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CHECK report for ASICS on machv2

This page was generated on 2020-10-17 11:58:04 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ASICS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 90/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASICS 2.4.3
Gaëlle Lefort
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ASICS
Branch: RELEASE_3_11
Last Commit: 1a78fbf
Last Changed Date: 2020-07-20 02:44:56 -0400 (Mon, 20 Jul 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ASICS
Version: 2.4.3
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_2.4.3.tar.gz
StartedAt: 2020-10-16 22:44:35 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 22:55:52 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 677.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ASICS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_2.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ASICS.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.4.3’
* 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  6.3Mb
  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 ... NOTE
.shift_spec: no visible binding for global variable ‘pure_library’
.shift_spec: no visible global function definition for ‘rnbinom’
simulate_spectra: no visible binding for global variable ‘pure_library’
simulate_spectra : <anonymous>: no visible binding for global variable
  ‘pure_library’
Undefined global functions or variables:
  pure_library rnbinom
Consider adding
  importFrom("stats", "rnbinom")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘simulate_spectra’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 32.965  2.639  35.696
* 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, 2 NOTEs
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
** 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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
> 
> test_check("ASICS")
Binning 

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Normalisation method : CS 

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Import spectra from txt or csv files... 
Normalisation method : CS 
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 0.022 s user time, 0.001 s system time and 0.024 s elapsed time.
Begin GroupDelayCorrection 
End GroupDelayCorrection 
It lasted 0.041 s user time, 0 s system time and 0.041 s elapsed time.
Begin SolventSuppression 
End SolventSuppression 
It lasted 0.008 s user time, 0 s system time and 0.008 s elapsed time.
Begin Apodization 
End Apodization 
It lasted 0.002 s user time, 0 s system time and 0.001 s elapsed time.
Begin ZeroFilling 
End ZeroFilling 
It lasted 0.056 s user time, 0 s system time and 0.057 s elapsed time.
Begin FourierTransform 
End FourierTransform 
It lasted 0.01 s user time, 0 s system time and 0.01 s elapsed time.
Begin ZeroOrderPhaseCorrection 
End ZeroOrderPhaseCorrection 
It lasted 0.199 s user time, 0.012 s system time and 0.212 s elapsed time.
Begin InternalReferencing 
End InternalReferencing 
It lasted 0.022 s user time, 0 s system time and 0.022 s elapsed time.
Begin WindowSelection 
End WindowSelection 
It lasted 0.095 s user time, 0 s system time and 0.096 s elapsed time.
End PreprocessingChain 
It lasted 0.46 s user time, 0.018 s system time and 0.478 s elapsed time.
Normalisation method : CS 
Import spectra from txt or csv files... 
Normalisation method : CS 
Normalisation method : CS 
Alignment... 
Peak detection 

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Finding reference spectrum 
Compute FFT correlations 

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The reference spectrum is the number 3 : AG_faq_Beck139 
Align spectra 

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Import spectra from txt or csv files... 
Normalisation method : CS 
Binning 

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Normalisation method : CS 
Import spectra from txt or csv files... 
Normalisation method : CS 
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 1r files... 

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Normalisation method : CS 
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 
Compute shifts for all maximum shift values 

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Put the median shift for extreme shift values 

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Compute correlations between buckets and quantifications 

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Shift all spectra according to the best shift 

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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 
Compute shifts for all maximum shift values 

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Put the median shift for extreme shift values 

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Compute correlations between buckets and quantifications 

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Shift all spectra according to the best shift 

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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 
352.586  65.125 418.813 

Example timings

ASICS.Rcheck/ASICS-Ex.timings

nameusersystemelapsed
ASICS32.965 2.63935.696
ASICSUsersGuide0.0010.0010.001
accessors-methods0.1350.1230.260
alignSpectra2.3910.0932.498
binning0.1800.0210.202
combineAndSubset-methods0.0720.0060.078
createPureLibrary0.1240.0050.132
createSpectra0.1170.0040.122
formatForAnalysis1.2900.0231.321
importSpectra0.7790.0410.826
importSpectraBruker0.0870.0020.089
kruskalWallis0.5200.0190.541
normaliseSpectra0.0490.0020.051
oplsda0.1740.0030.178
pca0.5480.0060.557
plotAlignment1.1460.0281.174
summary-methods0.0320.0020.033
visualisation-methods-analyses1.3410.0141.356
visualisation-methods-spectra0.9320.0170.950