Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:03 -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 371/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CluMSID 1.22.0 (landing page) Tobias Depke
| 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 | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the CluMSID package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CluMSID.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: CluMSID |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CluMSID.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CluMSID_1.22.0.tar.gz |
StartedAt: 2024-12-19 21:35:15 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 21:49:09 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 833.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CluMSID.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CluMSID.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CluMSID_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CluMSID.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘CluMSID/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CluMSID’ version ‘1.22.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘CluMSID’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘dbscan::as.dendrogram’ by ‘stats::as.dendrogram’ when loading ‘CluMSID’ See ‘/home/biocbuild/bbs-3.20-bioc/meat/CluMSID.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... NOTE checkRd: (-1) OPTICSplot.Rd:24: Lost braces 24 | see code{\link[dbscan:optics]{extractDBSCAN}}. | ^ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed mergeMS2spectra 17.273 0.303 17.577 extractMS2spectra 13.728 0.273 14.010 splitPolarities 13.511 0.119 13.632 * 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/CluMSID.Rcheck/00check.log’ for details.
CluMSID.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CluMSID ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘CluMSID’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘dbscan::as.dendrogram’ by ‘stats::as.dendrogram’ when loading ‘CluMSID’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘dbscan::as.dendrogram’ by ‘stats::as.dendrogram’ when loading ‘CluMSID’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘dbscan::as.dendrogram’ by ‘stats::as.dendrogram’ when loading ‘CluMSID’ ** testing if installed package keeps a record of temporary installation path * DONE (CluMSID)
CluMSID.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: 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(CluMSID) Warning message: replacing previous import 'dbscan::as.dendrogram' by 'stats::as.dendrogram' when loading 'CluMSID' > > test_check("CluMSID") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ] > > proc.time() user system elapsed 14.562 0.757 15.302
CluMSID.Rcheck/CluMSID-Ex.timings
name | user | system | elapsed | |
Featurelist | 0.009 | 0.000 | 0.009 | |
HCplot | 0.890 | 0.019 | 0.909 | |
HCtbl | 0.007 | 0.000 | 0.008 | |
MDSplot | 0.419 | 0.014 | 0.433 | |
OPTICSplot | 0.034 | 0.001 | 0.035 | |
OPTICStbl | 0.010 | 0.001 | 0.011 | |
accessors | 0.045 | 0.000 | 0.046 | |
addAnnotations | 0.045 | 0.016 | 0.062 | |
as.MS2spectrum | 0.101 | 0.003 | 0.105 | |
cossim | 0.013 | 0.000 | 0.014 | |
distanceMatrix | 0.412 | 0.029 | 0.442 | |
extractMS2spectra | 13.728 | 0.273 | 14.010 | |
extractPseudospectra | 1.392 | 0.487 | 1.703 | |
findFragment | 0.021 | 0.000 | 0.021 | |
findNL | 0.021 | 0.000 | 0.021 | |
getSimilarities | 2.026 | 0.021 | 2.049 | |
getSpectrum | 0.017 | 0.000 | 0.017 | |
mergeMS2spectra | 17.273 | 0.303 | 17.577 | |
networkplot | 0.173 | 0.000 | 0.174 | |
specplot | 0.007 | 0.002 | 0.009 | |
splitPolarities | 13.511 | 0.119 | 13.632 | |
writeFeaturelist | 0.011 | 0.000 | 0.011 | |