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CHECK report for procoil on riesling1

This page was generated on 2021-01-24 12:36:33 -0500 (Sun, 24 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE procoil PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1354/1932HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
procoil 2.19.0
Ulrich Bodenhofer
Snapshot Date: 2021-01-23 14:40:18 -0500 (Sat, 23 Jan 2021)
URL: https://git.bioconductor.org/packages/procoil
Branch: master
Last Commit: 5848f71
Last Changed Date: 2020-10-27 10:40:18 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: procoil
Version: 2.19.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:procoil.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings procoil_2.19.0.tar.gz
StartedAt: 2021-01-23 21:23:20 -0500 (Sat, 23 Jan 2021)
EndedAt: 2021-01-23 21:25:38 -0500 (Sat, 23 Jan 2021)
EllapsedTime: 138.0 seconds
RetCode: 0
Status:  OK  
CheckDir: procoil.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:procoil.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings procoil_2.19.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-bioc/meat/procoil.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 'procoil/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'procoil' version '2.19.0'
* 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 'procoil' 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 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

procoil.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/bioc/src/contrib/procoil_2.19.0.tar.gz && rm -rf procoil.buildbin-libdir && mkdir procoil.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=procoil.buildbin-libdir procoil_2.19.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL procoil_2.19.0.zip && rm procoil_2.19.0.tar.gz procoil_2.19.0.zip
###
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  % 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  831k  100  831k    0     0  42.7M      0 --:--:-- --:--:-- --:--:-- 42.7M

install for i386

* installing *source* package 'procoil' ...
** 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 'procoil'
    finding HTML links ... done
    CCModel-FileOps                         html  
REDIRECT:topic	 CCModel-FileOps -> CCModel-FileOps.html [ SUCCESS ]
REDIRECT:topic	 readCCModel -> CCModel-FileOps.html [ SUCCESS ]
REDIRECT:topic	 writeCCModel -> CCModel-FileOps.html [ SUCCESS ]
    CCModel-class                           html  
REDIRECT:topic	 CCModel-class -> CCModel-class.html [ SUCCESS ]
REDIRECT:topic	 CCModel -> CCModel-class.html [ SUCCESS ]
REDIRECT:topic	 PrOCoilModel -> CCModel-class.html [ SUCCESS ]
REDIRECT:topic	 PrOCoilModelBA -> CCModel-class.html [ SUCCESS ]
REDIRECT:topic	 weights,CCModel-method -> CCModel-class.html [ SUCCESS ]
REDIRECT:topic	 show,CCModel-method -> CCModel-class.html [ SUCCESS ]
REDIRECT:topic	 show.CCModel -> CCModel-class.html [ SUCCESS ]
REDIRECT:topic	 weights.CCModel -> CCModel-class.html [ SUCCESS ]
    CCProfile-class                         html  
REDIRECT:topic	 CCProfile-class -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 CCProfile -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 [,CCProfile,index,ANY,ANY-method -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 show,CCProfile-method -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 heatmap,CCProfile,missing-method -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 baselines,CCProfile-method -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 profiles,CCProfile-method -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 profile,CCProfile-method -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 sequences,CCProfile-method -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 fitted,CCProfile-method -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 show.CCProfile -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 heatmap.CCProfile -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 baselines.CCProfile -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 profiles.CCProfile -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 profile.CCProfile -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 sequences.CCProfile -> CCProfile-class.html [ SUCCESS ]
REDIRECT:topic	 fitted.CCProfile -> CCProfile-class.html [ SUCCESS ]
    finding level-2 HTML links ... done

    plot-methods                            html  
REDIRECT:topic	 plot -> plot-methods.html [ SUCCESS ]
REDIRECT:topic	 plot-methods -> plot-methods.html [ SUCCESS ]
REDIRECT:topic	 plot,CCProfile,missing-method -> plot-methods.html [ SUCCESS ]
REDIRECT:topic	 plot.CCProfile -> plot-methods.html [ SUCCESS ]
    predict-methods                         html  
REDIRECT:topic	 predict -> predict-methods.html [ SUCCESS ]
REDIRECT:topic	 predict-methods -> predict-methods.html [ SUCCESS ]
REDIRECT:topic	 predict,CCModel-method -> predict-methods.html [ SUCCESS ]
REDIRECT:topic	 predict.CCModel -> predict-methods.html [ SUCCESS ]
    procoil-package                         html  
REDIRECT:topic	 procoil-package -> procoil-package.html [ SUCCESS ]
REDIRECT:topic	 procoil -> procoil-package.html [ SUCCESS ]
** 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 'procoil' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'procoil' as procoil_2.19.0.zip
* DONE (procoil)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'procoil' successfully unpacked and MD5 sums checked

Tests output


Example timings

procoil.Rcheck/examples_i386/procoil-Ex.timings

nameusersystemelapsed
CCModel-FileOps000
CCModel-class0.090.000.09
CCProfile-class0.420.030.49
plot-methods0.090.020.11
predict-methods0.10.00.1
procoil-package0.010.030.08

procoil.Rcheck/examples_x64/procoil-Ex.timings

nameusersystemelapsed
CCModel-FileOps0.020.000.02
CCModel-class0.110.000.11
CCProfile-class0.370.020.41
plot-methods0.030.000.03
predict-methods0.060.000.07
procoil-package0.040.000.04