Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:05:39 -0400 (Fri, 24 Sep 2021).

CHECK results for ASICS on nebbiolo1

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 92/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASICS 2.8.0  (landing page)
Gaëlle Lefort
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/ASICS
git_branch: RELEASE_3_13
git_last_commit: 3169aa8
git_last_commit_date: 2021-05-19 12:34:32 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ASICS
Version: 2.8.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ASICS_2.8.0.tar.gz
StartedAt: 2021-09-23 08:51:54 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 09:00:24 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 510.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ASICS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ASICS_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ASICS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.8.0’
* 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  5.2Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   1.4Mb
* 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’
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
* 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 ... 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
simulate_spectra 37.597  3.540  41.138
ASICS            30.056  1.316  31.376
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/ASICS.Rcheck/00check.log’
for details.



Installation output

ASICS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ASICS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
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 0.009 s user time, 0 s system time and 0.009 s elapsed time.
Begin GroupDelayCorrection 
End GroupDelayCorrection 
It lasted 0.023 s user time, 0 s system time and 0.023 s elapsed time.
Begin SolventSuppression 
End SolventSuppression 
It lasted 0.006 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 0.027 s user time, 0 s system time and 0.027 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 0.102 s user time, 0.015 s system time and 0.118 s elapsed time.
Begin InternalReferencing 
End InternalReferencing 
It lasted 0.008 s user time, 0 s system time and 0.008 s elapsed time.
Begin WindowSelection 
End WindowSelection 
It lasted 0.047 s user time, 0 s system time and 0.047 s elapsed time.
End PreprocessingChain 
It lasted 0.235 s user time, 0.016 s system time and 0.25 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 
277.631  13.205 290.904 

Example timings

ASICS.Rcheck/ASICS-Ex.timings

nameusersystemelapsed
ASICS30.056 1.31631.376
ASICSUsersGuide0.0000.0010.001
accessors-methods0.0640.1360.200
alignSpectra1.8660.0241.890
binning0.1230.0000.123
combineAndSubset-methods0.030.000.03
createPureLibrary0.1100.0010.115
createSpectra0.0870.0000.090
formatForAnalysis0.8830.0520.936
importSpectra0.4970.0720.571
importSpectraBruker0.0970.0000.097
kruskalWallis0.3220.0040.326
normaliseSpectra0.0320.0000.032
oplsda0.120.000.12
pca0.2970.0040.301
plotAlignment0.5060.0120.518
simulate_spectra37.597 3.54041.138
summary-methods0.0160.0040.020
visualisation-methods-analyses0.7750.0080.782
visualisation-methods-spectra0.5510.0080.560