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 12:07 -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: /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_2.22.0.tar.gz |
| StartedAt: 2024-12-20 11:28:05 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 11:43:04 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 899.0 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_2.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ASICS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASICS’ version ‘2.22.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ASICS’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
data 1.1Mb
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
ASICS 55.734 7.215 63.050
simulate_spectra 54.251 4.604 58.885
* 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-3.20-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-arm64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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")
Binning
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
Normalisation method : CS
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
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 0.013 s user time, 0.004 s system time and 0.016 s elapsed time.
Begin GroupDelayCorrection
End GroupDelayCorrection
It lasted 0.036 s user time, 0.005 s system time and 0.041 s elapsed time.
Begin SolventSuppression
End SolventSuppression
It lasted 0.008 s user time, 0.008 s system time and 0.016 s elapsed time.
Begin Apodization
End Apodization
It lasted 0.001 s user time, 0.001 s system time and 0.002 s elapsed time.
Begin ZeroFilling
End ZeroFilling
It lasted 0.035 s user time, 0.002 s system time and 0.037 s elapsed time.
Begin FourierTransform
End FourierTransform
It lasted 0.012 s user time, 0.004 s system time and 0.016 s elapsed time.
Begin ZeroOrderPhaseCorrection
End ZeroOrderPhaseCorrection
It lasted 0.16 s user time, 0.02 s system time and 0.18 s elapsed time.
Begin InternalReferencing
End InternalReferencing
It lasted 0.011 s user time, 0.001 s system time and 0.013 s elapsed time.
Begin WindowSelection
End WindowSelection
It lasted 0.062 s user time, 0 s system time and 0.062 s elapsed time.
End PreprocessingChain
It lasted 0.339 s user time, 0.048 s system time and 0.386 s elapsed time.
Normalisation method : CS
Import spectra from txt or csv files...
Normalisation method : CS
Normalisation method : CS
Alignment...
Peak detection
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Finding reference spectrum
Compute FFT correlations
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
The reference spectrum is the number 3 : AG_faq_Beck139
Align spectra
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Import spectra from txt or csv files...
Normalisation method : CS
Binning
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Normalisation method : CS
Import spectra from txt or csv files...
Normalisation method : CS
Remove areas from spectrum and library
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Compute weights
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Remove metabolites that cannot belong to the mixture
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Translate library
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Deform library peaks
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Compute quantifications
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Format global results...
Remove areas from spectrum and library
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Compute weights
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Remove metabolites that cannot belong to the mixture
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Translate library
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Deform library peaks
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Compute quantifications
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Format global results...
Import spectra from 1r files...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Normalisation method : CS
Remove areas from spectrum and library
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Compute weights
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Remove metabolites that cannot belong to the mixture
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Translate library
Compute shifts for all maximum shift values
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
Put the median shift for extreme shift values
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
Compute correlations between buckets and quantifications
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
Shift all spectra according to the best shift
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Deform library peaks
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Compute quantifications
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Format global results...
Remove areas from spectrum and library
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Compute weights
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Remove metabolites that cannot belong to the mixture
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Translate library
Compute shifts for all maximum shift values
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
Put the median shift for extreme shift values
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
Compute correlations between buckets and quantifications
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
Shift all spectra according to the best shift
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Deform library peaks
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Compute quantifications
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
Format global results...
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 23 ]
>
> proc.time()
user system elapsed
462.309 83.796 547.215
ASICS.Rcheck/ASICS-Ex.timings
| name | user | system | elapsed | |
| ASICS | 55.734 | 7.215 | 63.050 | |
| ASICSUsersGuide | 0.001 | 0.001 | 0.001 | |
| accessors-methods | 0.097 | 0.079 | 0.176 | |
| alignSpectra | 1.424 | 0.052 | 1.477 | |
| binning | 0.286 | 0.041 | 0.328 | |
| combineAndSubset-methods | 0.034 | 0.001 | 0.034 | |
| createPureLibrary | 0.185 | 0.007 | 0.195 | |
| createSpectra | 0.134 | 0.008 | 0.144 | |
| formatForAnalysis | 0.427 | 0.005 | 0.437 | |
| importSpectra | 0.983 | 0.063 | 1.048 | |
| importSpectraBruker | 0.136 | 0.014 | 0.150 | |
| kruskalWallis | 0.189 | 0.003 | 0.192 | |
| normaliseSpectra | 0.089 | 0.006 | 0.097 | |
| oplsda | 0.101 | 0.002 | 0.102 | |
| pca | 0.051 | 0.001 | 0.053 | |
| plotAlignment | 0.874 | 0.065 | 0.939 | |
| simulate_spectra | 54.251 | 4.604 | 58.885 | |
| summary-methods | 0.028 | 0.001 | 0.029 | |
| visualisation-methods-analyses | 1.047 | 0.034 | 1.082 | |
| visualisation-methods-spectra | 0.611 | 0.029 | 0.641 | |