Gaëlle Lefort
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/ASICS |
| Branch: RELEASE_3_12 |
| Last Commit: 2165d0b |
| Last Changed Date: 2020-10-28 05:58:26 -0400 (Wed, 28 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:20 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the ASICS package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 93/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ASICS 2.6.1 (landing page) Gaëlle Lefort
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ASICS |
| Version: 2.6.1 |
| 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_2.6.1.tar.gz |
| StartedAt: 2021-05-05 23:19:09 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 23:31:47 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 757.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ASICS.Rcheck |
| Warnings: 0 |
##############################################################################
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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_2.6.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ASICS.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.6.1’
* 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 5.8Mb
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 ... 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 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 49.215 1.345 50.633
ASICS 43.288 2.694 46.209
* 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
‘/Users/biocbuild/bbs-3.12-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 ** 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)
ASICS.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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")
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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 0.013 s user time, 0.001 s system time and 0.014 s elapsed time.
Begin GroupDelayCorrection
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Begin SolventSuppression
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Begin FourierTransform
End FourierTransform
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Begin ZeroOrderPhaseCorrection
End ZeroOrderPhaseCorrection
It lasted 0.144 s user time, 0.011 s system time and 0.156 s elapsed time.
Begin InternalReferencing
End InternalReferencing
It lasted 0.013 s user time, 0 s system time and 0.013 s elapsed time.
Begin WindowSelection
End WindowSelection
It lasted 0.068 s user time, 0 s system time and 0.068 s elapsed time.
End PreprocessingChain
It lasted 0.323 s user time, 0.016 s system time and 0.339 s elapsed time.
Normalisation method : CS
Import spectra from txt or csv files...
Normalisation method : CS
Normalisation method : CS
Alignment...
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The reference spectrum is the number 3 : AG_faq_Beck139
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[ FAIL 0 | WARN 6 | SKIP 0 | PASS 23 ]
>
> proc.time()
user system elapsed
384.648 69.085 454.520
ASICS.Rcheck/ASICS-Ex.timings
| name | user | system | elapsed | |
| ASICS | 43.288 | 2.694 | 46.209 | |
| ASICSUsersGuide | 0.001 | 0.000 | 0.001 | |
| accessors-methods | 0.118 | 0.115 | 0.234 | |
| alignSpectra | 2.265 | 0.090 | 2.440 | |
| binning | 0.193 | 0.015 | 0.212 | |
| combineAndSubset-methods | 0.047 | 0.001 | 0.050 | |
| createPureLibrary | 0.148 | 0.009 | 0.204 | |
| createSpectra | 0.130 | 0.003 | 0.135 | |
| formatForAnalysis | 1.155 | 0.020 | 1.178 | |
| importSpectra | 0.594 | 0.025 | 0.620 | |
| importSpectraBruker | 0.106 | 0.004 | 0.110 | |
| kruskalWallis | 0.395 | 0.002 | 0.397 | |
| normaliseSpectra | 0.043 | 0.003 | 0.045 | |
| oplsda | 0.149 | 0.003 | 0.152 | |
| pca | 0.531 | 0.006 | 0.538 | |
| plotAlignment | 0.616 | 0.019 | 0.634 | |
| simulate_spectra | 49.215 | 1.345 | 50.633 | |
| summary-methods | 0.031 | 0.002 | 0.032 | |
| visualisation-methods-analyses | 1.184 | 0.026 | 1.212 | |
| visualisation-methods-spectra | 0.866 | 0.012 | 0.880 | |