Thomas Lieb
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/IPO |
| git_branch: RELEASE_3_17 |
| git_last_commit: e5631e2 |
| git_last_commit_date: 2023-04-25 10:48:45 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:10 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1018/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IPO 1.26.0 (landing page) Thomas Lieb
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the IPO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IPO.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: IPO |
| Version: 1.26.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IPO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IPO_1.26.0.tar.gz |
| StartedAt: 2023-10-16 02:57:35 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 03:21:46 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 1450.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IPO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IPO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IPO_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/IPO.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IPO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IPO’ version ‘1.26.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findIsotopes.IPO 4.232 1.997 8.031
combineParams 3.582 1.727 0.091
findIsotopes.CAMERA 3.351 1.801 6.484
calculateXcmsSet 3.090 1.726 6.899
calcPPS 3.416 0.058 10.479
* 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
‘/Users/biocbuild/bbs-3.17-bioc/meat/IPO.Rcheck/00check.log’
for details.
IPO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IPO ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘IPO’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (IPO)
IPO.Rcheck/tests/runTests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
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:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.26.0
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:base':
trimws
This is xcms version 3.22.0
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 -- Mon Oct 16 03:21:29 2023
***********************************************
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 30 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
515.062 102.800 812.515
IPO.Rcheck/IPO-Ex.timings
| name | user | system | elapsed | |
| IPO-package | 0.000 | 0.002 | 0.001 | |
| attachList | 0.000 | 0.001 | 0.002 | |
| calcPPS | 3.416 | 0.058 | 10.479 | |
| calculateXcmsSet | 3.090 | 1.726 | 6.899 | |
| combineParams | 3.582 | 1.727 | 0.091 | |
| createModel | 0.148 | 0.060 | 0.227 | |
| decode | 0.001 | 0.002 | 0.005 | |
| findIsotopes.CAMERA | 3.351 | 1.801 | 6.484 | |
| findIsotopes.IPO | 4.232 | 1.997 | 8.031 | |
| getBbdParameter | 0.006 | 0.001 | 0.006 | |
| getCcdParameter | 0.014 | 0.000 | 0.020 | |
| getDefaultRetCorCenterSample | 0.001 | 0.001 | 0.002 | |
| getDefaultRetGroupStartingParams | 0.001 | 0.001 | 0.003 | |
| getDefaultXcmsSetStartingParams | 0.001 | 0.002 | 0.003 | |
| getNormalizedResponse | 0.000 | 0.001 | 0.000 | |
| getRGTVValues | 0.000 | 0.001 | 0.001 | |
| optimizeRetGroup | 0.000 | 0.001 | 0.001 | |
| optimizeXcmsSet | 0.000 | 0.001 | 0.000 | |
| toMatrix | 0.001 | 0.001 | 0.002 | |
| typeCastParams | 0.001 | 0.000 | 0.001 | |
| writeParamsTable | 0.009 | 0.002 | 0.019 | |
| writeRScript | 0.004 | 0.001 | 0.006 | |