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CHECK report for ASICS on malbec2

This page was generated on 2019-10-16 12:13:47 -0400 (Wed, 16 Oct 2019).

Package 86/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASICS 2.0.1
Gaëlle Lefort
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ASICS
Branch: RELEASE_3_9
Last Commit: d165432
Last Changed Date: 2019-06-18 10:46:00 -0400 (Tue, 18 Jun 2019)
malbec2 Linux (Ubuntu 18.04.2 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: 2.0.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ASICS_2.0.1.tar.gz
StartedAt: 2019-10-15 23:51:13 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 23:58:52 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 458.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ASICS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ASICS_2.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ASICS.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘2.0.1’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.6Mb
* 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 or elapsed time > 5s
        user system elapsed
ASICS 33.288  0.184   33.49
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/ASICS.Rcheck/00check.log’
for details.



Installation output

ASICS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ASICS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ASICS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ASICS)

Tests output

ASICS.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> library(testthat)
> library(ASICS)
> 
> 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 0.05 s user time, 0 s system time and 0.049 s elapsed time.
Begin GroupDelayCorrection 
End GroupDelayCorrection 
It lasted 0.041 s user time, 0 s system time and 0.04 s elapsed time.
Begin SolventSuppression 
End SolventSuppression 
It lasted 0.006 s user time, 0 s system time and 0.007 s elapsed time.
Begin Apodization 
End Apodization 
It lasted 0.001 s user time, 0 s system time and 0.002 s elapsed time.
Begin ZeroFilling 
End ZeroFilling 
It lasted 0.049 s user time, 0 s system time and 0.05 s elapsed time.
Begin FourierTransform 
End FourierTransform 
It lasted 0.009 s user time, 0 s system time and 0.009 s elapsed time.
Begin ZeroOrderPhaseCorrection 
End ZeroOrderPhaseCorrection 
It lasted 0.157 s user time, 0.004 s system time and 0.161 s elapsed time.
Begin InternalReferencing 
End InternalReferencing 
It lasted 0.016 s user time, 0 s system time and 0.016 s elapsed time.
Begin WindowSelection 
End WindowSelection 
It lasted 0.079 s user time, 0 s system time and 0.08 s elapsed time.
End PreprocessingChain 
It lasted 0.413 s user time, 0.004 s system time and 0.416 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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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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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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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: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
252.559   1.768 255.287 

Example timings

ASICS.Rcheck/ASICS-Ex.timings

nameusersystemelapsed
ASICS33.288 0.18433.490
ASICSUsersGuide0.0010.0000.001
accessors-methods0.1140.0400.154
alignSpectra1.5520.0841.636
binning0.1650.0040.169
combineAndSubset-methods0.0350.0000.034
createPureLibrary0.1420.0000.164
createSpectra0.1330.0000.159
formatForAnalysis1.0320.0081.140
importSpectra0.8490.0040.910
importSpectraBruker0.0910.0000.091
kruskalWallis0.440.000.44
normaliseSpectra0.0510.0020.053
oplsda0.1990.0000.199
pca0.4930.0000.493
plotAlignment1.4530.0041.457
summary-methods0.0360.0000.036
visualisation-methods-analyses1.6580.0001.659
visualisation-methods-spectra1.8650.0001.866