Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for artMS on tokay1

This page was generated on 2020-10-29 12:24:34 -0400 (Thu, 29 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE artMS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 89/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.8.0
David Jimenez-Morales
Snapshot Date: 2020-10-28 14:42:40 -0400 (Wed, 28 Oct 2020)
URL: https://git.bioconductor.org/packages/artMS
Branch: RELEASE_3_12
Last Commit: b4aa374
Last Changed Date: 2020-10-27 11:40:21 -0400 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: artMS
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:artMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings artMS_1.8.0.tar.gz
StartedAt: 2020-10-29 00:20:13 -0400 (Thu, 29 Oct 2020)
EndedAt: 2020-10-29 00:27:13 -0400 (Thu, 29 Oct 2020)
EllapsedTime: 420.3 seconds
RetCode: 0
Status:  OK  
CheckDir: artMS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:artMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings artMS_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/artMS.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'artMS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'artMS' version '1.8.0'
* 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 'artMS' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
* 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
artmsEnrichLog2fc 1.17   0.46       6
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
artmsAnnotationUniprot  4.2    0.9    5.13
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/artMS.Rcheck/00check.log'
for details.



Installation output

artMS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/artMS_1.8.0.tar.gz && rm -rf artMS.buildbin-libdir && mkdir artMS.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=artMS.buildbin-libdir artMS_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL artMS_1.8.0.zip && rm artMS_1.8.0.tar.gz artMS_1.8.0.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
100 6827k  100 6827k    0     0  55.4M      0 --:--:-- --:--:-- --:--:-- 57.4M

install for i386

* installing *source* package 'artMS' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'artMS'
    finding HTML links ... done
    artmsAnalysisQuantifications            html  
    artmsAnnotateSpecie                     html  
    artmsAnnotationUniprot                  html  
    artmsAvgIntensityRT                     html  
    artmsChangeColumnName                   html  
    artmsConvertMetabolomics                html  
    artmsDataPlots                          html  
    artmsEnrichLog2fc                       html  
    artmsEnrichProfiler                     html  
    artmsEvidenceToSAINTq                   html  
    artmsEvidenceToSaintExpress             html  
    artmsFilterEvidenceContaminants         html  
    artmsGeneratePhSiteExtended             html  
    artmsIsEvidenceNewVersion               html  
    artmsIsSpeciesSupported                 html  
    artmsLeaveOnlyUniprotEntryID            html  
    artmsMapUniprot2Entrez                  html  
    artmsMergeEvidenceAndKeys               html  
    artmsMsstatsSummary                     html  
    artmsPhosfateOutput                     html  
    artmsPhotonOutput                       html  
    artmsPlotHeatmapQuant                   html  
    artmsProtein2SiteConversion             html  
    artmsQualityControlEvidenceBasic        html  
    artmsQualityControlEvidenceExtended     html  
    artmsQualityControlMetabolomics         html  
    artmsQualityControlSummaryExtended      html  
    artmsQuantification                     html  
    artmsResultsWide                        html  
    artmsSILACtoLong                        html  
    artmsSpectralCounts                     html  
    artmsVolcanoPlot                        html  
    artmsWriteConfigYamlFile                html  
    artms_config                            html  
    artms_data_corum_mito_database          html  
    artms_data_pathogen_LPN                 html  
    artms_data_pathogen_TB                  html  
    artms_data_ph_config                    html  
    artms_data_ph_contrast                  html  
    artms_data_ph_evidence                  html  
    artms_data_ph_keys                      html  
    artms_data_ph_msstats_modelqc           html  
    artms_data_ph_msstats_results           html  
    artms_data_randomDF                     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 'artMS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'artMS' as artMS_1.8.0.zip
* DONE (artMS)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'artMS' successfully unpacked and MD5 sums checked

Tests output

artMS.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> library(testthat)
> library(artMS)


> 
> test_check("artMS")
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  10.32    0.93   14.48 

artMS.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> library(testthat)
> library(artMS)


> 
> test_check("artMS")
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   9.73    0.51   13.56 

Example timings

artMS.Rcheck/examples_i386/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.050.000.04
artmsAnnotateSpecie0.000.020.02
artmsAnnotationUniprot3.641.034.68
artmsAvgIntensityRT1.940.041.98
artmsChangeColumnName000
artmsConvertMetabolomics000
artmsDataPlots000
artmsEnrichLog2fc1.170.466.00
artmsEnrichProfiler0.270.001.83
artmsEvidenceToSAINTq000
artmsEvidenceToSaintExpress000
artmsFilterEvidenceContaminants0.090.000.10
artmsGeneratePhSiteExtended000
artmsIsEvidenceNewVersion000
artmsIsSpeciesSupported0.130.000.12
artmsLeaveOnlyUniprotEntryID000
artmsMapUniprot2Entrez0.290.000.30
artmsMergeEvidenceAndKeys0.140.000.14
artmsMsstatsSummary000
artmsPhosfateOutput000
artmsPhotonOutput000
artmsPlotHeatmapQuant0.360.000.35
artmsProtein2SiteConversion000
artmsQualityControlEvidenceBasic1.230.001.50
artmsQualityControlEvidenceExtended0.020.000.02
artmsQualityControlMetabolomics000
artmsQualityControlSummaryExtended000
artmsQuantification000
artmsResultsWide0.290.020.31
artmsSILACtoLong000
artmsSpectralCounts0.580.000.58
artmsVolcanoPlot0.190.000.19
artmsWriteConfigYamlFile000

artMS.Rcheck/examples_x64/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications000
artmsAnnotateSpecie000
artmsAnnotationUniprot4.200.905.13
artmsAvgIntensityRT2.480.002.48
artmsChangeColumnName000
artmsConvertMetabolomics000
artmsDataPlots000
artmsEnrichLog2fc1.060.123.68
artmsEnrichProfiler0.420.001.83
artmsEvidenceToSAINTq000
artmsEvidenceToSaintExpress000
artmsFilterEvidenceContaminants0.080.000.07
artmsGeneratePhSiteExtended000
artmsIsEvidenceNewVersion000
artmsIsSpeciesSupported0.110.020.13
artmsLeaveOnlyUniprotEntryID000
artmsMapUniprot2Entrez0.210.000.20
artmsMergeEvidenceAndKeys0.110.000.11
artmsMsstatsSummary000
artmsPhosfateOutput000
artmsPhotonOutput000
artmsPlotHeatmapQuant0.340.000.34
artmsProtein2SiteConversion000
artmsQualityControlEvidenceBasic2.110.002.11
artmsQualityControlEvidenceExtended0.010.000.02
artmsQualityControlMetabolomics000
artmsQualityControlSummaryExtended000
artmsQuantification000
artmsResultsWide0.290.000.28
artmsSILACtoLong000
artmsSpectralCounts0.110.000.11
artmsVolcanoPlot0.210.010.23
artmsWriteConfigYamlFile000