Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-09-27 12:29 -0400 (Fri, 27 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4451
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4417
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4456
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4489
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4436
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4435
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 369/2262HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CluMSID 1.21.0  (landing page)
Tobias Depke
Snapshot Date: 2024-09-26 13:40 -0400 (Thu, 26 Sep 2024)
git_url: https://git.bioconductor.org/packages/CluMSID
git_branch: devel
git_last_commit: c4712fb
git_last_commit_date: 2024-04-30 11:11:45 -0400 (Tue, 30 Apr 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for CluMSID on lconway

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.

raw results


Summary

Package: CluMSID
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CluMSID.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CluMSID_1.21.0.tar.gz
StartedAt: 2024-09-26 19:58:12 -0400 (Thu, 26 Sep 2024)
EndedAt: 2024-09-26 20:04:40 -0400 (Thu, 26 Sep 2024)
EllapsedTime: 387.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CluMSID.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CluMSID.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CluMSID_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CluMSID.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CluMSID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CluMSID’ version ‘1.21.0’
* 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 ‘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 ‘/Users/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 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   24.834  0.184  25.184
extractMS2spectra 20.456  0.227  20.782
splitPolarities   19.381  0.111  19.588
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CluMSID.Rcheck/00check.log’
for details.


Installation output

CluMSID.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CluMSID
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output

CluMSID.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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(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 
 19.985   0.916  21.005 

Example timings

CluMSID.Rcheck/CluMSID-Ex.timings

nameusersystemelapsed
Featurelist0.0130.0020.016
HCplot0.2990.0090.310
HCtbl0.0090.0020.010
MDSplot1.3850.0241.418
OPTICSplot0.0260.0020.028
OPTICStbl0.0140.0020.016
accessors0.0620.0060.068
addAnnotations0.0930.1240.220
as.MS2spectrum0.2320.0250.259
cossim0.0170.0000.018
distanceMatrix0.5580.0250.586
extractMS2spectra20.456 0.22720.782
extractPseudospectra1.1200.5531.044
findFragment0.0220.0010.024
findNL0.0270.0030.030
getSimilarities3.6410.0663.739
getSpectrum0.0240.0040.027
mergeMS2spectra24.834 0.18425.184
networkplot0.2250.0030.229
specplot0.0090.0010.011
splitPolarities19.381 0.11119.588
writeFeaturelist0.0120.0010.013