Thomas Lieb
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/IPO |
| git_branch: RELEASE_3_20 |
| git_last_commit: a73e03b |
| git_last_commit_date: 2024-10-29 10:13:08 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 1049/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IPO 1.32.0 (landing page) Thomas Lieb
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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: 1.32.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IPO.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings IPO_1.32.0.tar.gz |
| StartedAt: 2024-12-20 02:43:01 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 03:12:49 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 1787.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IPO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IPO.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings IPO_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/IPO.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'IPO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IPO' version '1.32.0'
* 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 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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
calcPPS 3.36 0.04 22.50
findIsotopes.IPO 2.14 0.10 21.44
findIsotopes.CAMERA 1.20 0.00 20.53
calculateXcmsSet 0.92 0.02 20.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'runTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'F:/biocbuild/bbs-3.20-bioc/meat/IPO.Rcheck/00check.log'
for details.
IPO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL IPO ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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, saveRDS, setdiff, 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")'.
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found.
2
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
3
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 88 found.
4
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
5
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.
6
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 215 found.
7
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
8
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 149 found.
9
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 101 found.
10
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found.
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found.
2
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found!
3
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 143 found.
4
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found!
5
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 222 found.
6
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 805 regions of interest ... OK: 225 found.
7
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found!
8
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 144 found.
9
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 139 found.
10
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 628 regions of interest ... OK: 222 found.
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
3
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
5
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
8
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
3
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
5
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Detecting mass traces at 56 ppm ... OK
Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found!
8
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
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: BiocParallel
This is xcms version 4.4.0
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.
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.4.0
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.
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 179 peak groups.
Performing retention time correction using 179 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 179 peak groups.
Performing retention time correction using 179 peak groups.
Performing retention time correction using 183 peak groups.
Performing retention time correction using 183 peak groups.
Performing retention time correction using 183 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 183 peak groups.
Performing retention time correction using 183 peak groups.
Performing retention time correction using 183 peak groups.
Performing retention time correction using 183 peak groups.
Performing retention time correction using 183 peak groups.
Performing retention time correction using 185 peak groups.
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
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 181 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
Performing retention time correction using 185 peak groups.
no increase stopping
RUNIT TEST PROTOCOL -- Fri Dec 20 03:12:37 2024
***********************************************
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
408.50 17.07 1358.75
IPO.Rcheck/IPO-Ex.timings
| name | user | system | elapsed | |
| IPO-package | 0 | 0 | 0 | |
| attachList | 0 | 0 | 0 | |
| calcPPS | 3.36 | 0.04 | 22.50 | |
| calculateXcmsSet | 0.92 | 0.02 | 20.27 | |
| combineParams | 0.02 | 0.00 | 0.01 | |
| createModel | 0.09 | 0.01 | 0.11 | |
| decode | 0 | 0 | 0 | |
| findIsotopes.CAMERA | 1.20 | 0.00 | 20.53 | |
| findIsotopes.IPO | 2.14 | 0.10 | 21.44 | |
| getBbdParameter | 0 | 0 | 0 | |
| getCcdParameter | 0.02 | 0.00 | 0.01 | |
| getDefaultRetCorCenterSample | 0 | 0 | 0 | |
| getDefaultRetGroupStartingParams | 0 | 0 | 0 | |
| getDefaultXcmsSetStartingParams | 0 | 0 | 0 | |
| getNormalizedResponse | 0 | 0 | 0 | |
| getRGTVValues | 0 | 0 | 0 | |
| optimizeRetGroup | 0 | 0 | 0 | |
| optimizeXcmsSet | 0 | 0 | 0 | |
| toMatrix | 0 | 0 | 0 | |
| typeCastParams | 0 | 0 | 0 | |
| writeParamsTable | 0.00 | 0.01 | 0.02 | |
| writeRScript | 0 | 0 | 0 | |