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CHECK report for IPO on tokay2

This page was generated on 2019-04-09 12:27:03 -0400 (Tue, 09 Apr 2019).

Package 815/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IPO 1.9.1
Thomas Riebenbauer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/IPO
Branch: master
Last Commit: 388cc2b
Last Changed Date: 2019-01-04 13:36:23 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: IPO
Version: 1.9.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IPO.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IPO_1.9.1.tar.gz
StartedAt: 2019-04-09 03:41:25 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:58:59 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 1053.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: IPO.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IPO.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IPO_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/IPO.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IPO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IPO' version '1.9.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'IPO' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/calculateXcmsSet.Rd:19: file link 'findPeaks.centWave' in package 'xcms' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/calculateXcmsSet.Rd:24: file link 'SerialParam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/calculateXcmsSet.Rd:25: file link 'MulticoreParam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/calculateXcmsSet.Rd:26: file link 'SnowParam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/calculateXcmsSet.Rd:53: file link 'findPeaks' in package 'xcms' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/optimizeXcmsSet.Rd:31: file link 'SerialParam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/optimizeXcmsSet.Rd:32: file link 'MulticoreParam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/optimizeXcmsSet.Rd:33: file link 'SnowParam' in package 'BiocParallel' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/IPO.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
calcPPS 2.18   0.05    8.86
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/IPO.Rcheck/00check.log'
for details.



Installation output

IPO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/IPO_1.9.1.tar.gz && rm -rf IPO.buildbin-libdir && mkdir IPO.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IPO.buildbin-libdir IPO_1.9.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL IPO_1.9.1.zip && rm IPO_1.9.1.tar.gz IPO_1.9.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  211k  100  211k    0     0  1352k      0 --:--:-- --:--:-- --:--:-- 1418k

install for i386

* installing *source* package 'IPO' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'IPO'
    finding HTML links ... done
    IPO-package                             html  
    attachList                              html  
    calcPPS                                 html  
    calculateXcmsSet                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/calculateXcmsSet.Rd:19: file link 'findPeaks.centWave' in package 'xcms' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/calculateXcmsSet.Rd:24: file link 'SerialParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/calculateXcmsSet.Rd:25: file link 'MulticoreParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/calculateXcmsSet.Rd:26: file link 'SnowParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/calculateXcmsSet.Rd:53: file link 'findPeaks' in package 'xcms' does not exist and so has been treated as a topic
    combineParams                           html  
    createModel                             html  
    decode                                  html  
    findIsotopes.CAMERA                     html  
    findIsotopes.IPO                        html  
    getBbdParameter                         html  
    getCcdParameter                         html  
    getDefaultRetCorCenterSample            html  
    getDefaultRetGroupStartingParams        html  
    getDefaultXcmsSetStartingParams         html  
    getNormalizedResponse                   html  
    getRGTVValues                           html  
    optimizeRetGroup                        html  
    optimizeXcmsSet                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/optimizeXcmsSet.Rd:31: file link 'SerialParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/optimizeXcmsSet.Rd:32: file link 'MulticoreParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKYODBy/R.INSTALL106844fc3215/IPO/man/optimizeXcmsSet.Rd:33: file link 'SnowParam' in package 'BiocParallel' does not exist and so has been treated as a topic
    toMatrix                                html  
    typeCastParams                          html  
    writeParamsTable                        html  
    writeRScript                            html  
** 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

install for x64

* installing *source* package 'IPO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IPO' as IPO_1.9.1.zip
* DONE (IPO)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'IPO' successfully unpacked and MD5 sums checked

Tests output

IPO.Rcheck/tests_i386/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("msdata")
> 
> BiocGenerics:::testPackage("IPO")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

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

    expand.grid


This is MSnbase version 2.9.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws


This is xcms version 3.5.1 


Attaching package: 'xcms'

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

    sigma


Attaching package: 'IPO'

The following object is masked from 'package:S4Vectors':

    decode




starting new DoE with:
min_peakwidth: c(3, 9.5)
max_peakwidth: c(10, 20)
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE

1
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found.
2
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
3
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 88 found.
4
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
5
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.
6
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 215 found.
7
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
8
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 149 found.
9
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 101 found.
10
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 225 found.



starting new DoE with:
min_peakwidth: c(3, 8.2)
max_peakwidth: c(9.2, 19.2)
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE

1
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found.
2
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found!
3
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 143 found.
4
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found!
5
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 222 found.
6
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 225 found.
7
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found!
8
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 144 found.
9
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 139 found.
10
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 222 found.
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 718 regions of interest ... OK: 220 found.
no increase, stopping
best parameter settings:
min_peakwidth: 5.6
max_peakwidth: 13
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE




starting new DoE with:
min_peakwidth: c(3, 9.5)
max_peakwidth: c(10, 20)
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE

1
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 59 
2
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
3
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 88 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 18 
4
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
5
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 52 
6
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 215 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 55 
7
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
8
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 149 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 35 
9
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 101 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 26 
10
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 52 
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 718 regions of interest ... OK: 221 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 62 



starting new DoE with:
min_peakwidth: c(3, 9.5)
max_peakwidth: c(10.5, 20.5)
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE

1
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 244 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 57 
2
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
3
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 88 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 18 
4
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
5
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 192 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 50 
6
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 215 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 55 
7
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
8
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 149 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 35 
9
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 101 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 26 
10
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 192 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 50 
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 718 regions of interest ... OK: 218 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 60 
no increase, stopping
best parameter settings:
min_peakwidth: 4.95
max_peakwidth: 13.5
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE

Loading required package: xcms
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: ProtGenerics

This is MSnbase version 2.9.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws


This is xcms version 3.5.1 


Attaching package: 'xcms'

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

    sigma

Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 217 regions of interest ... OK: 194 found.
Loading required package: xcms
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: ProtGenerics

This is MSnbase version 2.9.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws


This is xcms version 3.5.1 


Attaching package: 'xcms'

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

    sigma

Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 211 regions of interest ... OK: 196 found.



starting new DoE with:

distFunc: cor_opt
gapInit: 0.34
gapExtend: c(2.1, 2.7)
profStep: 1
plottype: none
response: 1
factorDiag: 2
factorGap: 1
localAlignment: 0
retcorMethod: obiwarp
bw: c(22, 38)
minfrac: 1
mzwid: 0.026
minsamp: 1
max: 50
center: 2

center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK



starting new DoE with:

gapExtend: c(2.04, 2.76)
bw: c(12.4, 31.6)
distFunc: cor_opt
gapInit: 0.34
profStep: 1
plottype: none
response: 1
factorDiag: 2
factorGap: 1
localAlignment: 0
retcorMethod: obiwarp
minfrac: 1
mzwid: 0.026
minsamp: 1
max: 50
center: 2

center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
no increase stopping



starting new DoE with:

missing: 0
extra: 0
span: c(0.1, 0.3)
smooth: loess
family: gaussian
plottype: none
retcorMethod: loess
bw: c(22, 38)
minfrac: c(0.3, 0.7)
mzwid: c(0.015, 0.035)
minsamp: 1
max: 50
center: 2

Processing 95119 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 95119 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 179 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 179 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 179 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 179 peak groups.
Processing 40766 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 95119 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 40766 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK



starting new DoE with:

span: c(0.001, 0.22)
bw: c(12.4, 31.6)
minfrac: c(0.46, 0.94)
mzwid: c(0.009, 0.029)
missing: 0
extra: 0
smooth: loess
family: gaussian
plottype: none
retcorMethod: loess
minsamp: 1
max: 50
center: 2

Processing 158530 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 158530 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 49200 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 158530 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 49200 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
no increase stopping


RUNIT TEST PROTOCOL -- Tue Apr 09 03:52:44 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
IPO RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
There were 42 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 322.78   13.54  351.43 

IPO.Rcheck/tests_x64/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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("msdata")
> 
> BiocGenerics:::testPackage("IPO")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

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

    expand.grid


This is MSnbase version 2.9.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws


This is xcms version 3.5.1 


Attaching package: 'xcms'

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

    sigma


Attaching package: 'IPO'

The following object is masked from 'package:S4Vectors':

    decode




starting new DoE with:
min_peakwidth: c(3, 9.5)
max_peakwidth: c(10, 20)
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE

1
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found.
2
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
3
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 88 found.
4
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
5
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.
6
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 215 found.
7
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
8
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 149 found.
9
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 101 found.
10
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 225 found.



starting new DoE with:
min_peakwidth: c(3, 8.2)
max_peakwidth: c(9.2, 19.2)
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE

1
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found.
2
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found!
3
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 143 found.
4
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found!
5
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 222 found.
6
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 225 found.
7
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found!
8
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 144 found.
9
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 139 found.
10
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 222 found.
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 718 regions of interest ... OK: 220 found.
no increase, stopping
best parameter settings:
min_peakwidth: 5.6
max_peakwidth: 13
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE




starting new DoE with:
min_peakwidth: c(3, 9.5)
max_peakwidth: c(10, 20)
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE

1
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 59 
2
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
3
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 88 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 18 
4
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
5
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 52 
6
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 215 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 55 
7
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
8
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 149 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 35 
9
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 101 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 26 
10
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 52 
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 718 regions of interest ... OK: 221 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 62 



starting new DoE with:
min_peakwidth: c(3, 9.5)
max_peakwidth: c(10.5, 20.5)
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE

1
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 244 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 57 
2
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
3
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 88 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 18 
4
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
5
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 192 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 50 
6
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 215 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 55 
7
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
8
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 149 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 35 
9
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 101 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 26 
10
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 192 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 50 
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 718 regions of interest ... OK: 218 found.
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
 % finished: 100  
Found isotopes: 60 
no increase, stopping
best parameter settings:
min_peakwidth: 4.95
max_peakwidth: 13.5
ppm: 56
mzdiff: -0.001
snthresh: 10
noise: 0
prefilter: 3
value_of_prefilter: 100
mzCenterFun: wMean
integrate: 1
fitgauss: FALSE
verbose.columns: FALSE

Loading required package: xcms
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: ProtGenerics

This is MSnbase version 2.9.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws


This is xcms version 3.5.1 


Attaching package: 'xcms'

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

    sigma

Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 217 regions of interest ... OK: 194 found.
Loading required package: xcms
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: ProtGenerics

This is MSnbase version 2.9.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws


This is xcms version 3.5.1 


Attaching package: 'xcms'

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

    sigma

Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 211 regions of interest ... OK: 196 found.



starting new DoE with:

distFunc: cor_opt
gapInit: 0.34
gapExtend: c(2.1, 2.7)
profStep: 1
plottype: none
response: 1
factorDiag: 2
factorGap: 1
localAlignment: 0
retcorMethod: obiwarp
bw: c(22, 38)
minfrac: 1
mzwid: 0.026
minsamp: 1
max: 50
center: 2

center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK



starting new DoE with:

gapExtend: c(1.74, 2.46)
bw: c(12.4, 31.6)
distFunc: cor_opt
gapInit: 0.34
profStep: 1
plottype: none
response: 1
factorDiag: 2
factorGap: 1
localAlignment: 0
retcorMethod: obiwarp
minfrac: 1
mzwid: 0.026
minsamp: 1
max: 50
center: 2

center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
center sample:  MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 
Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818  Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK

Processing 54877 mz slices ... OK
no increase stopping



starting new DoE with:

missing: 0
extra: 0
span: c(0.1, 0.3)
smooth: loess
family: gaussian
plottype: none
retcorMethod: loess
bw: c(22, 38)
minfrac: c(0.3, 0.7)
mzwid: c(0.015, 0.035)
minsamp: 1
max: 50
center: 2

Processing 95119 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 95119 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 95119 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 179 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 179 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 179 peak groups.
Processing 40766 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 179 peak groups.
Processing 40766 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 95119 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 95119 mz slices ... OK
Processing 40766 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 40766 mz slices ... OK
Processing 57072 mz slices ... OK
Performing retention time correction using 183 peak groups.
Processing 57072 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK



starting new DoE with:

span: c(0.001, 0.22)
bw: c(12.4, 31.6)
minfrac: c(0.46, 0.94)
mzwid: c(0.009, 0.029)
missing: 0
extra: 0
smooth: loess
family: gaussian
plottype: none
retcorMethod: loess
minsamp: 1
max: 50
center: 2

Processing 158530 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 158530 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 158530 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 49200 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 49200 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 181 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 158530 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 158530 mz slices ... OK
Processing 49200 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 49200 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
Processing 75094 mz slices ... OK
Performing retention time correction using 185 peak groups.
Processing 75094 mz slices ... OK
no increase stopping


RUNIT TEST PROTOCOL -- Tue Apr 09 03:58:52 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
IPO RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
There were 42 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 339.76   12.10  367.12 

Example timings

IPO.Rcheck/examples_i386/IPO-Ex.timings

nameusersystemelapsed
IPO-package000
attachList000
calcPPS2.180.058.86
calculateXcmsSet2.350.032.38
combineParams0.010.000.01
createModel0.460.000.52
decode000
findIsotopes.CAMERA2.510.082.59
findIsotopes.IPO3.390.153.55
getBbdParameter000
getCcdParameter0.020.000.01
getDefaultRetCorCenterSample000
getDefaultRetGroupStartingParams000
getDefaultXcmsSetStartingParams000
getNormalizedResponse000
getRGTVValues000
optimizeRetGroup000
optimizeXcmsSet000
toMatrix000
typeCastParams000
writeParamsTable0.000.000.05
writeRScript000

IPO.Rcheck/examples_x64/IPO-Ex.timings

nameusersystemelapsed
IPO-package000
attachList000
calcPPS2.970.124.34
calculateXcmsSet2.590.092.69
combineParams0.020.000.01
createModel0.30.00.3
decode000
findIsotopes.CAMERA2.090.022.11
findIsotopes.IPO3.410.173.58
getBbdParameter000
getCcdParameter0.010.000.01
getDefaultRetCorCenterSample000
getDefaultRetGroupStartingParams000
getDefaultXcmsSetStartingParams000
getNormalizedResponse000
getRGTVValues000
optimizeRetGroup000
optimizeXcmsSet000
toMatrix000
typeCastParams000
writeParamsTable0.020.000.02
writeRScript000