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CHECK report for coRdon on tokay2

This page was generated on 2019-10-16 12:42:00 -0400 (Wed, 16 Oct 2019).

Package 346/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coRdon 1.2.0
Anamaria Elek
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/coRdon
Branch: RELEASE_3_9
Last Commit: 48eb007
Last Changed Date: 2019-05-02 11:54:12 -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: coRdon
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coRdon.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings coRdon_1.2.0.tar.gz
StartedAt: 2019-10-16 02:55:10 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:58:14 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 183.5 seconds
RetCode: 0
Status:  OK  
CheckDir: coRdon.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:coRdon.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings coRdon_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/coRdon.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 'coRdon/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'coRdon' version '1.2.0'
* 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 'coRdon' 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
reduceCrossTab 7.25    1.7    8.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
reduceCrossTab 7.37   1.06    7.83
* 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

coRdon.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/coRdon_1.2.0.tar.gz && rm -rf coRdon.buildbin-libdir && mkdir coRdon.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=coRdon.buildbin-libdir coRdon_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL coRdon_1.2.0.zip && rm coRdon_1.2.0.tar.gz coRdon_1.2.0.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  320k  100  320k    0     0  5013k      0 --:--:-- --:--:-- --:--:-- 5621k

install for i386

* installing *source* package 'coRdon' ...
** 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 'coRdon'
    finding HTML links ... done
    HD59                                    html  
    HD59_KO                                 html  
    HD59_PATHWAYS                           html  
    LD94                                    html  
    LD94_KO                                 html  
    LD94_PATHWAYS                           html  
    RPKOs                                   html  
    bplot                                   html  
    coRdon                                  html  
    codonTable-class                        html  
    codonUsage-expressivity                 html  
    codonUsage                              html  
    crossTab-class                          html  
    enrichBarplot                           html  
    enrichMAplot                            html  
    enrichMatrix                            html  
    enrichment                              html  
    genCode-class                           html  
    intraBplot                              html  
    length-codonTable                       html  
    length-crossTab                         html  
    readSet                                 html  
    reduceCrossTab                          html  
    show-codonTable                         html  
    show-crossTab                           html  
    subset                                  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 'coRdon' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'coRdon' as coRdon_1.2.0.zip
* DONE (coRdon)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'coRdon' successfully unpacked and MD5 sums checked

Tests output

coRdon.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(coRdon)
> 
> test_check("coRdon")
== testthat results  ===========================================================
[ OK: 26 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   7.20    0.50    7.64 

coRdon.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(coRdon)
> 
> test_check("coRdon")
== testthat results  ===========================================================
[ OK: 26 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   9.29    0.18    9.40 

Example timings

coRdon.Rcheck/examples_i386/coRdon-Ex.timings

nameusersystemelapsed
bplot0.720.080.80
codonTable-class0.140.010.15
codonUsage-expressivity2.410.192.58
codonUsage1.970.242.17
crossTab-class0.030.000.03
enrichBarplot0.670.010.69
enrichMAplot1.140.021.15
enrichMatrix0.620.000.59
enrichment0.990.081.00
intraBplot0.980.061.05
readSet0.110.000.11
reduceCrossTab7.251.708.14
subset0.110.000.11

coRdon.Rcheck/examples_x64/coRdon-Ex.timings

nameusersystemelapsed
bplot0.720.030.75
codonTable-class0.110.020.12
codonUsage-expressivity2.680.122.66
codonUsage2.210.032.22
crossTab-class0.040.000.03
enrichBarplot0.700.020.72
enrichMAplot1.510.001.51
enrichMatrix0.960.030.99
enrichment0.760.020.78
intraBplot0.940.060.98
readSet0.080.030.11
reduceCrossTab7.371.067.83
subset0.110.020.12