Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-21 15:04:53 -0400 (Wed, 21 Jul 2021).

CHECK results for CAMERA on nebbiolo1

To the developers/maintainers of the CAMERA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAMERA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 233/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAMERA 1.48.0  (landing page)
Steffen Neumann
Snapshot Date: 2021-07-20 04:50:13 -0400 (Tue, 20 Jul 2021)
URL: https://git.bioconductor.org/packages/CAMERA
Branch: RELEASE_3_13
Last Commit: 5ad3135
Last Changed Date: 2021-05-19 11:42:44 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAMERA
Version: 1.48.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CAMERA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CAMERA_1.48.0.tar.gz
StartedAt: 2021-07-20 09:06:41 -0400 (Tue, 20 Jul 2021)
EndedAt: 2021-07-20 09:18:27 -0400 (Tue, 20 Jul 2021)
EllapsedTime: 705.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CAMERA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CAMERA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CAMERA_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CAMERA.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAMERA/DESCRIPTION’ ... OK
* this is package ‘CAMERA’ version ‘1.48.0’
* 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 ... 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
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    mzdata      1.4Mb
    quantiles   3.1Mb
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
getIsotopeCluster  26.145  4.892  11.732
annotateDiffreport 17.558  3.239   8.498
groupCorr-methods  17.850  0.327  18.186
calcCaS-methods     7.477  1.294   1.736
annotate-methods    6.304  0.152   6.479
* 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: 8 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/CAMERA.Rcheck/00check.log’
for details.



Installation output

CAMERA.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CAMERA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘CAMERA’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fastMatch.c -o fastMatch.o
gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o CAMERA.so fastMatch.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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)

Tests output

CAMERA.Rcheck/tests/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("CAMERA") || stop("unable to load CAMERA")
Loading required package: CAMERA
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, 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 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 2.18.0 
  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 3.14.0 


Attaching package: 'xcms'

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

    sigma

[1] TRUE
> BiocGenerics:::testPackage("CAMERA")
Processing 3195 mz slices ... OK
/home/biocbuild/bbs-3.13-bioc/R/library/faahKO/cdf/WT/wt19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.13-bioc/R/library/faahKO/cdf/WT/wt21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.13-bioc/R/library/faahKO/cdf/WT/wt22.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.13-bioc/R/library/faahKO/cdf/KO/ko15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.13-bioc/R/library/faahKO/cdf/KO/ko16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.13-bioc/R/library/faahKO/cdf/KO/ko18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.13-bioc/R/library/faahKO/cdf/WT/wt15.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.13-bioc/R/library/faahKO/cdf/WT/wt16.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.13-bioc/R/library/faahKO/cdf/WT/wt18.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.13-bioc/R/library/faahKO/cdf/KO/ko19.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.13-bioc/R/library/faahKO/cdf/KO/ko21.CDF 
method:  bin 
step:  0.1 
/home/biocbuild/bbs-3.13-bioc/R/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 Jul 20 09:18:23 2021 
*********************************************** 
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 
332.730   8.512 319.365 

Example timings

CAMERA.Rcheck/CAMERA-Ex.timings

nameusersystemelapsed
annotate-methods6.3040.1526.479
annotateDiffreport17.558 3.239 8.498
calcCaS-methods7.4771.2941.736
cleanParallel0.0000.0010.000
combinexsAnnos0.0000.0010.000
compoundLibraries0.0000.0020.001
compoundQuantiles0.0760.0080.087
findAdducts-methods4.0030.1164.119
findIsotopes-methods2.1890.0322.222
findIsotopesWithValidation-methods2.6940.0402.734
findKendrickMasses1.3790.0161.395
findNeutralLoss1.9960.0262.023
findNeutralLossSpecs2.0850.0172.103
getAllPeakEICs-methods3.6370.0643.702
getAtomCount-compoundQuantiles-method0.0520.0040.057
getIsotopeCluster26.145 4.89211.732
getIsotopeProportion-compoundQuantiles-method0.0730.0000.073
getPeaklist-methods3.9860.1844.170
getReducedPeaklist-methods3.7900.0843.873
getpspectra2.0700.0242.094
groupCorr-methods17.850 0.32718.186
groupDen-methods3.3300.0443.374
groupFWHM-methods3.3690.0363.405
massWindowSizes0.0010.0000.001
pspec2metfrag3.3160.0283.343
ruleSet-class0.0390.0000.038
xsAnnotate1.3230.0161.338