Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-27 11:36:28 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 367/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CluMSID 1.19.0  (landing page)
Tobias Depke
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/CluMSID
git_branch: devel
git_last_commit: f6e24c8
git_last_commit_date: 2023-10-24 11:10:10 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for CluMSID on nebbiolo1


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: 1.19.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CluMSID.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CluMSID_1.19.0.tar.gz
StartedAt: 2024-03-26 21:07:55 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 21:19:05 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 669.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CluMSID.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CluMSID.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CluMSID_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CluMSID.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 ‘CluMSID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CluMSID’ version ‘1.19.0’
* 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 ‘/home/biocbuild/bbs-3.19-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   18.636  0.450  19.103
extractMS2spectra 14.900  0.804  15.709
splitPolarities   14.549  0.163  14.712
* 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-3.19-bioc/meat/CluMSID.Rcheck/00check.log’
for details.


Installation output

CluMSID.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CluMSID
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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)

Tests output

CluMSID.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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 
 16.942   0.752  17.689 

Example timings

CluMSID.Rcheck/CluMSID-Ex.timings

nameusersystemelapsed
Featurelist0.0070.0040.011
HCplot0.1600.0000.161
HCtbl0.0090.0000.010
MDSplot1.2530.0201.273
OPTICSplot0.0270.0000.027
OPTICStbl0.0130.0000.013
accessors0.0500.0000.051
addAnnotations0.0650.1040.169
as.MS2spectrum0.1330.0160.149
cossim0.0160.0000.016
distanceMatrix0.4210.0200.440
extractMS2spectra14.900 0.80415.709
extractPseudospectra0.9220.3750.925
findFragment0.0220.0000.023
findNL0.0210.0040.025
getSimilarities3.0420.1443.186
getSpectrum0.0160.0040.020
mergeMS2spectra18.636 0.45019.103
networkplot0.2440.0040.248
specplot0.0100.0000.011
splitPolarities14.549 0.16314.712
writeFeaturelist0.0090.0040.013