Gaëlle Lefort
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/ASICS |
| git_branch: devel |
| git_last_commit: 034bc20 |
| git_last_commit_date: 2024-10-29 10:26:59 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:15 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 103/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ASICS 2.23.0 (landing page) Gaëlle Lefort
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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: 2.23.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ASICS.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ASICS_2.23.0.tar.gz |
| StartedAt: 2024-11-27 22:09:59 -0500 (Wed, 27 Nov 2024) |
| EndedAt: 2024-11-27 22:24:48 -0500 (Wed, 27 Nov 2024) |
| EllapsedTime: 889.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ASICS.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ASICS.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ASICS_2.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/ASICS.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* 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 '2.23.0'
* 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 ... INFO
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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
AnalysisResults-class.Rd: SummarizedExperiment, opls, ropls
formatForAnalysis.Rd: SummarizedExperiment
kruskalWallis.Rd: SummarizedExperiment
oplsda.Rd: SummarizedExperiment, ropls, opls
pca.Rd: SummarizedExperiment, ropls
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 69.95 6.52 76.45
ASICS 49.18 4.45 53.67
* 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
'E:/biocbuild/bbs-3.21-bioc/meat/ASICS.Rcheck/00check.log'
for details.
ASICS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL ASICS ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
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 0.02 s user time, 0 s system time and 0.01 s elapsed time.
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Begin WindowSelection
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End PreprocessingChain
It lasted 0.33 s user time, 0.03 s system time and 0.36 s elapsed time.
Normalisation method : CS
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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
461.68 54.40 516.89
ASICS.Rcheck/ASICS-Ex.timings
| name | user | system | elapsed | |
| ASICS | 49.18 | 4.45 | 53.67 | |
| ASICSUsersGuide | 0 | 0 | 0 | |
| accessors-methods | 0.19 | 0.03 | 0.22 | |
| alignSpectra | 1.76 | 0.11 | 1.87 | |
| binning | 0.36 | 0.00 | 0.36 | |
| combineAndSubset-methods | 0.03 | 0.00 | 0.03 | |
| createPureLibrary | 0.19 | 0.02 | 0.30 | |
| createSpectra | 0.24 | 0.00 | 0.33 | |
| formatForAnalysis | 0.62 | 0.01 | 0.67 | |
| importSpectra | 1.08 | 0.08 | 1.20 | |
| importSpectraBruker | 0.25 | 0.00 | 0.25 | |
| kruskalWallis | 0.25 | 0.02 | 0.27 | |
| normaliseSpectra | 0.04 | 0.00 | 0.05 | |
| oplsda | 0.14 | 0.00 | 0.14 | |
| pca | 0.08 | 0.00 | 0.08 | |
| plotAlignment | 1.52 | 0.01 | 1.53 | |
| simulate_spectra | 69.95 | 6.52 | 76.45 | |
| summary-methods | 0.03 | 0.00 | 0.04 | |
| visualisation-methods-analyses | 1.39 | 0.00 | 1.39 | |
| visualisation-methods-spectra | 0.67 | 0.06 | 0.73 | |