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This page was generated on 2021-10-21 12:05:11 -0400 (Thu, 21 Oct 2021).

CHECK results for ASICS on merida1

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 88/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASICS 2.9.2  (landing page)
Gaëlle Lefort
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/ASICS
git_branch: master
git_last_commit: 7a52ccf
git_last_commit_date: 2021-10-08 02:42:06 -0400 (Fri, 08 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ASICS
Version: 2.9.2
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_2.9.2.tar.gz
StartedAt: 2021-10-21 00:43:41 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 00:58:12 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 870.3 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_2.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ASICS.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘2.9.2’
* 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    618Kb       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 73.848  1.575  75.524
ASICS            49.383  3.199  52.804
* 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 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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 
Normalisation method : CS 
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 0.02 s user time, 0.002 s system time and 0.022 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 0.009 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 0.048 s user time, 0 s system time and 0.048 s elapsed time.
Begin FourierTransform 
End FourierTransform 
It lasted 0.056 s user time, 0.014 s system time and 0.07 s elapsed time.
Begin ZeroOrderPhaseCorrection 
End ZeroOrderPhaseCorrection 
It lasted 0.097 s user time, 0 s system time and 0.098 s elapsed time.
Begin InternalReferencing 
End InternalReferencing 
It lasted 0.01 s user time, 0.001 s system time and 0.009 s elapsed time.
Begin WindowSelection 
End WindowSelection 
It lasted 0.081 s user time, 0 s system time and 0.081 s elapsed time.
End PreprocessingChain 
It lasted 0.366 s user time, 0.018 s system time and 0.384 s elapsed time.
Normalisation method : CS 
Import spectra from txt or csv files... 
Normalisation method : CS 
Normalisation method : CS 
Alignment... 
Peak detection 
Finding reference spectrum 
Compute FFT correlations 
The reference spectrum is the number 3 : AG_faq_Beck139 
Align spectra 
Import spectra from txt or csv files... 
Normalisation method : CS 
Binning 
Normalisation method : CS 
Import spectra from txt or csv files... 
Normalisation method : CS 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Deform library peaks 
Compute quantifications 
Format global results... 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Deform library peaks 
Compute quantifications 
Format global results... 
Import spectra from 1r files... 
Normalisation method : CS 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Compute shifts for all maximum shift values 
Put the median shift for extreme shift values 
Compute correlations between buckets and quantifications 
Shift all spectra according to the best shift 
Deform library peaks 
Compute quantifications 
Format global results... 
Remove areas from spectrum and library 
Compute weights 
Remove metabolites that cannot belong to the mixture 
Translate library 
Compute shifts for all maximum shift values 
Put the median shift for extreme shift values 
Compute correlations between buckets and quantifications 
Shift all spectra according to the best shift 
Deform library peaks 
Compute quantifications 
Format global results... 
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
428.900  68.856 498.488 

Example timings

ASICS.Rcheck/ASICS-Ex.timings

nameusersystemelapsed
ASICS49.383 3.19952.804
ASICSUsersGuide0.0000.0000.001
accessors-methods0.1060.0570.163
alignSpectra2.0470.1242.185
binning0.2140.0270.242
combineAndSubset-methods0.0500.0020.052
createPureLibrary0.2750.0070.287
createSpectra0.1160.0040.123
formatForAnalysis1.7730.0241.811
importSpectra1.5290.0301.561
importSpectraBruker0.0870.0010.089
kruskalWallis0.5810.0020.584
normaliseSpectra0.0380.0020.040
oplsda0.2040.0020.205
pca0.6000.0020.602
plotAlignment0.6640.0230.687
simulate_spectra73.848 1.57575.524
summary-methods0.0270.0010.027
visualisation-methods-analyses1.4210.0281.453
visualisation-methods-spectra0.7730.0100.788