Multiple platform build/check report for BioC 3.8 - CHECK report for IPO on malbec1

Package: IPO

Version: 1.8.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:IPO.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings IPO_1.8.1.tar.gz

StartedAt: 2019-04-16 00:52:17 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:01:11 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 533.7 seconds

RetCode: 0

Status: OK

CheckDir: IPO.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:IPO.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings IPO_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/IPO.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IPO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IPO’ version ‘1.8.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘IPO’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/IPO.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL IPO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘IPO’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IPO)


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, lengths, 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 2.8.3 
  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 3.4.4 


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

Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 211 regions of interest ... OK: 196 found.
Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 217 regions of interest ... OK: 194 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 16 01:01:08 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 
354.848   7.176 358.792

name	user	system	elapsed
IPO-package	0	0	0
attachList	0	0	0
calcPPS	2.188	0.168	2.513
calculateXcmsSet	2.600	0.048	2.651
combineParams	0.020	0.000	0.019
createModel	0.356	0.000	0.356
decode	0.000	0.004	0.001
findIsotopes.CAMERA	2.520	0.032	2.558
findIsotopes.IPO	3.100	0.048	3.178
getBbdParameter	0.004	0.000	0.004
getCcdParameter	0.008	0.000	0.011
getDefaultRetCorCenterSample	0.004	0.000	0.001
getDefaultRetGroupStartingParams	0.000	0.000	0.001
getDefaultXcmsSetStartingParams	0.000	0.000	0.001
getNormalizedResponse	0.000	0.000	0.001
getRGTVValues	0	0	0
optimizeRetGroup	0	0	0
optimizeXcmsSet	0	0	0
toMatrix	0.004	0.000	0.001
typeCastParams	0	0	0
writeParamsTable	0.008	0.000	0.008
writeRScript	0.004	0.000	0.002

CHECK report for IPO on malbec1

Summary

Command output

Installation output

Tests output

Example timings