Multiple platform build/check report for BioC 3.13 - CHECK results for OmaDB on tokay2

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: 2021-10-15 02:51:08 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 03:12:17 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 1268.9 seconds

RetCode: 0

Status: OK

CheckDir: OmaDB.Rcheck

Warnings: 0

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###
### 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
###
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* 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      186.36   1.97  274.87
getGenomePairs  14.80   0.20   31.52
getOMAGroup      2.50   0.01    9.01
mapSequence      1.54   0.03    5.81
searchProtein    0.02   0.00  187.60
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
getGenome      204.30   0.90  299.32
getGenomePairs  22.48   0.21   40.65
getOMAGroup      2.19   0.05    9.08
mapSequence      1.97   0.02    6.05
searchProtein    0.00   0.00  187.59
* 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

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###
### 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
###
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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
  7  211k    7 16227    0     0   137k      0  0:00:01 --:--:--  0:00:01  136k
100  211k  100  211k    0     0   793k      0 --:--:-- --:--:-- --:--:--  793k

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


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 
   0.93    0.06    2.89


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 
   0.96    0.12    2.75

name	user	system	elapsed
annotateSequence	0.31	0.01	4.33
formatTopGO	0.54	0.00	1.14
getAttribute	0.47	0.08	1.81
getGenome	186.36	1.97	274.87
getGenomePairs	14.80	0.20	31.52
getHOG	0.14	0.05	0.91
getLocus	0.57	0.02	1.81
getOMAGroup	2.50	0.01	9.01
getObjectAttributes	0.46	0.00	1.75
getProtein	0.39	0.00	1.40
getTaxonomy	0.11	0.02	0.92
getTopGO	1.12	0.14	1.89
getTree	0.03	0.00	0.19
getVersion	0.04	0.00	0.15
mapSequence	1.54	0.03	5.81
resolveURL	0.08	0.00	2.33
searchProtein	0.02	0.00	187.60

name	user	system	elapsed
annotateSequence	0.53	0.03	4.84
formatTopGO	0.17	0.00	0.77
getAttribute	0.48	0.08	1.83
getGenome	204.30	0.90	299.32
getGenomePairs	22.48	0.21	40.65
getHOG	0.19	0.00	0.89
getLocus	0.70	0.01	1.97
getOMAGroup	2.19	0.05	9.08
getObjectAttributes	0.50	0.00	1.75
getProtein	0.47	0.00	1.61
getTaxonomy	0.10	0.00	1.08
getTopGO	1.58	0.06	3.05
getTree	0.02	0.00	0.19
getVersion	0.01	0.00	0.17
mapSequence	1.97	0.02	6.05
resolveURL	0.09	0.00	0.49
searchProtein	0.00	0.00	187.59

CHECK results for OmaDB on tokay2

Summary

Command output

Installation output

Tests output

Example timings