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CHECK report for topconfects on tokay2

This page was generated on 2019-10-16 12:43:18 -0400 (Wed, 16 Oct 2019).

Package 1658/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
topconfects 1.0.0
Paul Harrison
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/topconfects
Branch: RELEASE_3_9
Last Commit: e0a49c1
Last Changed Date: 2019-05-02 11:54:14 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: topconfects
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topconfects.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings topconfects_1.0.0.tar.gz
StartedAt: 2019-10-16 07:35:50 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:38:47 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 177.3 seconds
RetCode: 0
Status:  OK  
CheckDir: topconfects.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topconfects.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings topconfects_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/topconfects.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'topconfects/DESCRIPTION' ... OK
* this is package 'topconfects' version '1.0.0'
* 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 'topconfects' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
deseq2_confects  29.95   1.06   31.04
confects_plot_me  6.50   0.11    6.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
deseq2_confects 34.61   0.36   34.97
edger_confects   5.22   0.00    5.44
* 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: OK


Installation output

topconfects.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/topconfects_1.0.0.tar.gz && rm -rf topconfects.buildbin-libdir && mkdir topconfects.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=topconfects.buildbin-libdir topconfects_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL topconfects_1.0.0.zip && rm topconfects_1.0.0.tar.gz topconfects_1.0.0.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  201k  100  201k    0     0  2858k      0 --:--:-- --:--:-- --:--:-- 3197k

install for i386

* installing *source* package 'topconfects' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'topconfects'
    finding HTML links ... done
    confects_plot                           html  
    confects_plot_me                        html  
    deseq2_confects                         html  
    edger_confects                          html  
    limma_confects                          html  
    nest_confects                           html  
    normal_confects                         html  
    rank_rank_plot                          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 'topconfects' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'topconfects' as topconfects_1.0.0.zip
* DONE (topconfects)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'topconfects' successfully unpacked and MD5 sums checked

Tests output

topconfects.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(topconfects)
> 
> test_check("topconfects")
== testthat results  ===========================================================
[ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.10    0.14   11.23 

topconfects.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(topconfects)
> 
> test_check("topconfects")
== testthat results  ===========================================================
[ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.82    0.14   13.95 

Example timings

topconfects.Rcheck/examples_i386/topconfects-Ex.timings

nameusersystemelapsed
confects_plot0.530.000.53
confects_plot_me6.500.116.92
deseq2_confects29.95 1.0631.04
edger_confects4.440.144.58
limma_confects1.780.101.88
nest_confects0.110.000.11
normal_confects0.120.000.12
rank_rank_plot0.250.000.25

topconfects.Rcheck/examples_x64/topconfects-Ex.timings

nameusersystemelapsed
confects_plot0.330.000.32
confects_plot_me4.370.064.44
deseq2_confects34.61 0.3634.97
edger_confects5.220.005.44
limma_confects2.730.002.73
nest_confects0.160.000.16
normal_confects0.150.000.16
rank_rank_plot0.220.000.21