Steffen Neumann
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/xcms |
| git_branch: RELEASE_3_18 |
| git_last_commit: b274757 |
| git_last_commit_date: 2023-12-20 08:47:02 -0400 (Wed, 20 Dec 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:28 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 | ||||
| Package 2250/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| xcms 4.0.2 (landing page) Steffen Neumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the xcms package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/xcms.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: xcms |
| Version: 4.0.2 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:xcms.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings xcms_4.0.2.tar.gz |
| StartedAt: 2024-04-16 06:15:17 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 06:36:20 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 1262.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: xcms.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:xcms.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings xcms_4.0.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/xcms.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '4.0.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'xcms' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
R 3.5Mb
libs 1.1Mb
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'MALDIquant:::.localMaxima' 'MSnbase:::.MSnExpReqFvarLabels'
'MSnbase:::.plotXIC' 'MSnbase:::.vertical_sub_layout'
'MSnbase:::formatFileSpectrumNames' 'Spectra:::.concatenate_spectra'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.copy_env' '.get_closest_index' '.validChromPeaksMatrix' 'MSW.cwt'
'MSW.getLocalMaximumCWT' 'MSW.getRidge' 'descendMin' 'descendMinTol'
'estimateChromNoise' 'getLocalNoiseEstimate' 'na.flatfill'
'patternVsRowScore'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.xcmsFragments.plotTree: no visible global function definition for
'edgemode<-'
.xcmsFragments.plotTree: no visible global function definition for
'addEdge'
buildAnalysisSummary: no visible global function definition for
'newXMLNode'
buildAssayList : <anonymous>: no visible global function definition for
'newXMLNode'
buildAssayList: no visible global function definition for 'newXMLNode'
buildAuditCollection: no visible global function definition for
'newXMLNode'
buildCVlist: no visible global function definition for 'newXMLNode'
buildCVlist: no visible global function definition for 'addChildren'
buildCvParams : <anonymous>: no visible global function definition for
'newXMLNode'
buildDataProcessingList: no visible global function definition for
'newXMLNode'
buildFeatureList : <anonymous>: no visible global function definition
for 'newXMLNode'
buildInputFiles : <anonymous>: no visible global function definition
for 'newXMLNode'
buildInputFiles: no visible global function definition for 'newXMLNode'
buildMzq: no visible global function definition for 'xmlTree'
buildSmallMoleculeList : <anonymous>: no visible global function
definition for 'newXMLNode'
buildSmallMoleculeList: no visible global function definition for
'newXMLNode'
buildSoftwareList: no visible global function definition for
'newXMLNode'
buildStudyVariableList : <anonymous>: no visible global function
definition for 'newXMLNode'
buildStudyVariableList : <anonymous> : <anonymous>: no visible global
function definition for 'newXMLNode'
buildStudyVariableList: no visible global function definition for
'newXMLNode'
plotQC: no visible global function definition for 'sampleNames'
running: multiple local function definitions for 'funct' with different
formal arguments
verify.mzQuantML: no visible global function definition for
'xmlTreeParse'
verify.mzQuantML: no visible global function definition for
'xmlInternalTreeParse'
verify.mzQuantML: no visible global function definition for
'xmlSchemaValidate'
xcmsClusterApply: no visible global function definition for
'checkCluster'
xcmsClusterApply : submit: no visible global function definition for
'sendCall'
xcmsClusterApply: no visible global function definition for
'recvOneResult'
xcmsClusterApply: no visible global function definition for
'checkForRemoteErrors'
xcmsPapply: no visible global function definition for 'mpi.comm.size'
xcmsPapply: no visible global function definition for
'mpi.spawn.Rslaves'
xcmsPapply: no visible global function definition for 'mpi.comm.rank'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.send.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.recv.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.any.source'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.any.tag'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for
'mpi.bcast.Robj2slave'
xcmsPapply: no visible global function definition for 'mpi.bcast.cmd'
xcmsPapply: no visible global function definition for 'mpi.recv.Robj'
xcmsPapply: no visible global function definition for 'mpi.any.source'
xcmsPapply: no visible global function definition for 'mpi.any.tag'
xcmsPapply: no visible global function definition for
'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for 'mpi.send.Robj'
xcmsParallelSetup: no visible global function definition for
'mpi.spawn.Rslaves'
xcmsParallelSetup: no visible global function definition for
'mpi.comm.size'
xcmsParallelSetup: no visible global function definition for
'mpi.comm.rank'
xcmsParallelSetup: no visible global function definition for
'makeCluster'
plotSurf,xcmsRaw: no visible global function definition for 'clear3d'
plotSurf,xcmsRaw: no visible global function definition for 'surface3d'
plotSurf,xcmsRaw: no visible global function definition for 'points3d'
plotSurf,xcmsRaw: no visible global function definition for 'bbox3d'
plotTree,xcmsFragments: no visible global function definition for
'edgemode<-'
plotTree,xcmsFragments: no visible global function definition for
'addEdge'
write.cdf,xcmsRaw: no visible global function definition for
'ncdim_def'
write.cdf,xcmsRaw: no visible global function definition for
'ncvar_def'
write.cdf,xcmsRaw: no visible global function definition for
'nc_create'
write.cdf,xcmsRaw: no visible global function definition for
'ncvar_put'
write.cdf,xcmsRaw: no visible global function definition for
'ncatt_put'
write.cdf,xcmsRaw: no visible global function definition for 'nc_close'
write.mzQuantML,xcmsSet: no visible global function definition for
'saveXML'
write.mzdata,xcmsRaw: no visible global function definition for
'base64encode'
Undefined global functions or variables:
addChildren addEdge base64encode bbox3d checkCluster
checkForRemoteErrors clear3d edgemode<- makeCluster mpi.any.source
mpi.any.tag mpi.bcast.Robj2slave mpi.bcast.cmd mpi.comm.rank
mpi.comm.size mpi.get.sourcetag mpi.recv.Robj mpi.send.Robj
mpi.spawn.Rslaves nc_close nc_create ncatt_put ncdim_def ncvar_def
ncvar_put newXMLNode points3d recvOneResult sampleNames saveXML
sendCall surface3d xmlInternalTreeParse xmlSchemaValidate xmlTree
xmlTreeParse
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/xcms/libs/x64/xcms.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
XcmsExperiment 11.64 0.50 13.00
findPeaks.massifquant-methods 6.88 0.15 7.03
findChromPeaks-Chromatogram-CentWaveParam 5.08 0.08 5.15
* 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
'F:/biocbuild/bbs-3.18-bioc/meat/xcms.Rcheck/00check.log'
for details.
xcms.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL xcms
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'xcms' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/SegProc.cpp -o massifquant/SegProc.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp: In member function 'void DynProg::find_path(VEC::MatF&, VEC::VecF&, int, float, float, int, float)':
obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable]
1113 | float bestscore;
| ^~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-inline -c fastMatch.c -o fastMatch.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzROI.c -o mzROI.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-inline -c util.c -o util.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-inline -c xcms.c -o xcms.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
357 | int idx = 0;
| ^~~
g++ -std=gnu++17 -shared -s -static-libgcc -o xcms.dll tmp.def 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 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-xcms/00new/xcms/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'group' in package 'xcms'
Creating a new generic function for 'sigma' in package 'xcms'
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xcms)
xcms.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(xcms)
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.28.1
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 4.0.2
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
> library(faahKO)
> library(msdata)
>
> if (.Platform$OS.type == "unix") {
+ prm <- MulticoreParam(3)
+ } else {
+ # prm <- SnowParam(3)
+ prm <- SerialParam()
+ }
> register(bpstart(prm))
>
> ## Create some objects we can re-use in different tests:
> faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+ system.file('cdf/KO/ko16.CDF', package = "faahKO"),
+ system.file('cdf/KO/ko18.CDF', package = "faahKO"))
>
> faahko_od <- readMSData(faahko_3_files, mode = "onDisk")
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
> faahko_xod <- findChromPeaks(
+ faahko_od, param = CentWaveParam(noise = 10000, snthresh = 40,
+ prefilter = c(3, 10000)))
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 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.
> od_x <- faahko_od
> mzr <- matrix(c(335, 335, 344, 344), ncol = 2, byrow = TRUE)
> od_chrs <- chromatogram(od_x, mz = mzr)
> xod_x <- faahko_xod
> pdp <- PeakDensityParam(sampleGroups = rep(1, 3))
> xod_xg <- groupChromPeaks(xod_x, param = pdp)
> xod_xgr <- adjustRtime(xod_xg, param = PeakGroupsParam(span = 0.4))
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
> xod_xgrg <- groupChromPeaks(xod_xgr, param = pdp)
> xod_r <- adjustRtime(as(od_x, "XCMSnExp"), param = ObiwarpParam())
Sample number 2 used as center sample.
Aligning 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 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.
>
> microtofq_fs <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+ system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_od <- readMSData(microtofq_fs, mode = "onDisk")
>
> ## Direct injection data:
> fticrf <- list.files(system.file("fticr-mzML", package = "msdata"),
+ recursive = TRUE, full.names = TRUE)
> fticr <- readMSData(fticrf[1:2], msLevel. = 1, mode = "onDisk")
> fticr_xod <- findChromPeaks(fticr, MSWParam(scales = c(1, 7),
+ peakThr = 80000, ampTh = 0.005,
+ SNR.method = "data.mean",
+ winSize.noise = 500))
>
> ## Pesticide data
> fl <- system.file("TripleTOF-SWATH", "PestMix1_SWATH.mzML", package = "msdata")
> pest_swth <- readMSData(fl, mode = "onDisk")
> cwp <- CentWaveParam(snthresh = 5, noise = 100, ppm = 10,
+ peakwidth = c(3, 20), prefilter = c(3, 1000))
> pest_swth <- findChromPeaks(pest_swth, param = cwp)
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 11 regions of interest ... OK: 11 found.
> pest_swth <- findChromPeaksIsolationWindow(pest_swth, param = cwp)
Detecting mass traces at 10 ppm ... OK
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 2 regions of interest ... OK: 2 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 7 regions of interest ... OK: 7 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3 regions of interest ... OK: 3 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 17 regions of interest ... OK: 17 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3 regions of interest ... OK: 2 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 10 regions of interest ... OK: 10 found.
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3 regions of interest ... OK: 3 found.
Warning messages:
1: In .centWave_orig(mz = mz, int = int, scantime = scantime, valsPerSpect = valsPerSpect, :
No ROIs found!
2: 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 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
8.00 16.00 28.00 32.00 40.00 64.00 80.00 96.00 100.00
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
8.00 16.00 28.00 32.00 40.00 56.00 64.00 80.00 88.00 96.00 100.00
8.00 16.00 24.00 28.00 32.00 40.00 48.00 52.00 56.00 60.00 64.00 72.00 80.00 84.00 88.00 96.00 100.00
Object of class: XChromatogram
length of object: 0
from file:
mz range: [NA, NA]
MS level: 1
Identified chromatographic peaks (0):
rt rtmin rtmax into maxo sn
[ FAIL 0 | WARN 1023 | SKIP 13 | PASS 3991 ]
══ Skipped tests (13) ══════════════════════════════════════════════════════════
• empty test (13): 'test_XcmsExperiment-plotting.R:13:1',
'test_XcmsExperiment-plotting.R:44:1', 'test_functions-XCMSnExp.R:80:1',
'test_functions-XCMSnExp.R:91:1', 'test_functions-XCMSnExp.R:449:1',
'test_functions-XChromatogram.R:60:1', 'test_functions-utils.R:49:1',
'test_matchpeaks.R:1:1', 'test_methods-MChromatograms.R:181:1',
'test_methods-XCMSnExp.R:2278:1', 'test_methods-XChromatogram.R:1:1',
'test_methods-XChromatogram.R:60:1', 'test_methods-XChromatograms.R:140:1'
[ FAIL 0 | WARN 1023 | SKIP 13 | PASS 3991 ]
>
> bpstop(prm)
>
> proc.time()
user system elapsed
694.34 29.68 725.79
xcms.Rcheck/xcms-Ex.timings
| name | user | system | elapsed | |
| AutoLockMass-methods | 0 | 0 | 0 | |
| GenericParam | 0.02 | 0.00 | 0.02 | |
| XCMSnExp-class | 2.83 | 0.06 | 2.95 | |
| XCMSnExp-filter-methods | 0.39 | 0.00 | 0.39 | |
| XChromatogram | 2.44 | 0.03 | 2.47 | |
| XcmsExperiment | 11.64 | 0.50 | 13.00 | |
| applyAdjustedRtime | 1.89 | 0.09 | 1.98 | |
| binYonX | 0 | 0 | 0 | |
| breaks_on_binSize | 0 | 0 | 0 | |
| breaks_on_nBins | 0 | 0 | 0 | |
| chromPeakChromatograms | 2.50 | 0.13 | 2.62 | |
| chromPeakSpectra | 2.60 | 0.05 | 3.15 | |
| chromatogram-method | 1.54 | 0.07 | 1.62 | |
| correlate-Chromatogram | 0.02 | 0.00 | 0.02 | |
| descendZero | 0 | 0 | 0 | |
| do_findChromPeaks_centWave | 0.61 | 0.05 | 0.65 | |
| do_findChromPeaks_massifquant | 1.83 | 0.06 | 1.89 | |
| do_findChromPeaks_matchedFilter | 0.81 | 0.08 | 0.89 | |
| do_groupChromPeaks_density | 0.33 | 0.02 | 0.35 | |
| extractMsData-method | 0.33 | 0.03 | 0.36 | |
| featureChromatograms | 1.00 | 0.01 | 1.01 | |
| fillChromPeaks | 1.07 | 0.02 | 1.10 | |
| filter-MChromatograms | 0.22 | 0.01 | 0.23 | |
| findChromPeaks-Chromatogram-CentWaveParam | 5.08 | 0.08 | 5.15 | |
| findChromPeaks-Chromatogram-MatchedFilter | 0.37 | 0.00 | 0.38 | |
| findChromPeaks-centWave | 2.74 | 0.05 | 2.83 | |
| findChromPeaks-centWaveWithPredIsoROIs | 0.01 | 0.00 | 0.01 | |
| findChromPeaks-massifquant | 3.85 | 0.14 | 3.99 | |
| findChromPeaks-matchedFilter | 2.14 | 0.08 | 2.21 | |
| findMZ | 0 | 0 | 0 | |
| findPeaks-MSW | 1.51 | 0.05 | 1.66 | |
| findPeaks.massifquant-methods | 6.88 | 0.15 | 7.03 | |
| findneutral | 0 | 0 | 0 | |
| group.mzClust | 0 | 0 | 0 | |
| group.nearest | 0 | 0 | 0 | |
| groupFeatures-abundance-correlation | 0.40 | 0.03 | 0.44 | |
| groupFeatures-eic-similarity | 2.42 | 0.21 | 2.62 | |
| groupFeatures-similar-rtime | 0.36 | 0.00 | 0.36 | |
| groupOverlaps | 0 | 0 | 0 | |
| highlightChromPeaks | 0.96 | 0.14 | 1.10 | |
| imputeLinInterpol | 0 | 0 | 0 | |
| imputeRowMin | 1.47 | 0.03 | 1.50 | |
| imputeRowMinRand | 1.50 | 0.03 | 1.53 | |
| loadXcmsData | 0.11 | 0.00 | 0.11 | |
| manualChromPeaks | 0.28 | 0.03 | 0.41 | |
| medianFilter | 0 | 0 | 0 | |
| msn2xcmsRaw | 1.22 | 0.01 | 1.35 | |
| overlappingFeatures | 0.36 | 0.00 | 0.36 | |
| peakTable-methods | 0 | 0 | 0 | |
| peaksWithCentWave | 1.13 | 0.05 | 1.18 | |
| peaksWithMatchedFilter | 0.26 | 0.00 | 0.26 | |
| phenoDataFromPaths | 0 | 0 | 0 | |
| plotAdjustedRtime | 0.4 | 0.0 | 0.4 | |
| plotChromPeakDensity | 0.03 | 0.01 | 0.05 | |
| plotChromPeaks | 0.35 | 0.00 | 0.34 | |
| plotChromatogramsOverlay | 2.92 | 0.04 | 2.97 | |
| plotMsData | 2.27 | 0.06 | 2.33 | |
| plotQC | 1.82 | 0.01 | 1.84 | |
| profGenerate | 0 | 0 | 0 | |
| profMat-xcmsSet | 1.19 | 0.03 | 1.22 | |
| profStep-methods | 0 | 0 | 0 | |
| rectUnique | 0 | 0 | 0 | |
| refineChromPeaks | 1.13 | 0.18 | 1.30 | |
| removeIntensity-Chromatogram | 0 | 0 | 0 | |
| rla | 0 | 0 | 0 | |
| stitch-methods | 0 | 0 | 0 | |
| sub-xcmsRaw-logicalOrNumeric-missing-missing-method | 1.03 | 0.01 | 1.05 | |
| writeMzTab | 1.48 | 0.02 | 1.50 | |
| xcmsRaw | 0 | 0 | 0 | |