| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-26 06:18:04 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 96/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ASICS 2.17.0 (landing page) Gaëlle Lefort
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: ASICS |
| Version: 2.17.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ASICS_2.17.0.tar.gz |
| StartedAt: 2023-05-26 03:19:06 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 03:38:26 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 1160.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ASICS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ASICS_2.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ASICS.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘ASICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASICS’ version ‘2.17.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ASICS’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
data 1.0Mb
doc 2.7Mb
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 loading without being on the library search path ... 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 ... 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 75.237 3.017 78.412
ASICS 56.893 1.213 58.235
* 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 ...
‘ASICS.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/ASICS.Rcheck/00check.log’
for details.
ASICS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ASICS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 0.014 s user time, 0 s system time and 0.021 s elapsed time.
Begin GroupDelayCorrection
End GroupDelayCorrection
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Begin SolventSuppression
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Begin Apodization
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Begin ZeroFilling
End ZeroFilling
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Begin FourierTransform
End FourierTransform
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Begin ZeroOrderPhaseCorrection
End ZeroOrderPhaseCorrection
It lasted 0.22 s user time, 0.008 s system time and 0.228 s elapsed time.
Begin InternalReferencing
End InternalReferencing
It lasted 0.043 s user time, 0 s system time and 0.043 s elapsed time.
Begin WindowSelection
End WindowSelection
It lasted 0.086 s user time, 0 s system time and 0.086 s elapsed time.
End PreprocessingChain
It lasted 0.483 s user time, 0.024 s system time and 0.517 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
517.239 4.607 522.869
ASICS.Rcheck/ASICS-Ex.timings
| name | user | system | elapsed | |
| ASICS | 56.893 | 1.213 | 58.235 | |
| ASICSUsersGuide | 0.001 | 0.000 | 0.001 | |
| accessors-methods | 0.093 | 0.036 | 0.129 | |
| alignSpectra | 2.225 | 0.088 | 2.318 | |
| binning | 0.288 | 0.052 | 0.340 | |
| combineAndSubset-methods | 0.06 | 0.00 | 0.06 | |
| createPureLibrary | 1.182 | 0.124 | 1.321 | |
| createSpectra | 0.182 | 0.004 | 0.197 | |
| formatForAnalysis | 0.562 | 0.008 | 0.579 | |
| importSpectra | 0.931 | 0.032 | 0.971 | |
| importSpectraBruker | 0.140 | 0.000 | 0.141 | |
| kruskalWallis | 0.244 | 0.008 | 0.254 | |
| normaliseSpectra | 0.092 | 0.007 | 0.099 | |
| oplsda | 0.144 | 0.000 | 0.145 | |
| pca | 0.072 | 0.000 | 0.073 | |
| plotAlignment | 0.776 | 0.056 | 0.834 | |
| simulate_spectra | 75.237 | 3.017 | 78.412 | |
| summary-methods | 0.039 | 0.000 | 0.040 | |
| visualisation-methods-analyses | 1.366 | 0.011 | 1.381 | |
| visualisation-methods-spectra | 0.761 | 0.004 | 0.766 | |