newXMLNode’
buildStudyVariableList : <anonymous>: no visible global function
definition for ‘newXMLNode’
buildStudyVariableList : <anonymous> : <anonymous>: no visible global
function definition for ‘newXMLNode’
buildStudyVariableList: no visible global function definition for
‘newXMLNode’
plotQC: no visible global function definition for ‘sampleNames’
running: multiple local function definitions for ‘funct’ with different
formal arguments
verify.mzQuantML: no visible global function definition for
‘xmlTreeParse’
verify.mzQuantML: no visible global function definition for
‘xmlInternalTreeParse’
verify.mzQuantML: no visible global function definition for
‘xmlSchemaValidate’
xcmsClusterApply: no visible global function definition for
‘checkCluster’
xcmsClusterApply : submit: no visible global function definition for
‘sendCall’
xcmsClusterApply: no visible global function definition for
‘recvOneResult’
xcmsClusterApply: no visible global function definition for
‘checkForRemoteErrors’
xcmsPapply: no visible global function definition for ‘mpi.comm.size’
xcmsPapply: no visible global function definition for
‘mpi.spawn.Rslaves’
xcmsPapply: no visible global function definition for ‘mpi.comm.rank’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.send.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.recv.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.any.source’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.any.tag’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for
‘mpi.bcast.Robj2slave’
xcmsPapply: no visible global function definition for ‘mpi.bcast.cmd’
xcmsPapply: no visible global function definition for ‘mpi.recv.Robj’
xcmsPapply: no visible global function definition for ‘mpi.any.source’
xcmsPapply: no visible global function definition for ‘mpi.any.tag’
xcmsPapply: no visible global function definition for
‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for ‘mpi.send.Robj’
xcmsParallelSetup: no visible global function definition for
‘mpi.spawn.Rslaves’
xcmsParallelSetup: no visible global function definition for
‘mpi.comm.size’
xcmsParallelSetup: no visible global function definition for
‘mpi.comm.rank’
xcmsParallelSetup: no visible global function definition for
‘makeCluster’
[,XChromatograms-ANY-ANY-ANY: no visible global function definition for
‘pData<-’
plotSurf,xcmsRaw: no visible global function definition for ‘clear3d’
plotSurf,xcmsRaw: no visible global function definition for ‘surface3d’
plotSurf,xcmsRaw: no visible global function definition for ‘points3d’
plotSurf,xcmsRaw: no visible global function definition for ‘bbox3d’
plotTree,xcmsFragments: no visible global function definition for
‘edgemode<-’
plotTree,xcmsFragments: no visible global function definition for
‘addEdge’
write.cdf,xcmsRaw: no visible global function definition for
‘ncdim_def’
write.cdf,xcmsRaw: no visible global function definition for
‘ncvar_def’
write.cdf,xcmsRaw: no visible global function definition for
‘nc_create’
write.cdf,xcmsRaw: no visible global function definition for
‘ncvar_put’
write.cdf,xcmsRaw: no visible global function definition for
‘ncatt_put’
write.cdf,xcmsRaw: no visible global function definition for ‘nc_close’
write.mzQuantML,xcmsSet: no visible global function definition for
‘saveXML’
write.mzdata,xcmsRaw: no visible global function definition for
‘base64encode’
Undefined global functions or variables:
addChildren addEdge base64encode bbox3d checkCluster
checkForRemoteErrors clear3d edgemode<- makeCluster mpi.any.source
mpi.any.tag mpi.bcast.Robj2slave mpi.bcast.cmd mpi.comm.rank
mpi.comm.size mpi.get.sourcetag mpi.recv.Robj mpi.send.Robj
mpi.spawn.Rslaves nc_close nc_create ncatt_put ncdim_def ncvar_def
ncvar_put newXMLNode pData<- points3d recvOneResult sampleNames
saveXML sendCall surface3d xmlInternalTreeParse xmlSchemaValidate
xmlTree xmlTreeParse
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
XcmsExperiment 11.210 0.323 11.561
findPeaks.massifquant-methods 8.946 0.076 9.036
findChromPeaks-Chromatogram-CentWaveParam 6.660 0.199 6.872
XCMSnExp-class 5.856 0.196 6.101
findChromPeaks-massifquant 5.591 0.016 5.616
* 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 ...
‘LC-MS-feature-grouping.Rmd’ using ‘UTF-8’... OK
‘xcms-direct-injection.Rmd’ using ‘UTF-8’... OK
‘xcms-lcms-ms.Rmd’ using ‘UTF-8’... OK
‘xcms.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 6 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/xcms.Rcheck/00check.log’
for details.
xcms.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL xcms ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘xcms’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fastMatch.c -o fastMatch.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c mzROI.c -o mzROI.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c util.c -o util.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c xcms.c -o xcms.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c binners.c -o binners.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-xcms/00new/xcms/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘group’ in package ‘xcms’ Creating a new generic function for ‘sigma’ in package ‘xcms’ ** 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 (xcms)
xcms.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> library(testthat)
> library(xcms)
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, 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.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.27.0
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:base':
trimws
This is xcms version 3.99.2
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
> library(faahKO)
> library(msdata)
>
> if (.Platform$OS.type == "unix") {
+ prm <- MulticoreParam(3)
+ } else {
+ # prm <- SnowParam(3)
+ prm <- SerialParam()
+ }
> register(bpstart(prm))
>
> ## Create some objects we can re-use in different tests:
> faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+ system.file('cdf/KO/ko16.CDF', package = "faahKO"),
+ system.file('cdf/KO/ko18.CDF', package = "faahKO"))
>
> faahko_od <- readMSData(faahko_3_files, mode = "onDisk")
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
> faahko_xod <- findChromPeaks(
+ faahko_od, param = CentWaveParam(noise = 10000, snthresh = 40,
+ prefilter = c(3, 10000)))
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
> od_x <- faahko_od
> mzr <- matrix(c(335, 335, 344, 344), ncol = 2, byrow = TRUE)
> od_chrs <- chromatogram(od_x, mz = mzr)
> xod_x <- faahko_xod
> pdp <- PeakDensityParam(sampleGroups = rep(1, 3))
> xod_xg <- groupChromPeaks(xod_x, param = pdp)
> xod_xgr <- adjustRtime(xod_xg, param = PeakGroupsParam(span = 0.4))
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
> xod_xgrg <- groupChromPeaks(xod_xgr, param = pdp)
> xod_r <- adjustRtime(as(od_x, "XCMSnExp"), param = ObiwarpParam())
Sample number 2 used as center sample.
Aligning ko18.CDF against ko16.CDF ... OK
Aligning ko15.CDF against ko16.CDF ... OK
>
> xod_chr <- findChromPeaks(filterMz(filterRt(od_x, rt = c(2500, 3500)),
+ mz = c(334.9, 344.1)),
+ param = CentWaveParam())
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 515 regions of interest ... OK: 20 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 551 regions of interest ... OK: 29 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 514 regions of interest ... OK: 23 found.
Warning message:
In .local(object, param, ...) :
Your data appears to be not centroided! CentWave works best on data in centroid mode.
>
> microtofq_fs <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+ system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_od <- readMSData(microtofq_fs, mode = "onDisk")
>
> ## Direct injection data:
> fticrf <- list.files(system.file("fticr-mzML", package = "msdata"),
+ recursive = TRUE, full.names = TRUE)
> fticr <- readMSData(fticrf[1:2], msLevel. = 1, mode = "onDisk")
> fticr_xod <- findChromPeaks(fticr, MSWParam(scales = c(1, 7),
+ peakThr = 80000, ampTh = 0.005,
+ SNR.method = "data.mean",
+ winSize.noise = 500))
>
> ## Pesticide data
> fl <- system.file("TripleTOF-SWATH", "PestMix1_SWATH.mzML", package = "msdata")
> pest_swth <- readMSData(fl, mode = "onDisk")
> cwp <- CentWaveParam(snthresh = 5, noise = 100, ppm = 10,
+ peakwidth = c(3, 20), prefilter = c(3, 1000))
> pest_swth <- findChromPeaks(pest_swth, param = cwp)
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 11 regions of interest ... OK: 11 found.
> pest_swth <- findChromPeaksIsolationWindow(pest_swth, param = cwp)
Detecting mass traces at 10 ppm ... OK
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 2 regions of interest ... OK: 2 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 7 regions of interest ... OK: 7 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3 regions of interest ... OK: 3 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 17 regions of interest ... OK: 17 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3 regions of interest ... OK: 2 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 10 regions of interest ... OK: 10 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3 regions of interest ... OK: 3 found.
Warning message:
In .processResultList(resList, getProcHist = return.type == "xcmsSet", :
No peaks found in sample number 1.
>
> fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
> pest_dda <- readMSData(fl, mode = "onDisk")
> pest_dda <- findChromPeaks(pest_dda, param = cwp)
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 29 regions of interest ... OK: 27 found.
>
> ## Sciex test data.
> ## fl <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
> ## sciex_data <- readMSData(fl, mode = "onDisk")
> ## sciex_data <- pickPeaks(sciex_data)
>
> test_check("xcms")
Object of class: CleanPeaksParam
Parameters:
- maxPeakwidth: [1] 13.2
Object of class: MergeNeighboringPeaksParam
Parameters:
- expandRt: [1] 5
- expandMz: [1] 0.1
- ppm: [1] 20
- minProp: [1] 0.9
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
8.00 16.00 28.00 32.00 40.00 64.00 80.00 96.00 100.00
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
8.00 16.00 28.00 32.00 40.00 56.00 64.00 80.00 88.00 96.00 100.00
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
Object of class: XChromatogram
length of object: 0
from file:
mz range: [NA, NA]
MS level: 1
Identified chromatographic peaks (0):
rt rtmin rtmax into maxo sn
[ FAIL 0 | WARN 679 | SKIP 13 | PASS 3924 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (13)
[ FAIL 0 | WARN 679 | SKIP 13 | PASS 3924 ]
>
> bpstop(prm)
>
> proc.time()
user system elapsed
449.014 35.629 915.018
xcms.Rcheck/xcms-Ex.timings
| name | user | system | elapsed | |
| AutoLockMass-methods | 0.001 | 0.000 | 0.000 | |
| GenericParam | 0.001 | 0.000 | 0.002 | |
| XCMSnExp-class | 5.856 | 0.196 | 6.101 | |
| XCMSnExp-filter-methods | 0.527 | 0.008 | 0.536 | |
| XChromatogram | 2.245 | 0.032 | 2.281 | |
| XcmsExperiment | 11.210 | 0.323 | 11.561 | |
| applyAdjustedRtime | 3.093 | 0.124 | 3.224 | |
| binYonX | 0.002 | 0.000 | 0.002 | |
| breaks_on_binSize | 0.001 | 0.000 | 0.001 | |
| breaks_on_nBins | 0 | 0 | 0 | |
| chromPeakSpectra | 3.813 | 0.259 | 4.068 | |
| chromatogram-method | 2.369 | 0.056 | 2.430 | |
| correlate-Chromatogram | 0.02 | 0.00 | 0.02 | |
| descendZero | 0.001 | 0.000 | 0.001 | |
| do_findChromPeaks_centWave | 1.100 | 0.028 | 1.130 | |
| do_findChromPeaks_massifquant | 1.734 | 0.028 | 1.765 | |
| do_findChromPeaks_matchedFilter | 2.410 | 0.080 | 2.495 | |
| do_groupChromPeaks_density | 0.402 | 0.011 | 0.414 | |
| extractMsData-method | 0.532 | 0.028 | 0.561 | |
| featureChromatograms | 1.556 | 0.016 | 1.576 | |
| fillChromPeaks | 1.748 | 0.024 | 1.775 | |
| filter-MChromatograms | 0.349 | 0.004 | 0.354 | |
| findChromPeaks-Chromatogram-CentWaveParam | 6.660 | 0.199 | 6.872 | |
| findChromPeaks-Chromatogram-MatchedFilter | 0.548 | 0.012 | 0.561 | |
| findChromPeaks-centWave | 3.973 | 0.068 | 4.051 | |
| findChromPeaks-centWaveWithPredIsoROIs | 0.013 | 0.000 | 0.013 | |
| findChromPeaks-massifquant | 5.591 | 0.016 | 5.616 | |
| findChromPeaks-matchedFilter | 3.068 | 0.008 | 3.081 | |
| findMZ | 0 | 0 | 0 | |
| findPeaks-MSW | 2.099 | 0.012 | 2.124 | |
| findPeaks.massifquant-methods | 8.946 | 0.076 | 9.036 | |
| findneutral | 0 | 0 | 0 | |
| group.mzClust | 0.001 | 0.000 | 0.000 | |
| group.nearest | 0.000 | 0.000 | 0.001 | |
| groupFeatures-abundance-correlation | 0.565 | 0.000 | 0.567 | |
| groupFeatures-eic-similarity | 4.002 | 0.092 | 4.099 | |
| groupFeatures-similar-rtime | 0.472 | 0.044 | 0.516 | |
| groupOverlaps | 0 | 0 | 0 | |
| highlightChromPeaks | 1.673 | 0.083 | 1.759 | |
| imputeLinInterpol | 0.007 | 0.001 | 0.007 | |
| imputeRowMin | 2.217 | 0.059 | 2.279 | |
| imputeRowMinRand | 2.358 | 0.092 | 2.453 | |
| loadXcmsData | 0.061 | 0.004 | 0.066 | |
| manualChromPeaks | 0.448 | 0.020 | 0.485 | |
| medianFilter | 0.000 | 0.000 | 0.001 | |
| msn2xcmsRaw | 1.638 | 0.100 | 1.757 | |
| overlappingFeatures | 0.501 | 0.008 | 0.510 | |
| peakTable-methods | 0 | 0 | 0 | |
| peaksWithCentWave | 1.588 | 0.048 | 1.637 | |
| peaksWithMatchedFilter | 0.441 | 0.012 | 0.454 | |
| phenoDataFromPaths | 0.001 | 0.000 | 0.001 | |
| plotAdjustedRtime | 0.566 | 0.012 | 0.579 | |
| plotChromPeakDensity | 0.039 | 0.000 | 0.039 | |
| plotChromPeaks | 0.537 | 0.020 | 0.558 | |
| plotChromatogramsOverlay | 4.410 | 0.088 | 4.518 | |
| plotMsData | 3.102 | 0.036 | 3.141 | |
| plotQC | 2.828 | 0.023 | 2.856 | |
| profGenerate | 0 | 0 | 0 | |
| profMat-xcmsSet | 1.859 | 0.060 | 1.921 | |
| profStep-methods | 0 | 0 | 0 | |
| rectUnique | 0.002 | 0.000 | 0.002 | |
| refineChromPeaks | 2.044 | 0.036 | 2.083 | |
| removeIntensity-Chromatogram | 0.003 | 0.000 | 0.002 | |
| rla | 0.001 | 0.000 | 0.001 | |
| stitch-methods | 0.000 | 0.000 | 0.001 | |
| sub-xcmsRaw-logicalOrNumeric-missing-missing-method | 1.410 | 0.032 | 1.443 | |
| writeMzTab | 2.224 | 0.040 | 2.267 | |
| xcmsRaw | 0 | 0 | 0 | |