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CHECK report for procoil on tokay1

This page was generated on 2021-01-19 11:56:05 -0500 (Tue, 19 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 1390/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
procoil 2.18.0
Ulrich Bodenhofer
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/procoil
Branch: RELEASE_3_12
Last Commit: bd35bcf
Last Changed Date: 2020-10-27 10:40:17 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 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 [ WARNINGS ] 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: procoil
Version: 2.18.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:procoil.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings procoil_2.18.0.tar.gz
StartedAt: 2021-01-19 06:02:13 -0500 (Tue, 19 Jan 2021)
EndedAt: 2021-01-19 06:05:19 -0500 (Tue, 19 Jan 2021)
EllapsedTime: 186.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: procoil.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:procoil.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings procoil_2.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/procoil.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 'procoil/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'procoil' version '2.18.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpgVqc3c/R.INSTALL23c871445da2/procoil/man/plot-methods.Rd:58: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/procoil.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
** 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/procoil.Rcheck/00check.log'
for details.



Installation output

procoil.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/procoil_2.18.0.tar.gz && rm -rf procoil.buildbin-libdir && mkdir procoil.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=procoil.buildbin-libdir procoil_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL procoil_2.18.0.zip && rm procoil_2.18.0.tar.gz procoil_2.18.0.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
 92  834k   92  768k    0     0  6092k      0 --:--:-- --:--:-- --:--:-- 6243k
100  834k  100  834k    0     0  6587k      0 --:--:-- --:--:-- --:--:-- 6729k

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  
    CCModel-class                           html  
    CCProfile-class                         html  
    finding level-2 HTML links ... done

    plot-methods                            html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpgVqc3c/R.INSTALL23c871445da2/procoil/man/plot-methods.Rd:58: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    predict-methods                         html  
    procoil-package                         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 'procoil' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'procoil' as procoil_2.18.0.zip
* DONE (procoil)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'procoil' successfully unpacked and MD5 sums checked

Tests output


Example timings

procoil.Rcheck/examples_i386/procoil-Ex.timings

nameusersystemelapsed
CCModel-FileOps0.020.000.01
CCModel-class0.150.000.16
CCProfile-class0.620.140.76
plot-methods0.050.000.05
predict-methods0.080.000.08
procoil-package0.050.000.04

procoil.Rcheck/examples_x64/procoil-Ex.timings

nameusersystemelapsed
CCModel-FileOps0.020.000.02
CCModel-class0.260.000.27
CCProfile-class0.690.050.74
plot-methods0.060.000.06
predict-methods0.090.000.09
procoil-package0.070.000.06