Steffen Neumann
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/CAMERA |
| git_branch: RELEASE_3_17 |
| git_last_commit: 8622c31 |
| git_last_commit_date: 2023-04-25 09:48:21 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 261/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CAMERA 1.56.0 (landing page) Steffen Neumann
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the CAMERA package: - 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: CAMERA |
| Version: 1.56.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAMERA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAMERA_1.56.0.tar.gz |
| StartedAt: 2023-10-17 07:22:32 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 07:39:56 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 1043.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAMERA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAMERA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAMERA_1.56.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CAMERA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAMERA/DESCRIPTION’ ... OK
* this is package ‘CAMERA’ version ‘1.56.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘Rmpi’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CAMERA’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 8.7Mb
sub-directories of 1Mb or more:
mzML 2.7Mb
quantiles 4.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘xcms’
A package should be listed in only one of these fields.
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
Please remove these calls from your code.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘annotateGrp’ ‘combineHypothese’ ‘fastMatch’ ‘naOmit’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call("getEIC", ..., PACKAGE = "xcms")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
File ‘CAMERA/R/zzz.R’:
.onLoad calls:
require(methods)
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
annotateGrp: no visible global function definition for ‘na.omit’
annotateGrpMPI2: no visible binding for global variable
‘papply_commondata’
cleanParallel: no visible global function definition for
‘mpi.close.Rslaves’
cleanParallel: no visible global function definition for ‘stopCluster’
compoundQuantiles: no visible global function definition for ‘tail’
createHypothese: no visible global function definition for ‘cutree’
createHypothese: no visible global function definition for ‘hclust’
createHypothese: no visible global function definition for ‘dist’
extractfragments: no visible global function definition for ‘median’
fast_corr: no visible global function definition for ‘pt’
findIsotopesForPS: no visible binding for global variable ‘tableMM48’
findKendrickMasses: no visible global function definition for ‘rainbow’
findKendrickMasses : <anonymous>: no visible global function definition
for ‘lines’
findNeutralLoss: no visible global function definition for ‘dist’
findNeutralLossSpecs : <anonymous>: no visible global function
definition for ‘dist’
fragments2metfrag : <anonymous>: no visible global function definition
for ‘write.table’
fragments2metfusion : <anonymous>: no visible binding for global
variable ‘object’
fragments2metfusion : <anonymous>: no visible global function
definition for ‘write.table’
getIsotopeCluster : <anonymous>: no visible global function definition
for ‘na.omit’
xsAnnotate: no visible global function definition for ‘mpi.comm.size’
xsAnnotate: no visible global function definition for
‘mpi.spawn.Rslaves’
xsAnnotate: no visible global function definition for ‘makeCluster’
xsAnnotate: no visible binding for global variable ‘graphMethod’
findAdducts,xsAnnotate: no visible global function definition for
‘mpi.comm.size’
findAdducts,xsAnnotate: no visible global function definition for
‘xcmsPapply’
findIsotopesWithValidation,xsAnnotate : <anonymous>: no visible global
function definition for ‘median’
getReducedPeaklist,xsAnnotate : <anonymous> : <anonymous>: no visible
global function definition for ‘median’
getReducedPeaklist,xsAnnotate : <anonymous>: no visible global function
definition for ‘prcomp’
getReducedPeaklist,xsAnnotate : <anonymous>: no visible global function
definition for ‘na.omit’
groupComplete,xsAnnotate: no visible global function definition for
‘dist’
groupComplete,xsAnnotate: no visible global function definition for
‘cutree’
groupComplete,xsAnnotate: no visible global function definition for
‘hclust’
groupDen,xsAnnotate: no visible global function definition for
‘density’
groupFWHM,xsAnnotate : <anonymous>: no visible global function
definition for ‘na.omit’
plotEICs,xsAnnotate: no visible global function definition for
‘rainbow’
plotEICs,xsAnnotate: no visible global function definition for
‘na.omit’
plotPeakEICs,xsAnnotate : <anonymous>: no visible binding for global
variable ‘pc’
plotPeakEICs,xsAnnotate: no visible binding for global variable ‘pspec’
plotPeakEICs,xsAnnotate: no visible global function definition for
‘rainbow’
plotPeakEICs,xsAnnotate: no visible global function definition for
‘na.omit’
plotPsSpectrum,xsAnnotate: no visible global function definition for
‘median’
plotPsSpectrum,xsAnnotate: no visible global function definition for
‘na.omit’
Undefined global functions or variables:
cutree density dist graphMethod hclust lines makeCluster median
mpi.close.Rslaves mpi.comm.size mpi.spawn.Rslaves na.omit object
papply_commondata pc prcomp pspec pt rainbow stopCluster tableMM48
tail write.table xcmsPapply
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "lines")
importFrom("stats", "cutree", "density", "dist", "hclust", "median",
"na.omit", "prcomp", "pt")
importFrom("utils", "tail", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: findKendrickMasses.Rd:21-22: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getIsotopeCluster 17.439 3.420 17.789
annotateDiffreport 17.462 2.844 14.120
groupCorr-methods 17.802 0.944 28.755
annotate-methods 6.762 0.714 10.796
findAdducts-methods 3.894 0.708 7.086
pspec2metfrag 3.857 0.662 6.821
getPeaklist-methods 3.762 0.678 6.854
getReducedPeaklist-methods 3.759 0.627 6.758
groupFWHM-methods 3.697 0.625 6.585
groupDen-methods 3.595 0.646 6.508
getAllPeakEICs-methods 3.824 0.264 6.278
* 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: 9 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CAMERA.Rcheck/00check.log’
for details.
CAMERA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAMERA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘CAMERA’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastMatch.c -o fastMatch.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CAMERA.so fastMatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-CAMERA/00new/CAMERA/libs ** R ** data ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CAMERA)
CAMERA.Rcheck/tests/runTests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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.
> require("CAMERA") || stop("unable to load CAMERA")
Loading required package: CAMERA
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, 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")'.
Loading required package: xcms
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.26.0
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
[1] TRUE
> BiocGenerics:::testPackage("CAMERA")
Processing 3195 mz slices ... OK
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/KO/ko15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/KO/ko16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/KO/ko18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/WT/wt19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/WT/wt21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/WT/wt22.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/WT/wt15.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/WT/wt16.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/WT/wt18.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/KO/ko19.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/KO/ko21.CDF
method: bin
step: 0.1
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/faahKO/cdf/KO/ko22.CDF
method: bin
step: 0.1
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 321
xsAnnotate has now 321 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 321 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating peak correlations across samples.
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 229
xsAnnotate has now 229 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 229 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Calculating peak correlations across samples.
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 244
xsAnnotate has now 244 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 244 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 321
xsAnnotate has now 321 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 321 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 321
xsAnnotate has now 321 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 321 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating isotope assignments in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 289
xsAnnotate has now 289 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 289 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 321
xsAnnotate has now 321 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 321 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 313
xsAnnotate has now 313 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 313 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating peak correlations across samples.
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 229
xsAnnotate has now 229 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 229 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating peak correlations across samples.
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 218
xsAnnotate has now 218 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 218 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 375
xsAnnotate has now 375 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 375 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 314
xsAnnotate has now 314 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 314 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 375
xsAnnotate has now 375 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 375 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 317
xsAnnotate has now 317 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 317 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 61
Start grouping after correlation.
Generating EIC's ..
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 314
xsAnnotate has now 314 groups, instead of 133
Generating peak matrix for peak annotation!
Calculating possible adducts in 314 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Processing 3195 mz slices ... OK
Start grouping after retention time.
Created 148 pseudospectra.
Start grouping after correlation.
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 148 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 148 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 333
xsAnnotate has now 333 groups, instead of 148
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 22
Generating peak matrix for peak annotation!
Found and use user-defined ruleset!
Calculating possible adducts in 333 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Start grouping after correlation.
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 254
xsAnnotate has now 254 groups, instead of 133
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 32
Generating peak matrix for peak annotation!
Found and use user-defined ruleset!
Calculating possible adducts in 254 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Start grouping after retention time.
Created 133 pseudospectra.
Start grouping after correlation.
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 329
xsAnnotate has now 329 groups, instead of 133
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 20
Generating peak matrix for peak annotation!
Found and use user-defined ruleset!
Calculating possible adducts in 329 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found.
Start grouping after retention time.
Created 14 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 20 50 60 70 80 90 100
Found isotopes: 32
Found and use user-defined ruleset!
Calculating possible adducts in 14 Groups...
% finished: 20 50 60 70 80 90 100
Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found.
Start grouping after retention time.
Created 14 pseudospectra.
Start grouping after correlation.
Calculating peak correlations in 14 Groups...
% finished: 20 50 60 70 80 90 100
Calculating graph cross linking in 14 Groups...
% finished: 20 50 60 70 80 90 100
New number of ps-groups: 35
xsAnnotate has now 35 groups, instead of 14
Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found.
Created 11 pseudospectra.
Processing 3195 mz slices ... OK
Start grouping after retention time.
Created 148 pseudospectra.
Start grouping after correlation.
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 148 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 148 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 333
xsAnnotate has now 333 groups, instead of 148
Start grouping after retention time.
Created 133 pseudospectra.
Start grouping after correlation.
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 133 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 329
xsAnnotate has now 329 groups, instead of 133
Start grouping after correlation.
Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks.
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 1 Groups...
% finished: 100
Calculating graph cross linking in 1 Groups...
% finished: 100
New number of ps-groups: 316
xsAnnotate has now 316 groups, instead of 1
Start grouping after correlation.
Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks.
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 1 Groups...
% finished: 100
Calculating graph cross linking in 1 Groups...
% finished: 100
New number of ps-groups: 316
xsAnnotate has now 316 groups, instead of 1
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 22
Generating peak matrix for peak annotation!
Found and use user-defined ruleset!
Calculating possible adducts in 316 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found.
Start grouping after retention time.
Created 14 pseudospectra.
Start grouping after correlation.
Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks.
Calculating peak correlations in 1 Groups...
% finished: 100
Calculating graph cross linking in 1 Groups...
% finished: 100
New number of ps-groups: 48
xsAnnotate has now 48 groups, instead of 1
Start grouping after correlation.
Calculating peak correlations in 14 Groups...
% finished: 20 50 60 70 80 90 100
Calculating graph cross linking in 14 Groups...
% finished: 20 50 60 70 80 90 100
New number of ps-groups: 48
xsAnnotate has now 48 groups, instead of 14
Start grouping after correlation.
Calculating peak correlations in 8 Groups...
% finished: 30 60 70 80 90 100
Calculating graph cross linking in 8 Groups...
% finished: 30 60 70 80 90 100
New number of ps-groups: 29
xsAnnotate has now 29 groups, instead of 14
Generating peak matrix!
Run isotope peak annotation
% finished: 20 50 60 70 80 90 100
Found isotopes: 32
Start grouping after correlation.
Calculating peak correlations in 14 Groups...
% finished: 20 50 60 70 80 90 100
Calculating graph cross linking in 14 Groups...
% finished: 20 50 60 70 80 90 100
New number of ps-groups: 48
xsAnnotate has now 48 groups, instead of 14
xsAnnotate contains no pseudospectra. Regroup all peaks into one!
Generating peak matrix!
Run isotope peak annotation
% finished: 100
Found isotopes: 32
Found and use user-defined ruleset!
Calculating possible adducts in 1 Groups...
% finished: 100
Generating peak matrix!
Run isotope peak annotation
% finished: 20 40 50 60 70 80 90 100
Found isotopes: 23
Calculating possible adducts in 48 Groups...
% finished: 20 40 50 60 70 80 90 100
Calculating possible adducts in 8 Groups...
% finished: 10
Processing 3195 mz slices ... OK
Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found.
Start grouping after retention time.
Created 14 pseudospectra.
Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found.
Start grouping after retention time.
Created 14 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 20 50 60 70 80 90 100
Found isotopes: 32
Calculating possible adducts in 14 Groups...
% finished: 20 50 60 70 80 90 100
RUNIT TEST PROTOCOL -- Tue Oct 17 07:39:39 2023
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
CAMERA RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
287.195 11.182 433.194
CAMERA.Rcheck/CAMERA-Ex.timings
| name | user | system | elapsed | |
| annotate-methods | 6.762 | 0.714 | 10.796 | |
| annotateDiffreport | 17.462 | 2.844 | 14.120 | |
| calcCaS-methods | 1.927 | 0.248 | 3.355 | |
| cleanParallel | 0 | 0 | 0 | |
| combinexsAnnos | 0.000 | 0.000 | 0.001 | |
| compoundLibraries | 0.001 | 0.001 | 0.003 | |
| compoundQuantiles | 0.071 | 0.014 | 0.128 | |
| findAdducts-methods | 3.894 | 0.708 | 7.086 | |
| findIsotopes-methods | 1.974 | 0.512 | 3.830 | |
| findIsotopesWithValidation-methods | 2.376 | 0.593 | 4.566 | |
| findKendrickMasses | 1.690 | 0.080 | 2.712 | |
| findNeutralLoss | 1.853 | 0.517 | 3.637 | |
| findNeutralLossSpecs | 1.869 | 0.489 | 3.624 | |
| getAllPeakEICs-methods | 3.824 | 0.264 | 6.278 | |
| getAtomCount-compoundQuantiles-method | 0.069 | 0.008 | 0.118 | |
| getIsotopeCluster | 17.439 | 3.420 | 17.789 | |
| getIsotopeProportion-compoundQuantiles-method | 0.071 | 0.026 | 0.136 | |
| getPeaklist-methods | 3.762 | 0.678 | 6.854 | |
| getReducedPeaklist-methods | 3.759 | 0.627 | 6.758 | |
| getpspectra | 1.833 | 0.453 | 3.524 | |
| groupCorr-methods | 17.802 | 0.944 | 28.755 | |
| groupDen-methods | 3.595 | 0.646 | 6.508 | |
| groupFWHM-methods | 3.697 | 0.625 | 6.585 | |
| massWindowSizes | 0.002 | 0.001 | 0.003 | |
| pspec2metfrag | 3.857 | 0.662 | 6.821 | |
| ruleSet-class | 0.055 | 0.003 | 0.084 | |
| xsAnnotate | 1.688 | 0.025 | 2.571 | |