Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-04 11:37:13 -0400 (Wed, 04 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 363/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CluMSID 1.16.0  (landing page)
Tobias Depke
Snapshot Date: 2023-10-03 14:00:15 -0400 (Tue, 03 Oct 2023)
git_url: https://git.bioconductor.org/packages/CluMSID
git_branch: RELEASE_3_17
git_last_commit: e71998f
git_last_commit_date: 2023-04-25 11:06:55 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for CluMSID on merida1


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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2023-10-03 23:50:50 -0400 (Tue, 03 Oct 2023)
EndedAt: 2023-10-04 00:00:40 -0400 (Wed, 04 Oct 2023)
EllapsedTime: 590.2 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/CluMSID.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CluMSID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CluMSID’ version ‘1.16.0’
* 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-3.17-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 ... 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   57.476  0.291  83.065
splitPolarities   48.418  0.246  71.083
extractMS2spectra 48.070  0.311  70.964
getSimilarities    6.733  0.052   9.872
* 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-3.17-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/4.3-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-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 
 25.143   0.961  38.370 

Example timings

CluMSID.Rcheck/CluMSID-Ex.timings

nameusersystemelapsed
Featurelist0.0210.0020.045
HCplot0.5760.0130.887
HCtbl0.0130.0030.026
MDSplot1.1460.0351.757
OPTICSplot0.0420.0040.062
OPTICStbl0.0240.0030.037
accessors0.0930.0090.136
addAnnotations0.2180.3350.795
as.MS2spectrum0.2590.0270.411
cossim0.0300.0020.041
distanceMatrix1.2850.1412.069
extractMS2spectra48.070 0.31170.964
extractPseudospectra1.5830.3752.241
findFragment0.0610.0020.114
findNL0.0620.0060.108
getSimilarities6.7330.0529.872
getSpectrum0.0430.0080.074
mergeMS2spectra57.476 0.29183.065
networkplot0.4320.0050.613
specplot0.0170.0020.030
splitPolarities48.418 0.24671.083
writeFeaturelist0.0250.0020.040