Gaëlle Lefort
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/ASICS |
| git_branch: RELEASE_3_20 |
| git_last_commit: 0851b6b |
| git_last_commit_date: 2024-10-29 10:26:59 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 103/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ASICS 2.22.0 (landing page) Gaëlle Lefort
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 2.22.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ASICS.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ASICS_2.22.0.tar.gz |
| StartedAt: 2024-12-19 22:58:41 -0500 (Thu, 19 Dec 2024) |
| EndedAt: 2024-12-19 23:14:17 -0500 (Thu, 19 Dec 2024) |
| EllapsedTime: 936.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ASICS.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ASICS.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ASICS_2.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ASICS.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ASICS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ASICS' version '2.22.0'
* 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 whether package 'ASICS' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.0Mb
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 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 1.0Mb 661Kb 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 70.00 7.40 77.32
ASICS 48.91 5.83 54.75
* 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
'F:/biocbuild/bbs-3.20-bioc/meat/ASICS.Rcheck/00check.log'
for details.
ASICS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ASICS ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 ** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 0.06 s user time, 0 s system time and 0.06 s elapsed time.
Begin GroupDelayCorrection
End GroupDelayCorrection
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Begin SolventSuppression
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Begin FourierTransform
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Begin ZeroOrderPhaseCorrection
End ZeroOrderPhaseCorrection
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Begin InternalReferencing
End InternalReferencing
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Begin WindowSelection
End WindowSelection
It lasted 0.08 s user time, 0 s system time and 0.08 s elapsed time.
End PreprocessingChain
It lasted 0.45 s user time, 0.03 s system time and 0.48 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 1 | SKIP 0 | PASS 23 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]
>
> proc.time()
user system elapsed
497.73 53.50 552.09
ASICS.Rcheck/ASICS-Ex.timings
| name | user | system | elapsed | |
| ASICS | 48.91 | 5.83 | 54.75 | |
| ASICSUsersGuide | 0 | 0 | 0 | |
| accessors-methods | 0.20 | 0.06 | 0.27 | |
| alignSpectra | 1.97 | 0.24 | 2.20 | |
| binning | 0.37 | 0.00 | 0.38 | |
| combineAndSubset-methods | 0.04 | 0.01 | 0.05 | |
| createPureLibrary | 0.15 | 0.03 | 0.26 | |
| createSpectra | 0.21 | 0.02 | 0.33 | |
| formatForAnalysis | 0.43 | 0.01 | 0.50 | |
| importSpectra | 2.00 | 0.08 | 2.09 | |
| importSpectraBruker | 0.17 | 0.00 | 0.17 | |
| kruskalWallis | 0.21 | 0.00 | 0.21 | |
| normaliseSpectra | 0.08 | 0.00 | 0.08 | |
| oplsda | 0.09 | 0.00 | 0.09 | |
| pca | 0.05 | 0.00 | 0.05 | |
| plotAlignment | 0.62 | 0.06 | 0.68 | |
| simulate_spectra | 70.00 | 7.40 | 77.32 | |
| summary-methods | 0.03 | 0.00 | 0.03 | |
| visualisation-methods-analyses | 1.38 | 0.06 | 1.44 | |
| visualisation-methods-spectra | 0.87 | 0.08 | 0.95 | |