Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 99/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASICS 2.20.1  (landing page)
Gaëlle Lefort
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/ASICS
git_branch: RELEASE_3_19
git_last_commit: 52b7c3d
git_last_commit_date: 2024-05-30 05:49:33 -0400 (Thu, 30 May 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for ASICS on nebbiolo1

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: 2.20.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ASICS_2.20.1.tar.gz
StartedAt: 2024-06-12 20:36:16 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 20:50:15 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 838.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ASICS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ASICS_2.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ASICS.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ASICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASICS’ version ‘2.20.1’
* 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  5.6Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    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 code 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 loading without being on the library search path ... 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    1.2Mb    791Kb       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 52.500  4.412  56.913
ASICS            47.461  0.977  48.440
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ASICS.Rcheck/00check.log’
for details.


Installation output

ASICS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ASICS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 0.006 s user time, 0.004 s system time and 0.01 s elapsed time.
Begin GroupDelayCorrection 
End GroupDelayCorrection 
It lasted 0.025 s user time, 0 s system time and 0.025 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 0.027 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 0.108 s user time, 0.004 s system time and 0.112 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 0.046 s elapsed time.
End PreprocessingChain 
It lasted 0.237 s user time, 0.008 s system time and 0.246 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 1 | SKIP 0 | PASS 23 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
367.678   8.516 376.191 

Example timings

ASICS.Rcheck/ASICS-Ex.timings

nameusersystemelapsed
ASICS47.461 0.97748.440
ASICSUsersGuide0.0010.0000.002
accessors-methods0.0550.1040.159
alignSpectra1.8630.0561.920
binning0.1590.0120.171
combineAndSubset-methods0.0230.0000.023
createPureLibrary0.1330.0080.144
createSpectra0.0970.0040.102
formatForAnalysis0.3600.0030.366
importSpectra0.4600.0080.468
importSpectraBruker0.0920.0040.096
kruskalWallis0.1540.0040.158
normaliseSpectra0.0370.0040.041
oplsda0.0860.0000.085
pca0.0400.0000.041
plotAlignment0.4930.0030.496
simulate_spectra52.500 4.41256.913
summary-methods0.0210.0000.021
visualisation-methods-analyses0.9480.0120.960
visualisation-methods-spectra0.5380.0190.559