Gaëlle Lefort
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 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) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:41 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 99/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ASICS 2.20.1 (landing page) Gaëlle Lefort
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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. |
| Package: ASICS |
| Version: 2.20.1 |
| 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_2.20.1.tar.gz |
| StartedAt: 2024-06-09 18:46:39 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 19:00:59 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 859.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ASICS.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_2.20.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ASICS.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘2.20.1’
* 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 6.3Mb
sub-directories of 1Mb or more:
data 1.2Mb
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 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 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 61.479 3.164 64.821
ASICS 51.413 6.558 58.267
* 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 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/ASICS.Rcheck/00check.log’
for details.
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)
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-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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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 0.012 s user time, 0.001 s system time and 0.014 s elapsed time.
Begin GroupDelayCorrection
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Begin FourierTransform
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Begin ZeroOrderPhaseCorrection
End ZeroOrderPhaseCorrection
It lasted 0.121 s user time, 0.018 s system time and 0.141 s elapsed time.
Begin InternalReferencing
End InternalReferencing
It lasted 0.011 s user time, 0 s system time and 0.012 s elapsed time.
Begin WindowSelection
End WindowSelection
It lasted 0.05 s user time, 0 s system time and 0.05 s elapsed time.
End PreprocessingChain
It lasted 0.249 s user time, 0.022 s system time and 0.273 s elapsed time.
Normalisation method : CS
Import spectra from txt or csv files...
Normalisation method : CS
Normalisation method : CS
Alignment...
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[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]
>
> proc.time()
user system elapsed
410.482 104.831 518.652
ASICS.Rcheck/ASICS-Ex.timings
| name | user | system | elapsed | |
| ASICS | 51.413 | 6.558 | 58.267 | |
| ASICSUsersGuide | 0.001 | 0.001 | 0.002 | |
| accessors-methods | 0.083 | 0.089 | 0.173 | |
| alignSpectra | 1.506 | 0.041 | 1.551 | |
| binning | 0.191 | 0.018 | 0.209 | |
| combineAndSubset-methods | 0.034 | 0.002 | 0.035 | |
| createPureLibrary | 0.184 | 0.012 | 0.200 | |
| createSpectra | 0.124 | 0.004 | 0.129 | |
| formatForAnalysis | 0.484 | 0.006 | 0.493 | |
| importSpectra | 0.845 | 0.045 | 0.894 | |
| importSpectraBruker | 0.117 | 0.008 | 0.125 | |
| kruskalWallis | 0.246 | 0.025 | 0.270 | |
| normaliseSpectra | 0.035 | 0.001 | 0.037 | |
| oplsda | 0.084 | 0.001 | 0.086 | |
| pca | 0.043 | 0.001 | 0.045 | |
| plotAlignment | 0.549 | 0.035 | 0.586 | |
| simulate_spectra | 61.479 | 3.164 | 64.821 | |
| summary-methods | 0.026 | 0.002 | 0.029 | |
| visualisation-methods-analyses | 1.130 | 0.044 | 1.177 | |
| visualisation-methods-spectra | 0.589 | 0.010 | 0.600 | |