Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-03 13:05:39 -0500 (Fri, 03 Dec 2021).

CHECK results for ASICS on machv2

To the developers/maintainers of the ASICS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ASICS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 88/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASICS 2.10.0  (landing page)
Gaëlle Lefort
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/ASICS
git_branch: RELEASE_3_14
git_last_commit: f29bce8
git_last_commit_date: 2021-10-26 12:43:14 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ASICS
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ASICS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ASICS_2.10.0.tar.gz
StartedAt: 2021-12-02 11:44:55 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 11:59:49 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 893.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ASICS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ASICS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ASICS_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ASICS.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.10.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda   1010Kb    615Kb       xz
* 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
simulate_spectra 76.926  2.069  79.321
ASICS            45.227  3.317  48.751
* 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-3.14-bioc/meat/ASICS.Rcheck/00check.log’
for details.



Installation output

ASICS.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 0.019 s user time, 0.001 s system time and 0.02 s elapsed time.
Begin GroupDelayCorrection 
End GroupDelayCorrection 
It lasted 0.034 s user time, 0 s system time and 0.035 s elapsed time.
Begin SolventSuppression 
End SolventSuppression 
It lasted 0.007 s user time, 0 s system time and 0.006 s elapsed time.
Begin Apodization 
End Apodization 
It lasted 0.001 s user time, 0 s system time and 0.001 s elapsed time.
Begin ZeroFilling 
End ZeroFilling 
It lasted 0.029 s user time, 0 s system time and 0.029 s elapsed time.
Begin FourierTransform 
End FourierTransform 
It lasted 0.008 s user time, 0 s system time and 0.008 s elapsed time.
Begin ZeroOrderPhaseCorrection 
End ZeroOrderPhaseCorrection 
It lasted 0.12 s user time, 0.006 s system time and 0.126 s elapsed time.
Begin InternalReferencing 
End InternalReferencing 
It lasted 0.01 s user time, 0 s system time and 0.009 s elapsed time.
Begin WindowSelection 
End WindowSelection 
It lasted 0.051 s user time, 0 s system time and 0.05 s elapsed time.
End PreprocessingChain 
It lasted 0.28 s user time, 0.009 s system time and 0.29 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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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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Translate library 

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Deform library peaks 

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Compute quantifications 

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Format global results... 
Remove areas from spectrum and library 

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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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Translate library 

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Deform library peaks 

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Compute quantifications 

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Format global results... 
Import spectra from 1r files... 

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Normalisation method : CS 
Remove areas from spectrum and library 

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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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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 global results... 
Remove areas from spectrum and library 

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Compute weights 

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Remove metabolites that cannot belong to the mixture 

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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 global results... 
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
439.809  85.116 525.528 

Example timings

ASICS.Rcheck/ASICS-Ex.timings

nameusersystemelapsed
ASICS45.227 3.31748.751
ASICSUsersGuide0.0010.0010.001
accessors-methods0.1210.1360.258
alignSpectra1.9880.0812.084
binning0.2380.0260.264
combineAndSubset-methods0.0460.0020.048
createPureLibrary0.1820.0060.191
createSpectra0.1530.0050.161
formatForAnalysis1.8060.0541.874
importSpectra0.8570.0280.892
importSpectraBruker0.1310.0050.138
kruskalWallis0.5950.0060.605
normaliseSpectra0.0400.0010.043
oplsda0.1910.0020.193
pca0.5590.0060.569
plotAlignment0.8720.0320.911
simulate_spectra76.926 2.06979.321
summary-methods0.0290.0020.032
visualisation-methods-analyses1.4520.0321.489
visualisation-methods-spectra0.9290.0160.948