Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:09 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for coRdon on tokay2


To the developers/maintainers of the coRdon package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/coRdon.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 398/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coRdon 1.12.0  (landing page)
Anamaria Elek
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/coRdon
git_branch: RELEASE_3_14
git_last_commit: ba08f6b
git_last_commit_date: 2021-10-26 12:45:57 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: coRdon
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coRdon.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings coRdon_1.12.0.tar.gz
StartedAt: 2022-01-20 18:05:19 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:08:07 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 167.1 seconds
RetCode: 0
Status:   OK  
CheckDir: coRdon.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coRdon.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings coRdon_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/coRdon.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.12.0'
* 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 LazyData ... 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
** 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: OK


Installation output

coRdon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/coRdon_1.12.0.tar.gz && rm -rf coRdon.buildbin-libdir && mkdir coRdon.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=coRdon.buildbin-libdir coRdon_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL coRdon_1.12.0.zip && rm coRdon_1.12.0.tar.gz coRdon_1.12.0.zip
###
##############################################################################
##############################################################################


  % 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  318k  100  318k    0     0  1217k      0 --:--:-- --:--:-- --:--:-- 1222k

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_1.12.0.zip
* DONE (coRdon)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'coRdon' successfully unpacked and MD5 sums checked

Tests output

coRdon.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
   6.59    0.40    6.96 

coRdon.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
   7.95    0.20    8.14 

Example timings

coRdon.Rcheck/examples_i386/coRdon-Ex.timings

nameusersystemelapsed
bplot0.440.020.45
codonTable-class0.110.030.14
codonUsage-expressivity1.610.001.62
codonUsage1.410.051.45
crossTab-class0.010.000.02
enrichBarplot0.380.000.37
enrichMAplot0.760.020.78
enrichMatrix0.470.040.52
enrichment0.940.020.95
intraBplot0.570.040.62
readSet0.080.000.08
reduceCrossTab3.850.164.00
subset0.010.050.06

coRdon.Rcheck/examples_x64/coRdon-Ex.timings

nameusersystemelapsed
bplot0.610.000.61
codonTable-class0.150.030.19
codonUsage-expressivity2.060.002.06
codonUsage1.550.001.55
crossTab-class0.030.000.03
enrichBarplot0.360.000.36
enrichMAplot0.760.030.79
enrichMatrix0.490.000.49
enrichment0.740.000.74
intraBplot0.680.020.69
readSet0.070.000.08
reduceCrossTab4.300.074.37
subset0.060.000.07