Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-04 11:38:51 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 99/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASICS 2.19.0  (landing page)
Gaëlle Lefort
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/ASICS
git_branch: devel
git_last_commit: 162f23f
git_last_commit_date: 2023-10-24 11:04:01 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for ASICS on merida1


To the developers/maintainers of the ASICS package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ASICS
Version: 2.19.0
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_2.19.0.tar.gz
StartedAt: 2024-03-02 00:10:15 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 00:33:06 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 1370.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ASICS.Rcheck
Warnings: 0

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_2.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ASICS.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASICS’ version ‘2.19.0’
* 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  6.1Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    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 ... 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 99.969  3.164 116.936
ASICS            56.846  3.286  70.488
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/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
** 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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")
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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 0.023 s user time, 0.002 s system time and 0.03 s elapsed time.
Begin GroupDelayCorrection 
End GroupDelayCorrection 
It lasted 0.049 s user time, 0 s system time and 0.064 s elapsed time.
Begin SolventSuppression 
End SolventSuppression 
It lasted 0.051 s user time, 0.02 s system time and 0.086 s elapsed time.
Begin Apodization 
End Apodization 
It lasted 0.002 s user time, 0 s system time and 0.002 s elapsed time.
Begin ZeroFilling 
End ZeroFilling 
It lasted 0.052 s user time, 0.001 s system time and 0.068 s elapsed time.
Begin FourierTransform 
End FourierTransform 
It lasted 0.011 s user time, 0 s system time and 0.013 s elapsed time.
Begin ZeroOrderPhaseCorrection 
End ZeroOrderPhaseCorrection 
It lasted 0.189 s user time, 0.011 s system time and 0.236 s elapsed time.
Begin InternalReferencing 
End InternalReferencing 
It lasted 0.016 s user time, 0 s system time and 0.02 s elapsed time.
Begin WindowSelection 
End WindowSelection 
It lasted 0.094 s user time, 0.001 s system time and 0.125 s elapsed time.
End PreprocessingChain 
It lasted 0.491 s user time, 0.04 s system time and 0.654 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 
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 
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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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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... 
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Compute weights 

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Translate library 
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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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  |===================================                                   |  50%
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  |======================================================================| 100%

Compute quantifications 

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Format global results... 
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
553.937  71.218 742.727 

Example timings

ASICS.Rcheck/ASICS-Ex.timings

nameusersystemelapsed
ASICS56.846 3.28670.488
ASICSUsersGuide0.0020.0010.003
accessors-methods0.1700.2730.508
alignSpectra3.6640.0694.519
binning0.3810.0310.477
combineAndSubset-methods0.0440.0030.051
createPureLibrary0.4150.0100.516
createSpectra0.2340.0070.281
formatForAnalysis0.9870.0181.143
importSpectra1.9010.0792.327
importSpectraBruker0.2150.0070.268
kruskalWallis0.4250.0110.527
normaliseSpectra0.0510.0020.063
oplsda0.2270.0080.277
pca0.1060.0040.131
plotAlignment1.0690.0621.286
simulate_spectra 99.969 3.164116.936
summary-methods0.0350.0030.045
visualisation-methods-analyses2.4960.0893.042
visualisation-methods-spectra1.0990.0221.312