Gaëlle Lefort
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/ASICS |
| Branch: RELEASE_3_11 |
| Last Commit: 1a78fbf |
| Last Changed Date: 2020-07-20 02:44:56 -0400 (Mon, 20 Jul 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:23 -0400 (Sat, 17 Oct 2020).
| 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 90/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ASICS 2.4.3 Gaëlle Lefort
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: ASICS |
| Version: 2.4.3 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ASICS_2.4.3.tar.gz |
| StartedAt: 2020-10-16 22:56:28 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 23:04:51 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 503.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ASICS.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ASICS_2.4.3.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/ASICS.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.4.3’
* 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 6.4Mb
sub-directories of 1Mb or more:
doc 3.2Mb
extdata 1.6Mb
* 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’
.shift_spec: no visible global function definition for ‘rnbinom’
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 rnbinom
Consider adding
importFrom("stats", "rnbinom")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘simulate_spectra’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 34.012 0.304 34.345
* 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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.11-bioc/meat/ASICS.Rcheck/00check.log’
for details.
ASICS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ASICS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-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)
ASICS.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
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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 0.008 s user time, 0.003 s system time and 0.011 s elapsed time.
Begin GroupDelayCorrection
End GroupDelayCorrection
It lasted 0.056 s user time, 0.004 s system time and 0.06 s elapsed time.
Begin SolventSuppression
End SolventSuppression
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Begin Apodization
End Apodization
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Begin ZeroFilling
End ZeroFilling
It lasted 0.032 s user time, 0 s system time and 0.032 s elapsed time.
Begin FourierTransform
End FourierTransform
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Begin ZeroOrderPhaseCorrection
End ZeroOrderPhaseCorrection
It lasted 0.109 s user time, 0 s system time and 0.108 s elapsed time.
Begin InternalReferencing
End InternalReferencing
It lasted 0.009 s user time, 0 s system time and 0.009 s elapsed time.
Begin WindowSelection
End WindowSelection
It lasted 0.051 s user time, 0 s system time and 0.051 s elapsed time.
End PreprocessingChain
It lasted 0.281 s user time, 0.007 s system time and 0.289 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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══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 23 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
312.224 3.932 316.268
ASICS.Rcheck/ASICS-Ex.timings
| name | user | system | elapsed | |
| ASICS | 34.012 | 0.304 | 34.345 | |
| ASICSUsersGuide | 0.000 | 0.000 | 0.001 | |
| accessors-methods | 0.115 | 0.020 | 0.134 | |
| alignSpectra | 1.884 | 0.060 | 1.956 | |
| binning | 0.099 | 0.020 | 0.119 | |
| combineAndSubset-methods | 0.039 | 0.000 | 0.039 | |
| createPureLibrary | 0.108 | 0.005 | 0.128 | |
| createSpectra | 0.717 | 0.004 | 0.723 | |
| formatForAnalysis | 1.331 | 0.000 | 1.402 | |
| importSpectra | 0.729 | 0.012 | 0.742 | |
| importSpectraBruker | 0.096 | 0.000 | 0.095 | |
| kruskalWallis | 0.287 | 0.004 | 0.291 | |
| normaliseSpectra | 0.041 | 0.000 | 0.042 | |
| oplsda | 0.099 | 0.000 | 0.100 | |
| pca | 0.327 | 0.000 | 0.327 | |
| plotAlignment | 0.453 | 0.008 | 0.460 | |
| summary-methods | 0.021 | 0.000 | 0.020 | |
| visualisation-methods-analyses | 0.92 | 0.00 | 0.92 | |
| visualisation-methods-spectra | 1.148 | 0.003 | 1.151 | |