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This page was generated on 2021-07-30 12:05:34 -0400 (Fri, 30 Jul 2021).

CHECK results for metaMS on merida1

To the developers/maintainers of the metaMS package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1072/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaMS 1.29.0  (landing page)
Yann Guitton
Snapshot Date: 2021-07-29 14:50:07 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/metaMS
Branch: master
Last Commit: 5a99fe0
Last Changed Date: 2021-05-19 12:04:21 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  NO, package depends on 'CAMERA' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: metaMS
Version: 1.29.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metaMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metaMS_1.29.0.tar.gz
StartedAt: 2021-07-30 04:05:40 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 04:11:54 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 374.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: metaMS.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metaMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metaMS_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/metaMS.Rcheck’
* using R version 4.1.0 RC (2021-05-16 r80304)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaMS’ version ‘1.29.0’
* 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 ‘metaMS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘bin’
See ‘/Users/biocbuild/bbs-3.14-bioc/meat/metaMS.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 contents of ‘data’ directory ... WARNING
Output for data("GCresults", package = "metaMS"):
  Warning message:
  multiple methods tables found for ‘bin’ 
Output for data("LCresults", package = "metaMS"):
  Warning message:
  multiple methods tables found for ‘bin’ 
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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 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: 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/metaMS.Rcheck/00check.log’
for details.



Installation output

metaMS.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metaMS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘metaMS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
multiple methods tables found for ‘bin’ 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for ‘bin’
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘bin’
** testing if installed package keeps a record of temporary installation path
* DONE (metaMS)

Tests output

metaMS.Rcheck/tests/runTests.Rout


R version 4.1.0 RC (2021-05-16 r80304) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> 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, 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, sort, 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")'.


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.19.1 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    trimws


This is xcms version 3.15.2 


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 Jul 30 04:11:45 2021 
*********************************************** 
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 
Warning message:
multiple methods tables found for 'bin' 
> 
> proc.time()
   user  system elapsed 
 20.319   0.883  21.210 

Example timings

metaMS.Rcheck/metaMS-Ex.timings

nameusersystemelapsed
AnnotateTable0.0660.0070.074
FEMsettings0.0010.0020.002
addRI0.0400.0030.043
alignmentLC0.1880.2320.420
constructExpPseudoSpectra0.0660.0160.082
createSTDdbGC0.0030.0020.006
createSTDdbLC0.0270.0030.030
errf0.0220.0040.027
getAnnotationLC0.8770.2461.123
getAnnotationMat0.0640.0070.071
getFeatureInfo0.0620.0080.072
getPeakTable0.1910.2300.449
matchExpSpec0.0250.0060.031
matchSamples2DB0.0030.0020.006
matchSamples2Samples0.0020.0020.004
metaMSsettings-class0.0030.0020.003
metaSetting-methods0.0010.0010.000
msp0.0020.0030.005
peakDetection0.0020.0030.005
plotPseudoSpectrum0.0210.0020.024
processStandards0.0630.0070.071
readStdInfo0.0220.0020.024
runCAMERA0.1990.2480.447
runGC0.0640.0070.071
runLC0.0350.0050.040
threeStdsDB0.0140.0080.023
treat.DB0.0040.0020.006