Steffen Neumann
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/xcms |
| Branch: RELEASE_3_9 |
| Last Commit: be5af29 |
| Last Changed Date: 2019-10-09 03:51:55 -0400 (Wed, 09 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:45:26 -0400 (Wed, 16 Oct 2019).
| Package 1728/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| xcms 3.6.2 Steffen Neumann
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: xcms |
| Version: 3.6.2 |
| 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_3.6.2.tar.gz |
| StartedAt: 2019-10-16 07:45:51 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 08:06:43 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1252.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: xcms.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_3.6.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/xcms.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 ‘xcms/DESCRIPTION’ ... OK * this is package ‘xcms’ version ‘3.6.2’ * 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:::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 :: 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 : : no visible global function definition for ‘newXMLNode’ buildDataProcessingList: no visible global function definition for ‘newXMLNode’ buildFeatureList : : no visible global function definition for ‘newXMLNode’ buildInputFiles : : no visible global function definition for ‘newXMLNode’ buildInputFiles: no visible global function definition for ‘newXMLNode’ buildMzq: no visible global function definition for ‘xmlTree’ buildSmallMoleculeList : : no visible global function definition for ‘newXMLNode’ buildSmallMoleculeList: no visible global function definition for ‘newXMLNode’ buildSoftwareList: no visible global function definition for ‘newXMLNode’ buildStudyVariableList : : no visible global function definition for ‘newXMLNode’ buildStudyVariableList : : : 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’ chromatogram,XCMSnExp: no visible global function definition for ‘selectFeatureData’ findChromPeaks,OnDiskMSnExp-CentWaveParam: no visible global function definition for ‘selectFeatureData’ 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’ show,XChromatograms: no visible global function definition for ‘varLabels’ show,XChromatograms: no visible global function definition for ‘fvarLabels’ 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<- fvarLabels 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 selectFeatureData sendCall varLabels 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 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 chromatogram-method 81.028 13.117 37.863 featureChromatograms 47.833 12.417 31.953 fillChromPeaks 16.727 7.298 16.221 findChromPeaks-massifquant 12.395 3.887 9.282 XCMSnExp-class 10.602 5.014 10.468 XCMSnExp-filter-methods 9.118 4.999 7.613 adjustRtime-obiwarp 8.916 3.547 9.273 findChromPeaks-Chromatogram-CentWaveParam 9.218 2.850 8.131 XChromatogram 8.743 2.988 7.824 adjustRtime-peakGroups 7.503 3.435 7.180 findChromPeaks-centWave 6.969 3.333 6.196 extractMsData-method 7.000 2.866 6.740 applyAdjustedRtime 6.582 3.219 6.671 plotChromPeakDensity 8.705 0.451 9.157 findPeaks.massifquant-methods 7.771 0.496 8.267 do_findChromPeaks_massifquant 5.422 0.605 6.030 plotChromPeaks 5.113 0.534 5.648 highlightChromPeaks 5.031 0.541 5.572 overlappingFeatures 4.885 0.256 5.141 * 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-3.9-bioc/meat/xcms.Rcheck/00check.log’ for details.
xcms.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL xcms
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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/3.6/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’
** 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 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.
> 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
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
This is xcms version 3.6.2
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(2)
+ } else {
+ prm <- SnowParam(2)
+ }
> 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"))
>
> ## 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 1025 regions of interest ... OK: 100 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 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 1025 regions of interest ... OK: 100 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 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 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 514 regions of interest ... OK: 23 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 515 regions of interest ... OK: 20 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/3.6/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/faahKO/cdf/WT/wt22.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 919 regions of interest ... OK: 41 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 937 regions of interest ... OK: 75 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 79 found.
>
>
>
>
> test_check("xcms")
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: 2679 | SKIPPED: 7 | WARNINGS: 625 | FAILED: 0 ]
>
> proc.time()
user system elapsed
499.460 29.898 687.305
xcms.Rcheck/xcms-Ex.timings
| name | user | system | elapsed | |
| AutoLockMass-methods | 0 | 0 | 0 | |
| GenericParam | 0.044 | 0.004 | 0.047 | |
| XCMSnExp-class | 10.602 | 5.014 | 10.468 | |
| XCMSnExp-filter-methods | 9.118 | 4.999 | 7.613 | |
| XChromatogram | 8.743 | 2.988 | 7.824 | |
| adjustRtime-obiwarp | 8.916 | 3.547 | 9.273 | |
| adjustRtime-peakGroups | 7.503 | 3.435 | 7.180 | |
| applyAdjustedRtime | 6.582 | 3.219 | 6.671 | |
| binYonX | 0.002 | 0.002 | 0.004 | |
| breaks_on_binSize | 0.003 | 0.002 | 0.004 | |
| breaks_on_nBins | 0.000 | 0.001 | 0.001 | |
| chromatogram-method | 81.028 | 13.117 | 37.863 | |
| descendZero | 0.002 | 0.000 | 0.002 | |
| do_findChromPeaks_centWave | 2.854 | 0.387 | 3.241 | |
| do_findChromPeaks_massifquant | 5.422 | 0.605 | 6.030 | |
| do_findChromPeaks_matchedFilter | 3.914 | 0.331 | 4.243 | |
| do_groupChromPeaks_density | 2.115 | 0.123 | 2.239 | |
| extractMsData-method | 7.000 | 2.866 | 6.740 | |
| featureChromatograms | 47.833 | 12.417 | 31.953 | |
| fillChromPeaks | 16.727 | 7.298 | 16.221 | |
| findChromPeaks-Chromatogram-CentWaveParam | 9.218 | 2.850 | 8.131 | |
| findChromPeaks-Chromatogram-MatchedFilter | 2.107 | 0.397 | 2.506 | |
| findChromPeaks-centWave | 6.969 | 3.333 | 6.196 | |
| findChromPeaks-centWaveWithPredIsoROIs | 0.060 | 0.013 | 0.072 | |
| findChromPeaks-massifquant | 12.395 | 3.887 | 9.282 | |
| findChromPeaks-matchedFilter | 3.593 | 0.467 | 4.060 | |
| findMZ | 0 | 0 | 0 | |
| findPeaks-MSW | 2.246 | 0.194 | 2.445 | |
| findPeaks.massifquant-methods | 7.771 | 0.496 | 8.267 | |
| findneutral | 0.000 | 0.001 | 0.000 | |
| group.mzClust | 0.000 | 0.000 | 0.001 | |
| group.nearest | 0.001 | 0.001 | 0.001 | |
| groupChromPeaks-density | 4.217 | 0.237 | 4.453 | |
| groupChromPeaks-mzClust | 2.336 | 0.203 | 2.538 | |
| groupChromPeaks-nearest | 4.363 | 0.287 | 4.649 | |
| highlightChromPeaks | 5.031 | 0.541 | 5.572 | |
| imputeLinInterpol | 0.007 | 0.004 | 0.012 | |
| imputeRowMin | 1.782 | 0.118 | 1.900 | |
| imputeRowMinRand | 1.779 | 0.065 | 1.845 | |
| medianFilter | 0.001 | 0.000 | 0.001 | |
| msn2xcmsRaw | 1.200 | 0.127 | 1.330 | |
| overlappingFeatures | 4.885 | 0.256 | 5.141 | |
| peakTable-methods | 0.000 | 0.000 | 0.001 | |
| peaksWithCentWave | 1.852 | 0.103 | 1.956 | |
| peaksWithMatchedFilter | 1.583 | 0.028 | 1.611 | |
| phenoDataFromPaths | 0.001 | 0.000 | 0.002 | |
| plotAdjustedRtime | 4.362 | 0.275 | 4.637 | |
| plotChromPeakDensity | 8.705 | 0.451 | 9.157 | |
| plotChromPeaks | 5.113 | 0.534 | 5.648 | |
| plotMsData | 1.734 | 0.091 | 1.826 | |
| plotQC | 2.119 | 0.098 | 2.219 | |
| profGenerate | 0.000 | 0.001 | 0.001 | |
| profMat-xcmsSet | 1.083 | 0.216 | 1.298 | |
| profStep-methods | 0.000 | 0.000 | 0.001 | |
| rectUnique | 0.002 | 0.001 | 0.003 | |
| rla | 0.002 | 0.000 | 0.002 | |
| stitch-methods | 0.000 | 0.000 | 0.001 | |
| sub-xcmsRaw-logicalOrNumeric-missing-missing-method | 0.833 | 0.052 | 0.885 | |
| writeMzTab | 1.753 | 0.092 | 1.846 | |
| xcmsPapply | 0.000 | 0.001 | 0.000 | |
| xcmsRaw | 0.000 | 0.000 | 0.001 | |