Steffen Neumann
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/xcms |
| git_branch: RELEASE_3_14 |
| git_last_commit: ed02588 |
| git_last_commit_date: 2021-11-19 10:10:20 -0400 (Fri, 19 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:09:00 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2070/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| xcms 3.16.1 (landing page) Steffen Neumann
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: xcms |
| Version: 3.16.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:xcms.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings xcms_3.16.1.tar.gz |
| StartedAt: 2022-04-12 19:59:59 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 20:17:23 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1044.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: xcms.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:xcms.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings xcms_3.16.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/xcms.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘3.16.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... 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
* checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
R 4.0Mb
* 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:
‘.copy_env’ ‘.getChromPeakData’ ‘.get_closest_index’
‘.spectra_for_peaks’ ‘.split_by_file2’ ‘.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’
chromPeakSpectra: no visible global function definition for ‘List’
featureSpectra: no visible global function definition for ‘List’
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 ‘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’
refineChromPeaks,XCMSnExp-FilterIntensityParam: no visible binding for
global variable ‘value’
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:
List 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 pData<- recvOneResult rgl.bbox rgl.clear
rgl.points rgl.surface sampleNames saveXML sendCall value
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
findPeaks.massifquant-methods 9.237 0.298 9.536
groupFeatures-eic-similarity 8.632 0.132 8.771
findChromPeaks-massifquant 5.764 0.253 6.018
* 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: 6 NOTEs
See
‘/Users/biocbuild/bbs-3.14-bioc/meat/xcms.Rcheck/00check.log’
for details.
xcms.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL xcms
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c fastMatch.c -o fastMatch.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mzROI.c -o mzROI.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c util.c -o util.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c xcms.c -o xcms.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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++ -mmacosx-version-min=10.13 -std=gnu++14 -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/4.1/Resources/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’
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 version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: 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, 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 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 2.20.4
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 3.16.1
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)
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 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", 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: 28 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 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 670 | SKIP 11 | PASS 2852 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (11)
[ FAIL 0 | WARN 670 | SKIP 11 | PASS 2852 ]
>
> bpstop(prm)
>
>
> proc.time()
user system elapsed
224.146 9.306 491.912
xcms.Rcheck/xcms-Ex.timings
| name | user | system | elapsed | |
| AutoLockMass-methods | 0.000 | 0.000 | 0.001 | |
| GenericParam | 0.001 | 0.000 | 0.002 | |
| XCMSnExp-class | 3.498 | 0.167 | 3.668 | |
| XCMSnExp-filter-methods | 0.477 | 0.019 | 0.497 | |
| XChromatogram | 3.443 | 0.098 | 3.584 | |
| adjustRtime-obiwarp | 3.019 | 0.158 | 3.178 | |
| adjustRtime-peakGroups | 0.605 | 0.016 | 0.623 | |
| applyAdjustedRtime | 2.335 | 0.099 | 2.434 | |
| binYonX | 0.001 | 0.001 | 0.004 | |
| breaks_on_binSize | 0.001 | 0.002 | 0.003 | |
| breaks_on_nBins | 0 | 0 | 0 | |
| chromPeakSpectra | 3.704 | 0.129 | 3.803 | |
| chromatogram-method | 2.283 | 0.097 | 2.384 | |
| correlate-Chromatogram | 0.015 | 0.001 | 0.016 | |
| descendZero | 0.001 | 0.000 | 0.001 | |
| do_findChromPeaks_centWave | 0.878 | 0.039 | 0.917 | |
| do_findChromPeaks_massifquant | 1.836 | 0.046 | 1.882 | |
| do_findChromPeaks_matchedFilter | 1.258 | 0.103 | 1.360 | |
| do_groupChromPeaks_density | 0.301 | 0.013 | 0.313 | |
| extractMsData-method | 1.027 | 0.037 | 1.063 | |
| featureChromatograms | 1.575 | 0.030 | 1.606 | |
| fillChromPeaks | 3.028 | 0.065 | 3.093 | |
| filter-MChromatograms | 0.283 | 0.002 | 0.285 | |
| findChromPeaks-Chromatogram-CentWaveParam | 4.889 | 0.099 | 4.995 | |
| findChromPeaks-Chromatogram-MatchedFilter | 0.731 | 0.031 | 0.765 | |
| findChromPeaks-centWave | 3.065 | 0.076 | 3.145 | |
| findChromPeaks-centWaveWithPredIsoROIs | 0.011 | 0.002 | 0.013 | |
| findChromPeaks-massifquant | 5.764 | 0.253 | 6.018 | |
| findChromPeaks-matchedFilter | 1.981 | 0.027 | 2.009 | |
| findMZ | 0 | 0 | 0 | |
| findPeaks-MSW | 1.402 | 0.032 | 1.435 | |
| findPeaks.massifquant-methods | 9.237 | 0.298 | 9.536 | |
| findneutral | 0.000 | 0.000 | 0.001 | |
| group.mzClust | 0.000 | 0.001 | 0.001 | |
| group.nearest | 0.000 | 0.001 | 0.001 | |
| groupChromPeaks-density | 0.398 | 0.007 | 0.404 | |
| groupChromPeaks-mzClust | 2.737 | 0.064 | 2.801 | |
| groupChromPeaks-nearest | 0.535 | 0.024 | 0.559 | |
| groupFeatures-abundance-correlation | 0.701 | 0.011 | 0.713 | |
| groupFeatures-eic-similarity | 8.632 | 0.132 | 8.771 | |
| groupFeatures-similar-rtime | 0.601 | 0.006 | 0.607 | |
| groupOverlaps | 0.001 | 0.000 | 0.001 | |
| highlightChromPeaks | 1.085 | 0.045 | 1.130 | |
| imputeLinInterpol | 0.006 | 0.002 | 0.008 | |
| imputeRowMin | 1.742 | 0.041 | 1.784 | |
| imputeRowMinRand | 1.674 | 0.020 | 1.694 | |
| medianFilter | 0.001 | 0.001 | 0.001 | |
| msn2xcmsRaw | 1.092 | 0.051 | 1.144 | |
| overlappingFeatures | 0.386 | 0.003 | 0.388 | |
| peakTable-methods | 0 | 0 | 0 | |
| peaksWithCentWave | 0.961 | 0.027 | 0.988 | |
| peaksWithMatchedFilter | 0.293 | 0.006 | 0.300 | |
| phenoDataFromPaths | 0.001 | 0.000 | 0.001 | |
| plotAdjustedRtime | 0.551 | 0.014 | 0.565 | |
| plotChromPeakDensity | 0.034 | 0.003 | 0.036 | |
| plotChromPeaks | 0.814 | 0.017 | 0.832 | |
| plotChromatogramsOverlay | 3.433 | 0.034 | 3.472 | |
| plotMsData | 2.006 | 0.037 | 2.044 | |
| plotQC | 2.192 | 0.023 | 2.217 | |
| profGenerate | 0.000 | 0.000 | 0.001 | |
| profMat-xcmsSet | 1.767 | 0.068 | 1.837 | |
| profStep-methods | 0 | 0 | 0 | |
| rectUnique | 0.002 | 0.001 | 0.002 | |
| refineChromPeaks-clean | 0.056 | 0.002 | 0.059 | |
| refineChromPeaks-filter-intensity | 3.375 | 0.051 | 3.427 | |
| refineChromPeaks-merge | 2.793 | 0.046 | 2.841 | |
| removeIntensity-Chromatogram | 0.002 | 0.001 | 0.003 | |
| rla | 0.000 | 0.000 | 0.002 | |
| stitch-methods | 0.000 | 0.001 | 0.000 | |
| sub-xcmsRaw-logicalOrNumeric-missing-missing-method | 0.994 | 0.038 | 1.033 | |
| writeMzTab | 1.642 | 0.022 | 1.666 | |
| xcmsRaw | 0.000 | 0.000 | 0.001 | |