Back to Multiple platform build/check report for BioC 3.12
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for CAMERA on tokay1

This page was generated on 2020-08-10 12:12:09 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CAMERA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 216/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAMERA 1.45.1
Steffen Neumann
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/CAMERA
Branch: master
Last Commit: 45384c6
Last Changed Date: 2020-06-02 05:43:49 -0400 (Tue, 02 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAMERA
Version: 1.45.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAMERA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CAMERA_1.45.1.tar.gz
StartedAt: 2020-08-10 00:05:33 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 00:20:07 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 873.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CAMERA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAMERA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CAMERA_1.45.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CAMERA.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAMERA/DESCRIPTION' ... OK
* this is package 'CAMERA' version '1.45.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... 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 whether package 'CAMERA' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CAMERA.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    mzdata      1.7Mb
    quantiles   5.0Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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.
Missing object imported by a ':::' call: 'xcms:::xcmsClusterApply'
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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/CAMERA/libs/i386/CAMERA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/CAMERA/libs/x64/CAMERA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
groupCorr-methods      20.56   0.35   20.91
getIsotopeCluster       7.27   0.25   33.90
getAllPeakEICs-methods  5.58   0.07    6.24
annotate-methods        5.16   0.48    7.93
findAdducts-methods     5.50   0.10    5.59
annotateDiffreport      2.65   0.14   32.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
groupCorr-methods      27.19   0.61   27.80
groupFWHM-methods       6.64   0.07    6.72
pspec2metfrag           6.28   0.10    6.40
groupDen-methods        6.12   0.11    6.26
annotate-methods        5.35   0.24    5.57
getIsotopeCluster       5.28   0.03   31.91
getAllPeakEICs-methods  5.00   0.02    5.01
annotateDiffreport      2.75   0.07   27.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 8 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/CAMERA.Rcheck/00check.log'
for details.



Installation output

CAMERA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CAMERA_1.45.1.tar.gz && rm -rf CAMERA.buildbin-libdir && mkdir CAMERA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CAMERA.buildbin-libdir CAMERA_1.45.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CAMERA_1.45.1.zip && rm CAMERA_1.45.1.tar.gz CAMERA_1.45.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1800k  100 1800k    0     0  3949k      0 --:--:-- --:--:-- --:--:-- 3982k

install for i386

* installing *source* package 'CAMERA' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fastMatch.c -o fastMatch.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CAMERA.dll tmp.def fastMatch.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CAMERA.buildbin-libdir/00LOCK-CAMERA/00new/CAMERA/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
** help
*** installing help indices
  converting help for package 'CAMERA'
    finding HTML links ... done
    annotate-methods                        html  
    annotateDiffreport                      html  
    finding level-2 HTML links ... done

    calcCaS-methods                         html  
    calcCiS-methods                         html  
    calcIsotopes-methods                    html  
    calcPC-methods                          html  
    calcPC.hcs-methods                      html  
    calcPC.lpc-methods                      html  
    cleanParallel                           html  
    combinexsAnnos                          html  
    compoundLibraries                       html  
    compoundQuantiles-class                 html  
    compoundQuantiles                       html  
    findAdducts-methods                     html  
    findIsotopes-methods                    html  
    findIsotopesWithValidation-methods      html  
    findKendrickMasses                      html  
    findNeutralLoss                         html  
    findNeutralLossSpecs                    html  
    getAllPeakEICs-methods                  html  
    getAtomCount-compoundQuantiles-method   html  
    getIsotopeCluster                       html  
    getIsotopeProportion-compoundQuantiles-method
                                            html  
    getPeaklist-methods                     html  
    getReducedPeaklist-methods              html  
    getpspectra                             html  
    groupCorr-methods                       html  
    groupDen-methods                        html  
    groupFWHM-methods                       html  
    massWindowSizes                         html  
    mm14                                    html  
    plotEIC.xsAnnotate                      html  
    plotPsSpectrum.xsAnnotate               html  
    psDist-methods                          html  
    pspec2metfrag                           html  
    ruleSet-class                           html  
    xsAnnotate-class                        html  
    xsAnnotate                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CAMERA' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fastMatch.c -o fastMatch.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CAMERA.dll tmp.def fastMatch.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CAMERA.buildbin-libdir/CAMERA/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
* MD5 sums
packaged installation of 'CAMERA' as CAMERA_1.45.1.zip
* DONE (CAMERA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CAMERA' successfully unpacked and MD5 sums checked

Tests output

CAMERA.Rcheck/tests_i386/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 object is masked from 'package:base':

    expand.grid

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.15.3 
  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 3.11.6 


Attaching package: 'xcms'

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

    sigma

[1] TRUE
Warning message:
replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA' 
> BiocGenerics:::testPackage("CAMERA")
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 -- Mon Aug 10 00:18:11 2020 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CAMERA RUnit Tests - 14 test functions, 0 errors, 0 failures
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  82.57    2.60   85.15 

CAMERA.Rcheck/tests_x64/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 object is masked from 'package:base':

    expand.grid

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.15.3 
  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 3.11.6 


Attaching package: 'xcms'

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

    sigma

[1] TRUE
Warning message:
replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA' 
> BiocGenerics:::testPackage("CAMERA")
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 -- Mon Aug 10 00:20:02 2020 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CAMERA RUnit Tests - 14 test functions, 0 errors, 0 failures
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 108.09    2.43  110.59 

Example timings

CAMERA.Rcheck/examples_i386/CAMERA-Ex.timings

nameusersystemelapsed
annotate-methods5.160.487.93
annotateDiffreport 2.65 0.1432.64
calcCaS-methods2.800.002.79
cleanParallel000
combinexsAnnos000
compoundLibraries000
compoundQuantiles0.130.000.13
findAdducts-methods5.500.105.59
findIsotopes-methods2.670.072.75
findIsotopesWithValidation-methods3.340.053.39
findKendrickMasses2.840.082.92
findNeutralLoss2.710.082.79
findNeutralLossSpecs2.510.042.57
getAllPeakEICs-methods5.580.076.24
getAtomCount-compoundQuantiles-method0.110.000.11
getIsotopeCluster 7.27 0.2533.90
getIsotopeProportion-compoundQuantiles-method0.110.000.11
getPeaklist-methods3.750.083.83
getReducedPeaklist-methods3.850.073.92
getpspectra1.650.081.73
groupCorr-methods20.56 0.3520.91
groupDen-methods4.440.034.47
groupFWHM-methods3.310.033.34
massWindowSizes000
pspec2metfrag4.070.084.15
ruleSet-class0.060.000.06
xsAnnotate1.900.001.89

CAMERA.Rcheck/examples_x64/CAMERA-Ex.timings

nameusersystemelapsed
annotate-methods5.350.245.57
annotateDiffreport 2.75 0.0727.22
calcCaS-methods2.160.002.15
cleanParallel000
combinexsAnnos000
compoundLibraries000
compoundQuantiles0.060.000.06
findAdducts-methods4.360.054.41
findIsotopes-methods2.610.062.67
findIsotopesWithValidation-methods2.780.082.86
findKendrickMasses1.830.001.83
findNeutralLoss2.290.012.32
findNeutralLossSpecs2.110.032.14
getAllPeakEICs-methods5.000.025.01
getAtomCount-compoundQuantiles-method0.080.000.08
getIsotopeCluster 5.28 0.0331.91
getIsotopeProportion-compoundQuantiles-method0.060.030.09
getPeaklist-methods4.270.054.31
getReducedPeaklist-methods4.000.054.05
getpspectra2.470.032.50
groupCorr-methods27.19 0.6127.80
groupDen-methods6.120.116.26
groupFWHM-methods6.640.076.72
massWindowSizes0.020.000.02
pspec2metfrag6.280.106.40
ruleSet-class0.050.000.05
xsAnnotate2.460.002.47