Steffen Neumann
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/xcms |
| Branch: master |
| Last Commit: 73ccc90 |
| Last Changed Date: 2020-01-09 10:11:46 -0500 (Thu, 09 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:29:36 -0500 (Thu, 16 Jan 2020).
| Package 1805/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| xcms 3.9.2 Steffen Neumann
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | TIMEOUT | NA | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: xcms |
| Version: 3.9.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:xcms.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings xcms_3.9.2.tar.gz |
| StartedAt: 2020-01-16 09:53:56 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 10:19:27 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 1530.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: xcms.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:xcms.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings xcms_3.9.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/xcms.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘3.9.2’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘xcms’ can be installed ... OK
* checking installed package size ... OK
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘MALDIquant:::.localMaxima’ ‘MSnbase:::.MSnExpReqFvarLabels’
‘MSnbase:::.plotXIC’ ‘MSnbase:::.vertical_sub_layout’
‘MSnbase:::formatFileSpectrumNames’
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:
‘.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’
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’
plotSurf,xcmsRaw: no visible global function definition for ‘rgl.clear’
plotSurf,xcmsRaw: no visible global function definition for
‘rgl.surface’
plotSurf,xcmsRaw: no visible global function definition for
‘rgl.points’
plotSurf,xcmsRaw: no visible global function definition for ‘rgl.bbox’
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 checkCluster checkForRemoteErrors
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
recvOneResult rgl.bbox rgl.clear rgl.points rgl.surface saveXML
sendCall 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 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
chromatogram-method 35.553 11.679 19.582
featureChromatograms 18.612 9.863 15.069
fillChromPeaks 16.883 7.855 16.698
adjustRtime-obiwarp 14.297 6.365 14.655
XCMSnExp-filter-methods 11.654 7.394 9.774
findChromPeaks-massifquant 13.455 5.267 10.646
XCMSnExp-class 11.254 5.704 10.793
adjustRtime-peakGroups 9.915 5.699 10.187
XChromatogram 9.586 3.378 8.412
findChromPeaks-centWave 8.100 4.508 7.454
findChromPeaks-Chromatogram-CentWaveParam 9.066 2.543 7.862
refineChromPeaks-merge 10.364 0.266 10.631
plotChromPeakDensity 9.467 0.473 9.942
extractMsData-method 6.841 2.727 6.531
findPeaks.massifquant-methods 8.870 0.536 9.407
applyAdjustedRtime 5.987 2.066 6.029
chromPeakSpectra 6.227 0.952 7.152
highlightChromPeaks 6.256 0.476 6.732
plotChromPeaks 5.763 0.437 6.202
do_findChromPeaks_massifquant 5.494 0.599 6.095
overlappingFeatures 5.752 0.301 6.054
groupChromPeaks-density 5.087 0.234 5.322
plotAdjustedRtime 5.103 0.213 5.318
groupChromPeaks-nearest 5.020 0.262 5.280
findChromPeaks-matchedFilter 4.502 0.569 5.071
* 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
‘/Users/biocbuild/bbs-3.11-bioc/meat/xcms.Rcheck/00check.log’
for details.
xcms.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL xcms
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘xcms’ ...
** using staged installation
** libs
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
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o
In file included from massifquant/Tracker.cpp:8:
massifquant/Tracker.h:49:16: warning: private field 'r_val_i' is not used [-Wunused-private-field]
double r_val_i;
^
massifquant/Tracker.h:50:16: warning: private field 'p_val_i' is not used [-Wunused-private-field]
double p_val_i;
^
massifquant/Tracker.h:53:16: warning: private field 'r_val_m' is not used [-Wunused-private-field]
double r_val_m;
^
massifquant/Tracker.h:54:16: warning: private field 'p_val_m' is not used [-Wunused-private-field]
double p_val_m;
^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
In file included from massifquant/DataKeeper.cpp:4:
massifquant/DataKeeper.h:36:26: warning: private field 'scbuf' is not used [-Wunused-private-field]
struct scanBuf * scbuf;
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c fastMatch.c -o fastMatch.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mzROI.c -o mzROI.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c util.c -o util.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c xcms.c -o xcms.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c binners.c -o binners.o
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
int idx = 0;
^
1 warning 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 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-xcms/00new/xcms/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘sigma’ in package ‘xcms’
Creating a generic function from function ‘hasFilledChromPeaks’ 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 Under development (unstable) (2019-12-14 r77572) -- "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.
> library(testthat)
> library(xcms)
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: BiocParallel
Loading required package: MSnbase
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 2.13.2
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 3.9.2
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
> library(faahKO)
> library(msdata)
>
> attr(faahko, "filepaths") <- sapply(
+ as.list(basename(attr(faahko, "filepaths"))),
+ function(x) system.file("cdf", if (length(grep("ko",x)) > 0) "KO" else "WT",
+ x, package = "faahKO"))
> if (.Platform$OS.type == "unix") {
+ prm <- MulticoreParam(3)
+ } else {
+ prm <- SnowParam(3)
+ }
> register(bpstart(prm))
> ## register(SerialParam())
>
> ## 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"))
>
> ## An xcmsRaw for the first file:
> faahko_xr_1 <- xcmsRaw(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+ profstep = 0)
> 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))
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
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.
> faahko_xs <- xcmsSet(faahko_3_files, profparam = list(step = 0),
+ method = "centWave", noise = 10000, snthresh = 40)
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
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.
> faahko_xsg <- group(faahko_xs)
Processing 2572 mz slices ... OK
> ## Doing also the retention time correction etc
> 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)
Processing 2572 mz slices ... OK
> 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)
Processing 2572 mz slices ... OK
> xod_r <- adjustRtime(as(od_x, "XCMSnExp"), param = ObiwarpParam())
Sample number 2 used as center sample.
Aligning ko15.CDF against ko16.CDF ... OK
Aligning ko18.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 514 regions of interest ... OK: 23 found.
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.
Warning message:
In .local(object, param, ...) :
Your data appears to be not centroided! CentWave works best on data in centroid mode.
>
> faahko_grouped_filled <- fillPeaks(group(faahko))
Processing 3195 mz slices ... OK
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt22.CDF
method: bin
step: 0.1
> faahko_grouped_retcor_filled <-
+ fillPeaks(group(retcor(group(updateObject(faahko)))))
Processing 3195 mz slices ... OK
Performing retention time correction using 132 peak groups.
Processing 3195 mz slices ... OK
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt22.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
>
> microtofq_fs <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+ system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_xr <- xcmsRaw(microtofq_fs[1], profstep = 0)
> microtofq_od <- readMSData(microtofq_fs, mode = "onDisk")
>
> ## Direct injection data:
> fticrf <- list.files(system.file("fticr", 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))
> fticr_xs <- xcmsSet(method="MSW", files=fticrf[1:2], scales=c(1,7),
+ SNR.method='data.mean' , winSize.noise=500,
+ peakThr=80000, amp.Th=0.005)
>
> fs <- 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"),
+ system.file('cdf/KO/ko19.CDF', package = "faahKO"))
> xs_1 <- xcmsSet(fs, profparam = list(step = 0), method = "centWave",
+ noise = 10000, snthresh = 50)
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 75 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 781 regions of interest ... OK: 46 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 79 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 41 found.
>
> ## 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))
> pest_swth <- findChromPeaks(pest_swth, param = cwp)
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 69 regions of interest ... OK: 63 found.
> pest_swth <- findChromPeaksIsolationWindow(pest_swth, param = cwp)
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 5 regions of interest ... OK: 5 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 32 regions of interest ... OK: 31 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 29 regions of interest ... OK: 21 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 13 regions of interest ... OK: 10 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 92 regions of interest ... OK: 83 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 20 regions of interest ... OK: 18 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 56 regions of interest ... OK: 48 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 29 regions of interest ... OK: 29 found.
>
> 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 101 regions of interest ... OK: 97 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: 13.2
Object of class: MergeNeighboringPeaksParam
Parameters:
expandRt: 5
expandMz: 0.1
ppm: 20
minProp: 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 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
center sample: ko16
Processing: ko15 ko18
center sample: ko18
Processing: ko15 ko16
center sample: ko18
Processing: ko15 ko16
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 56.00 64.00 80.00 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
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
HAM004_641fE_14-11-07--Exp1.extracted HAM004_641fE_14-11-07--Exp2.extracted
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
method: bin
step: 0.1
method: bin
step: 0.3
method: binlin
step: 0.2
method: binlinbase
step: 0.2
method: intlin
step: 0.2
center sample: ko15
Processing: ko16
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
center sample: ko16
Processing: ko15
Comparing peaks...OK
Comparing peaks...OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 2903 | SKIPPED: 8 | WARNINGS: 680 | FAILED: 0 ]
>
> proc.time()
user system elapsed
705.466 50.522 880.021
xcms.Rcheck/xcms-Ex.timings
| name | user | system | elapsed | |
| AutoLockMass-methods | 0.001 | 0.001 | 0.001 | |
| GenericParam | 0.046 | 0.008 | 0.054 | |
| XCMSnExp-class | 11.254 | 5.704 | 10.793 | |
| XCMSnExp-filter-methods | 11.654 | 7.394 | 9.774 | |
| XChromatogram | 9.586 | 3.378 | 8.412 | |
| adjustRtime-obiwarp | 14.297 | 6.365 | 14.655 | |
| adjustRtime-peakGroups | 9.915 | 5.699 | 10.187 | |
| align-Chromatogram | 0.015 | 0.005 | 0.019 | |
| applyAdjustedRtime | 5.987 | 2.066 | 6.029 | |
| binYonX | 0.004 | 0.005 | 0.008 | |
| breaks_on_binSize | 0.003 | 0.003 | 0.006 | |
| breaks_on_nBins | 0.001 | 0.000 | 0.002 | |
| chromPeakSpectra | 6.227 | 0.952 | 7.152 | |
| chromatogram-method | 35.553 | 11.679 | 19.582 | |
| descendZero | 0.001 | 0.001 | 0.002 | |
| do_findChromPeaks_centWave | 2.847 | 0.559 | 3.406 | |
| do_findChromPeaks_massifquant | 5.494 | 0.599 | 6.095 | |
| do_findChromPeaks_matchedFilter | 3.966 | 0.291 | 4.257 | |
| do_groupChromPeaks_density | 1.683 | 0.030 | 1.712 | |
| extractMsData-method | 6.841 | 2.727 | 6.531 | |
| featureChromatograms | 18.612 | 9.863 | 15.069 | |
| fillChromPeaks | 16.883 | 7.855 | 16.698 | |
| findChromPeaks-Chromatogram-CentWaveParam | 9.066 | 2.543 | 7.862 | |
| findChromPeaks-Chromatogram-MatchedFilter | 2.401 | 0.524 | 2.927 | |
| findChromPeaks-centWave | 8.100 | 4.508 | 7.454 | |
| findChromPeaks-centWaveWithPredIsoROIs | 0.062 | 0.015 | 0.077 | |
| findChromPeaks-massifquant | 13.455 | 5.267 | 10.646 | |
| findChromPeaks-matchedFilter | 4.502 | 0.569 | 5.071 | |
| findMZ | 0 | 0 | 0 | |
| findPeaks-MSW | 2.879 | 0.219 | 3.103 | |
| findPeaks.massifquant-methods | 8.870 | 0.536 | 9.407 | |
| findneutral | 0.001 | 0.000 | 0.000 | |
| group.mzClust | 0.001 | 0.001 | 0.001 | |
| group.nearest | 0.001 | 0.000 | 0.001 | |
| groupChromPeaks-density | 5.087 | 0.234 | 5.322 | |
| groupChromPeaks-mzClust | 2.777 | 0.166 | 2.944 | |
| groupChromPeaks-nearest | 5.020 | 0.262 | 5.280 | |
| highlightChromPeaks | 6.256 | 0.476 | 6.732 | |
| imputeLinInterpol | 0.007 | 0.003 | 0.010 | |
| imputeRowMin | 1.694 | 0.082 | 1.776 | |
| imputeRowMinRand | 1.77 | 0.12 | 1.89 | |
| medianFilter | 0.000 | 0.000 | 0.001 | |
| msn2xcmsRaw | 1.083 | 0.109 | 1.196 | |
| overlappingFeatures | 5.752 | 0.301 | 6.054 | |
| peakTable-methods | 0.000 | 0.000 | 0.001 | |
| peaksWithCentWave | 2.014 | 0.082 | 2.111 | |
| peaksWithMatchedFilter | 1.771 | 0.029 | 1.802 | |
| phenoDataFromPaths | 0.001 | 0.001 | 0.002 | |
| plotAdjustedRtime | 5.103 | 0.213 | 5.318 | |
| plotChromPeakDensity | 9.467 | 0.473 | 9.942 | |
| plotChromPeaks | 5.763 | 0.437 | 6.202 | |
| plotMsData | 2.039 | 0.065 | 2.105 | |
| plotQC | 2.082 | 0.086 | 2.169 | |
| profGenerate | 0 | 0 | 0 | |
| profMat-xcmsSet | 1.323 | 0.231 | 1.554 | |
| profStep-methods | 0 | 0 | 0 | |
| rectUnique | 0.002 | 0.001 | 0.003 | |
| refineChromPeaks-clean | 2.106 | 0.096 | 2.202 | |
| refineChromPeaks-merge | 10.364 | 0.266 | 10.631 | |
| rla | 0.002 | 0.000 | 0.002 | |
| stitch-methods | 0.001 | 0.001 | 0.001 | |
| sub-xcmsRaw-logicalOrNumeric-missing-missing-method | 1.085 | 0.029 | 1.114 | |
| writeMzTab | 1.718 | 0.053 | 1.770 | |
| xcmsPapply | 0.001 | 0.001 | 0.001 | |
| xcmsRaw | 0.001 | 0.000 | 0.001 | |