Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:02:49 -0400 (Fri, 31 May 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" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | |||||||||
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ASICS_2.20.1.tar.gz |
StartedAt: 2024-05-31 01:15:20 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 01:29:00 -0400 (Fri, 31 May 2024) |
EllapsedTime: 820.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ASICS.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ASICS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ASICS_2.20.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ASICS.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 5.6Mb sub-directories of 1Mb or more: data 1.1Mb doc 2.3Mb extdata 1.4Mb * 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 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 ... 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 53.640 4.680 58.322 ASICS 43.094 1.411 44.508 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/ASICS.Rcheck/00check.log’ for details.
ASICS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ASICS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 0.011 s user time, 0 s system time and 0.011 s elapsed time. Begin GroupDelayCorrection End GroupDelayCorrection It lasted 0.03 s user time, 0 s system time and 0.029 s elapsed time. Begin SolventSuppression End SolventSuppression It lasted 0.029 s user time, 0.008 s system time and 0.038 s elapsed time. Begin Apodization End Apodization It lasted 0.001 s user time, 0 s system time and 0 s elapsed time. Begin ZeroFilling End ZeroFilling It lasted 0.028 s user time, 0 s system time and 0.028 s elapsed time. Begin FourierTransform End FourierTransform It lasted 0.008 s user time, 0 s system time and 0.009 s elapsed time. Begin ZeroOrderPhaseCorrection End ZeroOrderPhaseCorrection It lasted 0.095 s user time, 0.012 s system time and 0.107 s elapsed time. Begin InternalReferencing End InternalReferencing It lasted 0.008 s user time, 0 s system time and 0.008 s elapsed time. Begin WindowSelection End WindowSelection It lasted 0.05 s user time, 0 s system time and 0.051 s elapsed time. End PreprocessingChain It lasted 0.266 s user time, 0.02 s system time and 0.285 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 352.640 9.739 362.393
ASICS.Rcheck/ASICS-Ex.timings
name | user | system | elapsed | |
ASICS | 43.094 | 1.411 | 44.508 | |
ASICSUsersGuide | 0.002 | 0.000 | 0.001 | |
accessors-methods | 0.065 | 0.100 | 0.165 | |
alignSpectra | 1.301 | 0.036 | 1.337 | |
binning | 0.180 | 0.016 | 0.195 | |
combineAndSubset-methods | 0.027 | 0.000 | 0.026 | |
createPureLibrary | 0.253 | 0.012 | 0.267 | |
createSpectra | 0.104 | 0.008 | 0.114 | |
formatForAnalysis | 0.398 | 0.008 | 0.407 | |
importSpectra | 0.596 | 0.012 | 0.609 | |
importSpectraBruker | 0.1 | 0.0 | 0.1 | |
kruskalWallis | 0.157 | 0.004 | 0.161 | |
normaliseSpectra | 0.024 | 0.003 | 0.027 | |
oplsda | 0.082 | 0.004 | 0.086 | |
pca | 0.041 | 0.000 | 0.041 | |
plotAlignment | 0.587 | 0.016 | 0.603 | |
simulate_spectra | 53.640 | 4.680 | 58.322 | |
summary-methods | 0.02 | 0.00 | 0.02 | |
visualisation-methods-analyses | 0.945 | 0.016 | 0.960 | |
visualisation-methods-spectra | 0.559 | 0.004 | 0.563 | |