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CHECK report for RforProteomics on riesling1

This page was generated on 2021-01-14 15:59:11 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE RforProteomics PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 293/385HostnameOS / ArchINSTALLBUILDCHECK
RforProteomics 1.29.2
Laurent Gatto
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/RforProteomics
Branch: master
Last Commit: 68db25d
Last Changed Date: 2020-12-09 16:21:27 -0500 (Wed, 09 Dec 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

Package: RforProteomics
Version: 1.29.2
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RforProteomics.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RforProteomics_1.29.2.tar.gz
StartedAt: 2021-01-14 11:36:19 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:39:53 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 214.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RforProteomics.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RforProteomics.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RforProteomics_1.29.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/RforProteomics.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RforProteomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RforProteomics' version '1.29.2'
* 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 'RforProteomics' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'MSnbase::plot' by 'graphics::plot' when loading 'RforProteomics'
See 'D:/biocbuild/bbs-3.13-data-experiment/meat/RforProteomics.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
* 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
id 4.81   0.04     8.7
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
   user system elapsed
id 4.98   0.16     9.3
* 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 WARNING
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/RforProteomics.Rcheck/00check.log'
for details.



Installation output

RforProteomics.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/RforProteomics_1.29.2.tar.gz && rm -rf RforProteomics.buildbin-libdir && mkdir RforProteomics.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RforProteomics.buildbin-libdir RforProteomics_1.29.2.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RforProteomics_1.29.2.zip && rm RforProteomics_1.29.2.tar.gz RforProteomics_1.29.2.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 2576k  100 2576k    0     0  52.4M      0 --:--:-- --:--:-- --:--:-- 52.4M

install for i386

* installing *source* package 'RforProteomics' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'MSnbase::plot' by 'graphics::plot' when loading 'RforProteomics'
** help
*** installing help indices
  converting help for package 'RforProteomics'
    finding HTML links ... done
    RforProteomics                          html  
REDIRECT:topic	 RforProteomics -> RforProteomics.html [ SUCCESS ]
REDIRECT:topic	 RProtVis -> RforProteomics.html [ SUCCESS ]
REDIRECT:topic	 RProtViz -> RforProteomics.html [ SUCCESS ]
    downloadData                            html  
REDIRECT:topic	 downloadData -> downloadData.html [ SUCCESS ]
    getPXD000001mzData                      html  
REDIRECT:topic	 getPXD000001mzData -> getPXD000001mzData.html [ SUCCESS ]
    getPXD000001mzTab                       html  
REDIRECT:topic	 getPXD000001mzTab -> getPXD000001mzTab.html [ SUCCESS ]
    getPXD000001mzXML                       html  
REDIRECT:topic	 getPXD000001mzXML -> getPXD000001mzXML.html [ SUCCESS ]
    getPackagesInBiocView                   html  
REDIRECT:topic	 getPackagesInBiocView -> getPackagesInBiocView.html [ SUCCESS ]
    getThermoHelaPRTC                       html  
REDIRECT:topic	 getThermoHelaPRTC -> getThermoHelaPRTC.html [ SUCCESS ]
    id                                      html  
REDIRECT:topic	 TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzid -> id.html [ SUCCESS ]
REDIRECT:file	 id.html -> id.html [ SUCCESS ]
    mstut                                   html  
REDIRECT:topic	 new_ions -> mstut.html [ SUCCESS ]
REDIRECT:topic	 mstut -> mstut.html [ SUCCESS ]
REDIRECT:topic	 analyse -> mstut.html [ SUCCESS ]
REDIRECT:topic	 analyze -> mstut.html [ SUCCESS ]
REDIRECT:topic	 detect -> mstut.html [ SUCCESS ]
REDIRECT:topic	 spectrum -> mstut.html [ SUCCESS ]
    packageDF                               html  
REDIRECT:topic	 packageDF -> packageDF.html [ SUCCESS ]
    proteomicsPackages                      html  
REDIRECT:topic	 proteomicsPackages -> proteomicsPackages.html [ SUCCESS ]
REDIRECT:topic	 massSpectrometryPackages -> proteomicsPackages.html [ SUCCESS ]
REDIRECT:topic	 massSpectrometryDataPackages -> proteomicsPackages.html [ SUCCESS ]
    qnt                                     html  
REDIRECT:topic	 qnt -> qnt.html [ SUCCESS ]
    finding level-2 HTML links ... done

** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'MSnbase::plot' by 'graphics::plot' when loading 'RforProteomics'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'MSnbase::plot' by 'graphics::plot' when loading 'RforProteomics'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'RforProteomics' ...
** testing if installed package can be loaded
Warning: replacing previous import 'MSnbase::plot' by 'graphics::plot' when loading 'RforProteomics'
* MD5 sums
packaged installation of 'RforProteomics' as RforProteomics_1.29.2.zip
* DONE (RforProteomics)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'RforProteomics' successfully unpacked and MD5 sums checked

Tests output


Example timings

RforProteomics.Rcheck/examples_i386/RforProteomics-Ex.timings

nameusersystemelapsed
getThermoHelaPRTC000
id4.810.048.70
mstut0.000.000.58
proteomicsPackages3.260.033.58
qnt0.020.000.02

RforProteomics.Rcheck/examples_x64/RforProteomics-Ex.timings

nameusersystemelapsed
getThermoHelaPRTC000
id4.980.169.30
mstut0.010.000.61
proteomicsPackages3.250.083.56
qnt0.020.000.02