CHECK report for CAMERA on veracruz1
This page was generated on 2018-04-12 13:33:07 -0400 (Thu, 12 Apr 2018).
CAMERA 1.34.0 Steffen Neumann
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
URL: https://git.bioconductor.org/packages/CAMERA |
Branch: RELEASE_3_6 |
Last Commit: 3cb5610 |
Last Changed Date: 2017-10-30 12:39:25 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
Summary
Command output
Installation output
CAMERA.Rcheck/00install.out
Tests output
CAMERA.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
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: ProtGenerics
This is MSnbase version 2.4.2
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
This is xcms version 3.0.2
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
[1] TRUE
> 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 -- Thu Apr 12 01:20:18 2018
***********************************************
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
86.002 1.429 90.121
Example timings
CAMERA.Rcheck/CAMERA-Ex.timings