Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:06:04 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 biodbKegg on tokay2


To the developers/maintainers of the biodbKegg package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbKegg.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 178/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbKegg 1.0.0  (landing page)
Pierrick Roger
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/biodbKegg
git_branch: RELEASE_3_14
git_last_commit: 5bb8a8a
git_last_commit_date: 2021-10-26 13:13:42 -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: biodbKegg
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biodbKegg.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings biodbKegg_1.0.0.tar.gz
StartedAt: 2022-01-13 16:10:16 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 16:31:33 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 1276.9 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbKegg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biodbKegg.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings biodbKegg_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/biodbKegg.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 'biodbKegg/DESCRIPTION' ... OK
* this is package 'biodbKegg' 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 'biodbKegg' can be installed ... OK
* checking installed package size ... OK
* checking package 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 (user + system) or elapsed time > 5s
                 user system elapsed
KeggCompoundConn 4.82   0.85    8.46
KeggEnzymeConn   5.09   0.03   11.75
KeggPathwayConn  2.70   0.02    7.58
** 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

biodbKegg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/biodbKegg_1.0.0.tar.gz && rm -rf biodbKegg.buildbin-libdir && mkdir biodbKegg.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biodbKegg.buildbin-libdir biodbKegg_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL biodbKegg_1.0.0.zip && rm biodbKegg_1.0.0.tar.gz biodbKegg_1.0.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  163k  100  163k    0     0  1024k      0 --:--:-- --:--:-- --:--:-- 1022k

install for i386

* installing *source* package 'biodbKegg' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biodbKegg'
    finding HTML links ... done
    KeggCircle                              html  
    KeggCompoundConn                        html  
    KeggCompoundEntry                       html  
    KeggConn                                html  
    KeggEntry                               html  
    KeggEnzymeConn                          html  
    KeggEnzymeEntry                         html  
    KeggGenesConn                           html  
    KeggGenesEntry                          html  
    KeggGlycanConn                          html  
    KeggGlycanEntry                         html  
    KeggModuleConn                          html  
    KeggModuleEntry                         html  
    KeggOrthologyConn                       html  
    KeggOrthologyEntry                      html  
    KeggPathwayConn                         html  
    KeggPathwayEntry                        html  
    KeggReactionConn                        html  
    KeggReactionEntry                       html  
    KeggRect                                html  
    KeggShape                               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 'biodbKegg' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biodbKegg' as biodbKegg_1.0.0.zip
* DONE (biodbKegg)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'biodbKegg' successfully unpacked and MD5 sums checked

Tests output

biodbKegg.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.

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbKegg)
> Sys.setenv(TESTTHAT_REPORTER = "summary")
> test_check("biodbKegg")
trying URL 'https://www.kegg.jp/kegg/pathway/map/map00260.png'
Content type 'image/png' length unknown
.......... .......... .......... .......... ....
downloaded 44 KB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1549 ]
> 
> proc.time()
   user  system elapsed 
 189.03    9.64  681.57 

biodbKegg.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.

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbKegg)
> Sys.setenv(TESTTHAT_REPORTER = "summary")
> test_check("biodbKegg")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1516 ]
> 
> proc.time()
   user  system elapsed 
 168.46    9.70  432.92 

Example timings

biodbKegg.Rcheck/examples_i386/biodbKegg-Ex.timings

nameusersystemelapsed
KeggCircle000
KeggCompoundConn4.820.858.46
KeggCompoundEntry0.730.001.55
KeggConn0.570.001.00
KeggEntry0.720.000.73
KeggEnzymeConn 5.09 0.0311.75
KeggEnzymeEntry0.590.011.00
KeggGenesConn0.820.021.31
KeggGenesEntry0.70.00.7
KeggGlycanConn0.400.000.41
KeggGlycanEntry0.660.001.03
KeggModuleConn0.700.001.28
KeggModuleEntry0.690.000.69
KeggOrthologyConn0.890.002.90
KeggOrthologyEntry0.800.010.81
KeggPathwayConn2.700.027.58
KeggPathwayEntry0.600.001.49
KeggReactionConn0.760.001.00
KeggReactionEntry0.830.000.86
KeggRect000
KeggShape000

biodbKegg.Rcheck/examples_x64/biodbKegg-Ex.timings

nameusersystemelapsed
KeggCircle0.020.000.02
KeggCompoundConn3.650.784.83
KeggCompoundEntry0.470.010.49
KeggConn0.360.000.36
KeggEntry0.430.000.43
KeggEnzymeConn3.690.023.71
KeggEnzymeEntry0.390.010.40
KeggGenesConn0.490.000.49
KeggGenesEntry0.530.000.53
KeggGlycanConn0.360.000.36
KeggGlycanEntry0.480.020.50
KeggModuleConn0.470.000.47
KeggModuleEntry0.450.000.45
KeggOrthologyConn0.440.030.47
KeggOrthologyEntry0.490.000.48
KeggPathwayConn1.760.031.80
KeggPathwayEntry0.470.000.47
KeggReactionConn0.50.00.5
KeggReactionEntry0.470.020.48
KeggRect000
KeggShape000