Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-07-04 11:45 -0400 (Thu, 04 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4411
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4413
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4395
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4390
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 (2024-04-24) -- "Puppy Cup" 4407
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 1177/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaboAnnotation 1.9.1  (landing page)
Johannes Rainer
Snapshot Date: 2024-07-03 14:00 -0400 (Wed, 03 Jul 2024)
git_url: https://git.bioconductor.org/packages/MetaboAnnotation
git_branch: devel
git_last_commit: b96137d
git_last_commit_date: 2024-05-16 03:13:56 -0400 (Thu, 16 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for MetaboAnnotation on kunpeng2

To the developers/maintainers of the MetaboAnnotation package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetaboAnnotation.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: MetaboAnnotation
Version: 1.9.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MetaboAnnotation.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MetaboAnnotation_1.9.1.tar.gz
StartedAt: 2024-07-04 06:40:37 -0000 (Thu, 04 Jul 2024)
EndedAt: 2024-07-04 06:47:27 -0000 (Thu, 04 Jul 2024)
EllapsedTime: 409.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MetaboAnnotation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:MetaboAnnotation.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MetaboAnnotation_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MetaboAnnotation.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaboAnnotation/DESCRIPTION’ ... OK
* this is package ‘MetaboAnnotation’ version ‘1.9.1’
* 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 ‘MetaboAnnotation’ can be installed ... OK
* 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 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 ... 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
CompareSpectraParam 7.344  0.776   8.107
CompDbSource        5.996  0.583  10.741
* 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: OK


Installation output

MetaboAnnotation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MetaboAnnotation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.0/site-library’
* installing *source* package ‘MetaboAnnotation’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MetaboAnnotation)

Tests output

MetaboAnnotation.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(MetaboAnnotation)
> library(msdata)
> library(Spectra)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:MetaboAnnotation':

    endoapply

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: BiocParallel
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth

> library(testthat)

Attaching package: 'testthat'

The following object is masked from 'package:MetaboAnnotation':

    matches

> 
> fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
> pest_ms2 <- filterMsLevel(Spectra(fl), 2L)
> pest_ms2 <- pest_ms2[c(808, 809, 945:955)]
> load(system.file("extdata", "minimb.RData", package = "MetaboAnnotation"))
> 
> test_check("MetaboAnnotation")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 1153 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 1153 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 60.683   4.118  72.028 

Example timings

MetaboAnnotation.Rcheck/MetaboAnnotation-Ex.timings

nameusersystemelapsed
CompDbSource 5.996 0.58310.741
CompareSpectraParam7.3440.7768.107
Matched0.5120.0560.569
MatchedSpectra0.3280.0160.345
createStandardMixes0.0030.0000.003
matchFormula0.1940.0110.206
matchValues0.8460.0240.871
validateMatchedSpectra1.2740.1911.414