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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1209/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaMS 1.42.0  (landing page)
Yann Guitton
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/metaMS
git_branch: RELEASE_3_20
git_last_commit: cd5932c
git_last_commit_date: 2024-10-29 09:51:29 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'CAMERA' which is only available as a source package that needs compilation
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'CAMERA' which is only available as a source package that needs compilation


CHECK results for metaMS on nebbiolo2

To the developers/maintainers of the metaMS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaMS.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: metaMS
Version: 1.42.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:metaMS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings metaMS_1.42.0.tar.gz
StartedAt: 2024-12-20 02:23:26 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 02:32:50 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 563.4 seconds
RetCode: 0
Status:   OK  
CheckDir: metaMS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:metaMS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings metaMS_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/metaMS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘metaMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaMS’ version ‘1.42.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘metaMS’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK


Installation output

metaMS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL metaMS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘metaMS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (metaMS)

Tests output

metaMS.Rcheck/tests/runTests.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.

> BiocGenerics:::testPackage("metaMS")

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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


This is xcms version 4.4.0 


Attaching package: 'xcms'

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

    sigma

< -------- Experiment of 4 samples ------------------------------------- >
< -------- Instrument: TSQXLS.QQQ.GC ----------------------------------- >
< -------- Annotation using database of 3 spectra ---------------------- >
< -------- Using xcmsSet object - only doing annotation ---------------- >
< -------- Removing artefacts (Bleeding, Plasticizers) ----------------- >
< -------- Matching with database of standards ------------------------- >
< -------- Matching unknowns across samples ---------------------------- >
< -------- Formatting results ------------------------------------------ >
< -------- Done! ------------------------------------------------------- >
< -------- Experiment of 4 samples ------------------------------------- >
< -------- Instrument: Synapt.QTOF.RP  - polarity: positive ------------ >
< -------- Database of 4 compounds ------------------------------------- >
< -------- Using xcmsSet object - only doing annotation ---------------- >
< -------- Performing annotation --------------------------------------- >
	 Fixed mass tolerance 0.005
	 Feature-wise Annotation ...
< -------- Formatting the output --------------------------------------- >
< -------- Done ! ------------------------------------------------------ >


RUNIT TEST PROTOCOL -- Fri Dec 20 02:32:13 2024 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metaMS RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 14.497   0.680  15.168 

Example timings

metaMS.Rcheck/metaMS-Ex.timings

nameusersystemelapsed
AnnotateTable0.0390.0030.042
FEMsettings0.0010.0000.000
addRI0.0250.0000.026
alignmentLC0.0770.0250.102
constructExpPseudoSpectra0.1750.0030.179
createSTDdbGC0.0030.0010.002
createSTDdbLC0.0120.0010.014
errf0.0150.0000.015
getAnnotationLC0.0790.0200.100
getAnnotationMat0.0370.0030.040
getFeatureInfo0.0350.0030.039
getPeakTable0.0720.0280.100
matchExpSpec0.0130.0000.013
matchSamples2DB0.0020.0000.001
matchSamples2Samples0.0010.0000.001
metaMSsettings-class0.0000.0000.001
metaSetting-methods000
msp0.0010.0000.001
peakDetection0.0010.0000.001
plotPseudoSpectrum0.0120.0000.013
processStandards0.0380.0000.039
readStdInfo0.0160.0010.015
runCAMERA0.9100.0220.932
runGC0.0360.0000.037
runLC0.0190.0010.020
threeStdsDB0.0090.0000.009
treat.DB0.0030.0000.002