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CHECK report for ASICS on celaya2

This page was generated on 2020-01-16 13:50:48 -0500 (Thu, 16 Jan 2020).

Package 89/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASICS 2.3.0
Gaëlle Lefort
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/ASICS
Branch: master
Last Commit: e067e00
Last Changed Date: 2019-10-29 13:43:00 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ASICS
Version: 2.3.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASICS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASICS_2.3.0.tar.gz
StartedAt: 2020-01-16 01:50:04 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 02:03:41 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 817.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ASICS.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASICS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASICS_2.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ASICS.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASICS’ version ‘2.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ASICS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/ASICS.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
ASICS 58.474  1.207  59.685
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ASICS.Rcheck/00check.log’
for details.



Installation output

ASICS.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ASICS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ASICS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘ASICS.Rmd’ using ‘UTF-8’ 
   ‘ASICSUsersGuide.Rmd’ using ‘UTF-8’ 
** testing if installed package can be loaded from temporary location
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** testing if installed package can be loaded from final location
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** testing if installed package keeps a record of temporary installation path
* DONE (ASICS)

Tests output

ASICS.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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.

> library(testthat)
> library(ASICS)
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
> 
> test_check("ASICS")
OPLS-DA
26 samples x 33 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE RMSEP pre ort
Total    0.202    0.845   0.316 0.209  0.35   1   1
Binning 

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Normalisation... 
OPLS-DA
26 samples x 881 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE RMSEP pre ort
Total    0.245    0.895   0.548 0.173  0.37   1   1

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Import spectra from txt or csv files... 
Normalisation... 
Import spectra from fid files...  
Begin PreprocessingChain 
Begin ReadFids 
dim Fid_data:  2 16384 
IDs:  AG_faq_Beck01 AG_faq_Beck051 
non-unique IDs? 0 
End ReadFids 
It lasted 0.015 s user time, 0.003 s system time and 0.018 s elapsed time.
Begin GroupDelayCorrection 
End GroupDelayCorrection 
It lasted 0.036 s user time, 0.005 s system time and 0.042 s elapsed time.
Begin SolventSuppression 
End SolventSuppression 
It lasted 0.01 s user time, 0.007 s system time and 0.017 s elapsed time.
Begin Apodization 
End Apodization 
It lasted 0.002 s user time, 0.001 s system time and 0.003 s elapsed time.
Begin ZeroFilling 
End ZeroFilling 
It lasted 0.035 s user time, 0.002 s system time and 0.039 s elapsed time.
Begin FourierTransform 
End FourierTransform 
It lasted 0.012 s user time, 0.01 s system time and 0.021 s elapsed time.
Begin ZeroOrderPhaseCorrection 
End ZeroOrderPhaseCorrection 
It lasted 0.306 s user time, 0.088 s system time and 0.395 s elapsed time.
Begin InternalReferencing 
End InternalReferencing 
It lasted 0.022 s user time, 0.008 s system time and 0.03 s elapsed time.
Begin WindowSelection 
End WindowSelection 
It lasted 0.059 s user time, 0.003 s system time and 0.062 s elapsed time.
End PreprocessingChain 
It lasted 0.501 s user time, 0.131 s system time and 0.633 s elapsed time.
Normalisation... 
Import spectra from txt or csv files... 
Normalisation... 
Normalisation... 
Alignment... 
Peak detection 

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Finding reference spectrum 
Binning 

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Normalisation... 
Compute LCSS similarities 

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The reference spectrum is the number 2 : AG_faq_Beck051 
Align spectra 

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Import spectra from txt or csv files... 
Normalisation... 
Binning 

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Normalisation... 
Import spectra from txt or csv files... 
Normalisation... 
Remove areas from spectrum and library 

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Remove metabolites that cannot belong to the mixture 

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Compute weights 

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Translate library 

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Deform library peaks 

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Compute quantifications 

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Format results... 
Remove areas from spectrum and library 

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Remove metabolites that cannot belong to the mixture 

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Compute weights 

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Translate library 

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Deform library peaks 

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Compute quantifications 

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  |======================================================================| 100%

Format results... 
Import spectra from txt or csv files... 
Normalisation... 
Remove areas from spectrum and library 

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  |======================================================================| 100%

Remove metabolites that cannot belong to the mixture 

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Compute weights 

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Translate library 

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  |======================================================================| 100%

Deform library peaks 

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Compute quantifications 

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  |======================================================================| 100%

Format results... 
Remove areas from spectrum and library 

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  |======================================================================| 100%

Remove metabolites that cannot belong to the mixture 

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  |======================================================================| 100%

Compute weights 

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  |======================================================================| 100%

Translate library 

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  |======================================================================| 100%

Deform library peaks 

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Compute quantifications 

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Format results... 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 23 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
411.139  35.891 454.534 

Example timings

ASICS.Rcheck/ASICS-Ex.timings

nameusersystemelapsed
ASICS58.474 1.20759.685
ASICSUsersGuide0.0010.0000.001
accessors-methods0.2620.1690.431
alignSpectra2.4180.3052.724
binning0.2350.0510.287
combineAndSubset-methods0.0450.0020.047
createPureLibrary0.1570.0320.195
createSpectra0.1270.0180.149
formatForAnalysis1.3630.0261.393
importSpectra0.9890.1801.171
importSpectraBruker0.1020.0180.120
kruskalWallis0.4710.0040.473
normaliseSpectra0.0430.0020.045
oplsda0.2740.0060.280
pca0.8440.0150.860
plotAlignment1.3330.1621.495
summary-methods0.0450.0020.047
visualisation-methods-analyses2.0910.0462.142
visualisation-methods-spectra1.8470.2532.100