Gaëlle Lefort
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/ASICS |
| Branch: master |
| Last Commit: e067e00 |
| Last Changed Date: 2019-10-29 13:43:00 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:50:48 -0500 (Thu, 16 Jan 2020).
| Package 89/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ASICS 2.3.0 Gaëlle Lefort
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: ASICS |
| Version: 2.3.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASICS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASICS_2.3.0.tar.gz |
| StartedAt: 2020-01-16 01:50:04 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:03:41 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 817.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ASICS.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASICS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASICS_2.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ASICS.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.3.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/ASICS.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
doc 3.2Mb
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 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
ASICS 58.474 1.207 59.685
* 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-3.11-bioc/meat/ASICS.Rcheck/00check.log’
for details.
ASICS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ASICS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE ** 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 Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE ** testing if installed package can be loaded from final location Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE ** testing if installed package keeps a record of temporary installation path * DONE (ASICS)
ASICS.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
>
> test_check("ASICS")
OPLS-DA
26 samples x 33 variables and 1 response
standard scaling of predictors and response(s)
R2X(cum) R2Y(cum) Q2(cum) RMSEE RMSEP pre ort
Total 0.202 0.845 0.316 0.209 0.35 1 1
Binning
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Normalisation...
OPLS-DA
26 samples x 881 variables and 1 response
standard scaling of predictors and response(s)
R2X(cum) R2Y(cum) Q2(cum) RMSEE RMSEP pre ort
Total 0.245 0.895 0.548 0.173 0.37 1 1
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Import spectra from txt or csv files...
Normalisation...
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 0.015 s user time, 0.003 s system time and 0.018 s elapsed time.
Begin GroupDelayCorrection
End GroupDelayCorrection
It lasted 0.036 s user time, 0.005 s system time and 0.042 s elapsed time.
Begin SolventSuppression
End SolventSuppression
It lasted 0.01 s user time, 0.007 s system time and 0.017 s elapsed time.
Begin Apodization
End Apodization
It lasted 0.002 s user time, 0.001 s system time and 0.003 s elapsed time.
Begin ZeroFilling
End ZeroFilling
It lasted 0.035 s user time, 0.002 s system time and 0.039 s elapsed time.
Begin FourierTransform
End FourierTransform
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Begin ZeroOrderPhaseCorrection
End ZeroOrderPhaseCorrection
It lasted 0.306 s user time, 0.088 s system time and 0.395 s elapsed time.
Begin InternalReferencing
End InternalReferencing
It lasted 0.022 s user time, 0.008 s system time and 0.03 s elapsed time.
Begin WindowSelection
End WindowSelection
It lasted 0.059 s user time, 0.003 s system time and 0.062 s elapsed time.
End PreprocessingChain
It lasted 0.501 s user time, 0.131 s system time and 0.633 s elapsed time.
Normalisation...
Import spectra from txt or csv files...
Normalisation...
Normalisation...
Alignment...
Peak detection
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Finding reference spectrum
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Normalisation...
Compute LCSS similarities
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The reference spectrum is the number 2 : AG_faq_Beck051
Align spectra
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Normalisation...
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Remove metabolites that cannot belong to the mixture
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Format results...
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Normalisation...
Remove areas from spectrum and library
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Remove metabolites that cannot belong to the mixture
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Compute weights
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Translate library
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Deform library peaks
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Format results...
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Remove metabolites that cannot belong to the mixture
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Format results...
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 23 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
411.139 35.891 454.534
ASICS.Rcheck/ASICS-Ex.timings
| name | user | system | elapsed | |
| ASICS | 58.474 | 1.207 | 59.685 | |
| ASICSUsersGuide | 0.001 | 0.000 | 0.001 | |
| accessors-methods | 0.262 | 0.169 | 0.431 | |
| alignSpectra | 2.418 | 0.305 | 2.724 | |
| binning | 0.235 | 0.051 | 0.287 | |
| combineAndSubset-methods | 0.045 | 0.002 | 0.047 | |
| createPureLibrary | 0.157 | 0.032 | 0.195 | |
| createSpectra | 0.127 | 0.018 | 0.149 | |
| formatForAnalysis | 1.363 | 0.026 | 1.393 | |
| importSpectra | 0.989 | 0.180 | 1.171 | |
| importSpectraBruker | 0.102 | 0.018 | 0.120 | |
| kruskalWallis | 0.471 | 0.004 | 0.473 | |
| normaliseSpectra | 0.043 | 0.002 | 0.045 | |
| oplsda | 0.274 | 0.006 | 0.280 | |
| pca | 0.844 | 0.015 | 0.860 | |
| plotAlignment | 1.333 | 0.162 | 1.495 | |
| summary-methods | 0.045 | 0.002 | 0.047 | |
| visualisation-methods-analyses | 2.091 | 0.046 | 2.142 | |
| visualisation-methods-spectra | 1.847 | 0.253 | 2.100 | |