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This page was generated on 2021-07-23 15:06:10 -0400 (Fri, 23 Jul 2021).

CHECK results for metaMS on tokay2

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.
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raw results

Package 1089/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaMS 1.28.0  (landing page)
Yann Guitton
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/metaMS
Branch: RELEASE_3_13
Last Commit: 1f3d024
Last Changed Date: 2021-05-19 12:04:21 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: metaMS
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings metaMS_1.28.0.tar.gz
StartedAt: 2021-07-23 01:52:24 -0400 (Fri, 23 Jul 2021)
EndedAt: 2021-07-23 01:58:38 -0400 (Fri, 23 Jul 2021)
EllapsedTime: 374.4 seconds
RetCode: 0
Status:   OK  
CheckDir: metaMS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings metaMS_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/metaMS.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metaMS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metaMS' version '1.28.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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: OK


Installation output

metaMS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/metaMS_1.28.0.tar.gz && rm -rf metaMS.buildbin-libdir && mkdir metaMS.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaMS.buildbin-libdir metaMS_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL metaMS_1.28.0.zip && rm metaMS_1.28.0.tar.gz metaMS_1.28.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 25 3425k   25  888k    0     0  1877k      0  0:00:01 --:--:--  0:00:01 1878k
100 3425k  100 3425k    0     0  2931k      0  0:00:01  0:00:01 --:--:-- 2935k

install for i386

* installing *source* package 'metaMS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'metaMS'
    finding HTML links ... done
    AnnotateTable                           html  
    FEMsettings                             html  
    finding level-2 HTML links ... done

    GCresults                               html  
    LCDBtest                                html  
    LCresults                               html  
    addRI                                   html  
    alignmentLC                             html  
    annotations2tab                         html  
    constructExpPseudoSpectra               html  
    createSTDdbGC                           html  
    createSTDdbLC                           html  
    errf                                    html  
    exptable                                html  
    getAnnotationLC                         html  
    getAnnotationMat                        html  
    getFeatureInfo                          html  
    getPeakTable                            html  
    match2ExtDB                             html  
    matchExpSpec                            html  
    matchSamples2DB                         html  
    matchSamples2Samples                    html  
    metaMS-package                          html  
    metaMSsettings-class                    html  
    metaSetting-methods                     html  
REDIRECT:topic	 metaSetting<- -> metaSetting-methods.html [ FAIL ]
REDIRECT:topic	 metaSetting<-,metaMSsettings-method -> metaSetting-methods.html [ FAIL ]
    msp                                     html  
    peakDetection                           html  
    plotPseudoSpectrum                      html  
    printString                             html  
    processStandards                        html  
    readStdInfo                             html  
    removeDoubleMasses                      html  
    runCAMERA                               html  
    runGC                                   html  
    runLC                                   html  
    threeStdsDB                             html  
    treat.DB                                html  
** 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

install for x64

* installing *source* package 'metaMS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metaMS' as metaMS_1.28.0.zip
* DONE (metaMS)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'metaMS' successfully unpacked and MD5 sums checked

Tests output

metaMS.Rcheck/tests_i386/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 2.18.0 
  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 3.14.0 


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 Jul 23 01:58:14 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 
> 
> proc.time()
   user  system elapsed 
  15.62    1.65   17.31 

metaMS.Rcheck/tests_x64/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 2.18.0 
  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 3.14.0 


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 Jul 23 01:58:29 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 
> 
> proc.time()
   user  system elapsed 
  13.73    0.59   14.31 

Example timings

metaMS.Rcheck/examples_i386/metaMS-Ex.timings

nameusersystemelapsed
AnnotateTable0.060.020.08
FEMsettings000
addRI0.030.000.04
alignmentLC0.110.050.16
constructExpPseudoSpectra0.050.010.06
createSTDdbGC000
createSTDdbLC0.020.000.02
errf0.020.000.02
getAnnotationLC0.150.000.15
getAnnotationMat0.070.000.07
getFeatureInfo0.040.000.04
getPeakTable0.080.080.16
matchExpSpec0.580.030.61
matchSamples2DB000
matchSamples2Samples000
metaMSsettings-class0.020.000.01
metaSetting-methods000
msp000
peakDetection000
plotPseudoSpectrum0.020.000.02
processStandards0.040.000.04
readStdInfo0.020.000.02
runCAMERA0.160.000.15
runGC0.040.020.07
runLC0.030.000.03
threeStdsDB0.000.010.01
treat.DB0.020.000.02

metaMS.Rcheck/examples_x64/metaMS-Ex.timings

nameusersystemelapsed
AnnotateTable0.050.010.06
FEMsettings000
addRI0.030.000.04
alignmentLC0.110.050.15
constructExpPseudoSpectra0.110.000.11
createSTDdbGC000
createSTDdbLC0.030.000.03
errf0.020.000.02
getAnnotationLC0.090.060.15
getAnnotationMat0.050.000.05
getFeatureInfo0.050.000.05
getPeakTable0.860.060.92
matchExpSpec0.010.000.02
matchSamples2DB0.000.020.01
matchSamples2Samples000
metaMSsettings-class000
metaSetting-methods000
msp0.000.020.02
peakDetection000
plotPseudoSpectrum0.020.010.03
processStandards0.040.000.04
readStdInfo0.020.000.02
runCAMERA0.090.060.16
runGC0.050.020.06
runLC0.030.000.03
threeStdsDB0.020.000.02
treat.DB0.010.000.01