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This page was generated on 2024-04-18 11:32:08 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 367/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CluMSID 1.18.0  (landing page)
Tobias Depke
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/CluMSID
git_branch: RELEASE_3_18
git_last_commit: ce1d21e
git_last_commit_date: 2023-10-24 11:10:10 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for CluMSID on kjohnson1


To the developers/maintainers of the CluMSID package:
- 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: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2024-04-17 09:19:36 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 09:23:32 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 236.3 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/CluMSID.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CluMSID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CluMSID’ version ‘1.18.0’
* 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-3.18-bioc-mac-arm64/meat/CluMSID.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
mergeMS2spectra   20.561  0.137  22.073
splitPolarities   17.853  0.126  20.216
extractMS2spectra 17.391  0.176  18.999
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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/4.3-arm64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(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 
 11.833   0.511  17.029 

Example timings

CluMSID.Rcheck/CluMSID-Ex.timings

nameusersystemelapsed
Featurelist0.0150.0020.020
HCplot0.3490.0060.391
HCtbl0.0130.0010.014
MDSplot1.0960.0221.246
OPTICSplot0.0370.0030.040
OPTICStbl0.0170.0010.019
accessors0.0750.0040.096
addAnnotations0.0690.1010.180
as.MS2spectrum0.1940.0160.215
cossim0.0190.0010.020
distanceMatrix0.4500.0370.490
extractMS2spectra17.391 0.17618.999
extractPseudospectra1.0340.1481.217
findFragment0.0260.0010.027
findNL0.0420.0080.058
getSimilarities2.3590.0162.439
getSpectrum0.0230.0030.026
mergeMS2spectra20.561 0.13722.073
networkplot0.2220.0040.235
specplot0.0150.0020.017
splitPolarities17.853 0.12620.216
writeFeaturelist0.0170.0020.021