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CHECK report for semisup on tokay1

This page was generated on 2019-04-13 11:27:46 -0400 (Sat, 13 Apr 2019).

Package 1412/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
semisup 1.6.0
Armin Rauschenberger
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/semisup
Branch: RELEASE_3_8
Last Commit: ae6f2b4
Last Changed Date: 2018-10-30 11:42:04 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: semisup
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:semisup.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings semisup_1.6.0.tar.gz
StartedAt: 2019-04-13 05:23:45 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:25:27 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 102.4 seconds
RetCode: 0
Status:  OK  
CheckDir: semisup.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:semisup.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings semisup_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/semisup.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'semisup/DESCRIPTION' ... OK
* this is package 'semisup' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'semisup' 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 '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-3.8-bioc/meat/semisup.Rcheck/00check.log'
for details.



Installation output

semisup.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/semisup_1.6.0.tar.gz && rm -rf semisup.buildbin-libdir && mkdir semisup.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=semisup.buildbin-libdir semisup_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL semisup_1.6.0.zip && rm semisup_1.6.0.tar.gz semisup_1.6.0.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 50642  100 50642    0     0  1520k      0 --:--:-- --:--:-- --:--:-- 1705k

install for i386

* installing *source* package 'semisup' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'semisup'
    finding HTML links ... done
    arguments                               html  
    debug                                   html  
    estim.nbinom                            html  
    fit.nbinom                              html  
    fit.norm                                html  
    fit.wrap                                html  
    fit.zinb                                html  
    internal                                html  
    mixtura                                 html  
    resam.lrts                              html  
    scrutor                                 html  
    semisup-package                         html  
    table                                   html  
    toydata                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'semisup' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'semisup' as semisup_1.6.0.zip
* DONE (semisup)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'semisup' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

semisup.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(semisup)
> 
> testthat::test_check("semisup")

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== testthat results  ===========================================================
OK: 20 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   5.92    0.10    6.01 

semisup.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(semisup)
> 
> testthat::test_check("semisup")

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  |========================================| 100%

  |                                              
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  |                                              
  |========================================| 100%

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  |========================================| 100%
== testthat results  ===========================================================
OK: 20 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   5.09    0.06    5.20 

Example timings

semisup.Rcheck/examples_i386/semisup-Ex.timings

nameusersystemelapsed
debug000
estim.nbinom0.500.020.52
fit.nbinom0.000.010.02
fit.norm0.000.020.01
fit.wrap000
fit.zinb000
mixtura0.040.000.05
resam.lrts0.020.000.01
scrutor0.110.030.14

semisup.Rcheck/examples_x64/semisup-Ex.timings

nameusersystemelapsed
debug000
estim.nbinom0.640.020.66
fit.nbinom0.020.000.02
fit.norm0.020.000.01
fit.wrap0.010.000.02
fit.zinb000
mixtura0.010.000.02
resam.lrts0.020.000.01
scrutor0.080.010.10