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This page was generated on 2024-03-28 11:40:16 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 2254/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xcms 4.1.11  (landing page)
Steffen Neumann
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/xcms
git_branch: devel
git_last_commit: c37baa78
git_last_commit_date: 2024-03-18 02:59:02 -0400 (Mon, 18 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for xcms on lconway


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.

raw results


Summary

Package: xcms
Version: 4.1.11
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_4.1.11.tar.gz
StartedAt: 2024-03-28 00:53:20 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 01:09:24 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 964.1 seconds
RetCode: 0
Status:   OK  
CheckDir: xcms.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_4.1.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/xcms.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘4.1.11’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘xcms’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   3.5Mb
* 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 code 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 whether 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’ ‘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’
xcmsSet: no visible global function definition for ‘bpstopOnError’
xcmsSet: no visible global function definition for ‘bptry’
xcmsSet: no visible global function definition for ‘bpok’
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 bpok bpstopOnError bptry
  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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
XcmsExperiment                9.756  0.570  10.301
findPeaks.massifquant-methods 5.783  0.245   6.028
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/xcms.Rcheck/00check.log’
for details.


Installation output

xcms.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL xcms
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘xcms’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
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++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -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++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c massifquant/SegProc.cpp -o massifquant/SegProc.o
clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -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++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c obiwarp/mat.cpp -o obiwarp/mat.o
clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c obiwarp/vec.cpp -o obiwarp/vec.o
clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable]
  float bestscore;
        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c xcms_obiwarp.cpp -o xcms_obiwarp.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fastMatch.c -o fastMatch.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mzClust_hclust.c -o mzClust_hclust.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c mzROI.c -o mzROI.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c util.c -o util.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c xcms.c -o xcms.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -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++ -arch x86_64 -std=gnu++11 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.4-x86_64/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’
in method for ‘storeResults’ with signature ‘object="XcmsExperiment",param="PlainTextParam"’: no definition for class “XcmsExperiment”
in method for ‘storeResults’ with signature ‘object="XcmsExperiment",param="RDataParam"’: no definition for class “XcmsExperiment”
** help
*** installing help indices
*** copying figures
** 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)

Tests output

xcms.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

This is xcms version 4.1.11 


Attaching package: 'xcms'

The following object is masked from 'package:stats':

    sigma

> library(faahKO)
> library(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, 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 2.29.4 
  Visit https://lgatto.github.io/MSnbase/ to get started.
 Consider switching to the 'R for Mass Spectrometry'
 packages - see https://RforMassSpectrometry.org for details.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws

> 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"))
> 
> cwp <- CentWaveParam(noise = 10000, snthresh = 40, prefilter = c(3, 10000))
> 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 = cwp)
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 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.

> od_x <- faahko_od
> mzr <- matrix(c(335, 335, 344, 344), ncol = 2, byrow = TRUE)
> od_chrs <- chromatogram(od_x, mz = mzr)
> xod_x <- faahko_xod
> pdp <- PeakDensityParam(sampleGroups = rep(1, 3))
> xod_xg <- groupChromPeaks(xod_x, param = pdp)
> xod_xgr <- adjustRtime(xod_xg, param = PeakGroupsParam(span = 0.4))
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
> xod_xgrg <- groupChromPeaks(xod_xgr, param = pdp)
> xod_r <- adjustRtime(as(od_x, "XCMSnExp"), param = ObiwarpParam())
Sample number 2 used as center sample.
Aligning ko18.CDF against ko16.CDF ... OK

Aligning ko15.CDF against ko16.CDF ... OK

> 
> xod_chr <- findChromPeaks(filterMz(filterRt(od_x, rt = c(2500, 3500)),
+                                    mz = c(334.9, 344.1)),
+                           param = CentWaveParam())
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 515 regions of interest ... OK: 20 found.

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 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.

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")
> cwp2 <- CentWaveParam(snthresh = 5, noise = 100, ppm = 10,
+                       peakwidth = c(3, 20), prefilter = c(3, 1000))
> pest_swth <- findChromPeaks(pest_swth, param = cwp2)
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 11 regions of interest ... OK: 11 found.

> pest_swth <- findChromPeaksIsolationWindow(pest_swth, param = cwp2)
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 = cwp2)
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)
> 
> library(MsExperiment)
> fls <- normalizePath(faahko_3_files)
> df <- data.frame(mzML_file = basename(fls),
+                  dataOrigin = fls,
+                  sample = c("ko15", "ko16", "ko18"))
> mse <- readMsExperiment(spectraFiles = fls, sampleData = df)
> xmse <- findChromPeaks(mse, param = cwp)
> expect_true(length(processHistory(xmse)) == 1L)
> pdp <- PeakDensityParam(sampleGroups = rep(1, 3))
> xmseg <- groupChromPeaks(xmse, param = pdp, add = FALSE)
> expect_true(length(processHistory(xmseg)) == 2L)
> 
> test_check("xcms")
Object of class:  CleanPeaksParam 
 Parameters:
 - maxPeakwidth: [1] 13.2
Object of class:  MergeNeighboringPeaksParam 
 Parameters:
 - expandRt: [1] 5
 - expandMz: [1] 0.1
 - ppm: [1] 20
 - minProp: [1] 0.9
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
8.00  16.00  28.00  32.00  40.00  64.00  80.00  96.00  100.00  
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
8.00  16.00  28.00  32.00  40.00  56.00  64.00  80.00  88.00  96.00  100.00  
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
Object of class: XChromatogram
length of object: 0
from file: 
mz range: [NA, NA]
MS level: 1
Identified chromatographic peaks (0):
 rt	rtmin	rtmax	into	maxo	sn 
[ FAIL 0 | WARN 679 | SKIP 13 | PASS 4127 ]

══ 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 679 | SKIP 13 | PASS 4127 ]
> 
> bpstop(prm)
> 
> proc.time()
   user  system elapsed 
250.103  16.690 508.254 

Example timings

xcms.Rcheck/xcms-Ex.timings

nameusersystemelapsed
AutoLockMass-methods000
GenericParam0.0010.0010.001
PlainTextParam3.1380.2613.252
RDataParam0.0520.0050.056
XCMSnExp-class1.1250.1321.259
XCMSnExp-filter-methods0.4120.0270.439
XChromatogram1.2930.0761.374
XcmsExperiment 9.756 0.57010.301
applyAdjustedRtime1.5960.1341.861
binYonX0.0000.0010.002
breaks_on_binSize0.0010.0010.002
breaks_on_nBins000
chromPeakChromatograms2.0690.1012.170
chromPeakSpectra1.4380.0901.510
chromatogram-method1.3800.0921.474
correlate-Chromatogram0.0850.0070.093
descendZero0.0000.0000.001
do_findChromPeaks_centWave0.6610.0340.696
do_findChromPeaks_massifquant1.0100.0491.064
do_findChromPeaks_matchedFilter0.8260.0860.911
do_groupChromPeaks_density0.2710.0240.295
extractMsData-method0.3690.0290.398
featureChromatograms1.4630.0741.537
fillChromPeaks0.8870.0360.924
filter-MChromatograms0.2620.0090.270
filterFeatures0.1820.0040.186
findChromPeaks-Chromatogram-CentWaveParam1.8890.0911.981
findChromPeaks-Chromatogram-MatchedFilter0.2780.0050.283
findChromPeaks-centWave0.7570.0350.795
findChromPeaks-centWaveWithPredIsoROIs0.0110.0010.012
findChromPeaks-massifquant3.5940.1763.773
findChromPeaks-matchedFilter1.8130.0291.843
findMZ000
findPeaks-MSW1.2250.0351.273
findPeaks.massifquant-methods5.7830.2456.028
findneutral0.0000.0010.000
group.mzClust000
group.nearest000
groupFeatures-abundance-correlation0.2890.0040.293
groupFeatures-eic-similarity1.9630.0852.048
groupFeatures-similar-rtime0.2530.0040.256
groupOverlaps000
highlightChromPeaks0.8800.0540.933
imputeLinInterpol0.0030.0020.005
imputeRowMin1.1060.0421.148
imputeRowMinRand1.1260.0411.168
loadXcmsData0.0470.0020.049
manualChromPeaks0.2350.0210.259
medianFilter0.0000.0000.001
msn2xcmsRaw0.9100.0300.942
overlappingFeatures0.3210.0100.331
peakTable-methods000
peaksWithCentWave0.2250.0140.239
peaksWithMatchedFilter0.2810.0240.304
phenoDataFromPaths0.0010.0000.001
plotAdjustedRtime0.2690.0030.271
plotChromPeakDensity0.0960.0090.105
plotChromPeaks0.2440.0130.257
plotChromatogramsOverlay2.2650.1152.391
plotQC1.3150.0241.341
profGenerate0.0000.0010.000
profMat-xcmsSet0.9860.0421.029
profStep-methods000
rectUnique0.0090.0010.010
refineChromPeaks1.0130.0431.055
removeIntensity-Chromatogram0.0860.0190.104
rla0.0010.0000.001
stitch-methods0.0000.0010.000
storeResults0.0740.0040.079
sub-xcmsRaw-logicalOrNumeric-missing-missing-method0.8260.0470.874
writeMzTab1.0360.0221.058
xcmsRaw000