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This page was generated on 2021-09-20 15:05:21 -0400 (Mon, 20 Sep 2021).

CHECK results for OmaDB on tokay2

To the developers/maintainers of the OmaDB package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmaDB.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 1295/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmaDB 2.8.0  (landing page)
Klara Kaleb , Adrian Altenhoff
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/OmaDB
git_branch: RELEASE_3_13
git_last_commit: 73c1e16
git_last_commit_date: 2021-05-19 12:32:07 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: OmaDB
Version: 2.8.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmaDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings OmaDB_2.8.0.tar.gz
StartedAt: 2021-09-20 02:09:54 -0400 (Mon, 20 Sep 2021)
EndedAt: 2021-09-20 02:33:15 -0400 (Mon, 20 Sep 2021)
EllapsedTime: 1400.8 seconds
RetCode: 0
Status:   OK  
CheckDir: OmaDB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmaDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings OmaDB_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/OmaDB.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OmaDB/DESCRIPTION' ... OK
* this is package 'OmaDB' version '2.8.0'
* 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 'OmaDB' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
getGenome      170.56   2.23  263.55
getGenomePairs  14.97   0.21   31.36
getOMAGroup      2.45   0.02    9.31
mapSequence      1.66   0.04    5.86
searchProtein    0.00   0.00  187.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
getGenome      221.40   1.03  322.29
getGenomePairs  24.05   0.33   41.06
getOMAGroup      2.45   0.02    9.22
mapSequence      1.88   0.00    5.84
searchProtein    0.02   0.00  187.61
* 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

OmaDB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/OmaDB_2.8.0.tar.gz && rm -rf OmaDB.buildbin-libdir && mkdir OmaDB.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmaDB.buildbin-libdir OmaDB_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL OmaDB_2.8.0.zip && rm OmaDB_2.8.0.tar.gz OmaDB_2.8.0.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  211k  100  211k    0     0   416k      0 --:--:-- --:--:-- --:--:--  417k

install for i386

* installing *source* package 'OmaDB' ...
** 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 'OmaDB'
    finding HTML links ... done
    OmaDB-deprecated                        html  
    OmaDB-package                           html  
    annotateSequence                        html  
    cash-.omadb_obj                         html  
    formatTopGO                             html  
    getAnnotation-deprecated                html  
    getAttribute                            html  
    getData-deprecated                      html  
    getGenome                               html  
    getGenomeAlignment-deprecated           html  
    getGenomePairs                          html  
    getHOG                                  html  
    getLocus                                html  
    getOMAGroup                             html  
    getObjectAttributes                     html  
    getProtein                              html  
    getTaxonomy                             html  
    getTopGO                                html  
    getTree                                 html  
    getVersion                              html  
    getXref-deprecated                      html  
    group                                   html  
    hog                                     html  
    mapSequence                             html  
    orthologs                               html  
    pairs                                   html  
    protein                                 html  
    resolveURL                              html  
    searchProtein                           html  
    sequence_annotation                     html  
    sequence_map                            html  
    setAPI                                  html  
    taxonomy                                html  
    xref                                    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 'OmaDB' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmaDB' as OmaDB_2.8.0.zip
* DONE (OmaDB)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'OmaDB' successfully unpacked and MD5 sums checked

Tests output

OmaDB.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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)
> 
> test_that("Testing the URL validity", {
+   expect_equal(httr::status_code(httr::GET("https://omabrowser.org/api")), 200 ) #checking that the server is live and accesible
+ 
+ })
Test passed 
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
   0.85    0.10    2.79 

OmaDB.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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)
> 
> test_that("Testing the URL validity", {
+   expect_equal(httr::status_code(httr::GET("https://omabrowser.org/api")), 200 ) #checking that the server is live and accesible
+ 
+ })
Test passed 
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
   1.17    0.18    3.40 

Example timings

OmaDB.Rcheck/examples_i386/OmaDB-Ex.timings

nameusersystemelapsed
annotateSequence0.440.002.66
formatTopGO0.520.002.98
getAttribute0.470.081.84
getGenome170.56 2.23263.55
getGenomePairs14.97 0.2131.36
getHOG0.170.020.87
getLocus0.570.031.89
getOMAGroup2.450.029.31
getObjectAttributes0.450.001.75
getProtein0.360.001.43
getTaxonomy0.140.000.89
getTopGO1.160.123.73
getTree0.010.000.18
getVersion0.020.000.14
mapSequence1.660.045.86
resolveURL0.040.000.46
searchProtein 0.00 0.00187.59

OmaDB.Rcheck/examples_x64/OmaDB-Ex.timings

nameusersystemelapsed
annotateSequence0.590.001.92
formatTopGO0.160.000.73
getAttribute0.440.141.91
getGenome221.40 1.03322.29
getGenomePairs24.05 0.3341.06
getHOG0.190.031.13
getLocus0.860.002.65
getOMAGroup2.450.029.22
getObjectAttributes0.560.002.10
getProtein0.500.001.53
getTaxonomy0.110.001.00
getTopGO1.160.091.84
getTree0.00.00.2
getVersion0.030.000.16
mapSequence1.880.005.84
resolveURL0.070.000.47
searchProtein 0.02 0.00187.61