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CHECK report for OmaDB on tokay2

This page was generated on 2019-10-16 12:40:05 -0400 (Wed, 16 Oct 2019).

Package 1127/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmaDB 2.0.0
Klara Kaleb , Adrian Altenhoff
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/OmaDB
Branch: RELEASE_3_9
Last Commit: f310294
Last Changed Date: 2019-05-02 11:54:09 -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: OmaDB
Version: 2.0.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmaDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings OmaDB_2.0.0.tar.gz
StartedAt: 2019-10-16 05:40:37 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:47:34 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 417.2 seconds
RetCode: 0
Status:  OK  
CheckDir: OmaDB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmaDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings OmaDB_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/OmaDB.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 'OmaDB/DESCRIPTION' ... OK
* this is package 'OmaDB' version '2.0.0'
* 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 '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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getGenome      43.92   0.34   64.25
getGenomePairs 15.67   0.42   21.69
searchProtein   2.24   0.03    5.58
getOMAGroup     1.12   0.01    5.88
mapSequence     0.79   0.02    8.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getGenome      50.53   0.55   72.60
getGenomePairs 15.84   0.23   22.86
searchProtein   4.22   0.02    7.58
getOMAGroup     1.81   0.02    6.50
mapSequence     0.91   0.01    8.90
* 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 https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/OmaDB_2.0.0.tar.gz && rm -rf OmaDB.buildbin-libdir && mkdir OmaDB.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmaDB.buildbin-libdir OmaDB_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL OmaDB_2.0.0.zip && rm OmaDB_2.0.0.tar.gz OmaDB_2.0.0.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  198k  100  198k    0     0  2741k      0 --:--:-- --:--:-- --:--:-- 2959k

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_2.0.0.zip
* DONE (OmaDB)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'OmaDB' successfully unpacked and MD5 sums checked

Tests output

OmaDB.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)
> 
> 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
+ 
+ })
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
   0.28    0.10    2.00 

OmaDB.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)
> 
> 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
+ 
+ })
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
   0.32    0.04    2.00 

Example timings

OmaDB.Rcheck/examples_i386/OmaDB-Ex.timings

nameusersystemelapsed
annotateSequence0.140.031.32
formatTopGO0.110.000.65
getAttribute0.100.020.36
getGenome43.92 0.3464.25
getGenomePairs15.67 0.4221.69
getHOG0.110.020.73
getLocus0.110.000.36
getOMAGroup1.120.015.88
getObjectAttributes0.100.000.34
getProtein0.210.002.73
getTaxonomy0.110.000.95
getTopGO1.200.101.83
getTree0.020.000.17
getVersion0.020.000.13
mapSequence0.790.028.97
resolveURL0.060.000.40
searchProtein2.240.035.58

OmaDB.Rcheck/examples_x64/OmaDB-Ex.timings

nameusersystemelapsed
annotateSequence0.080.021.31
formatTopGO0.130.010.64
getAttribute0.080.000.33
getGenome50.53 0.5572.60
getGenomePairs15.84 0.2322.86
getHOG0.130.000.75
getLocus0.110.000.37
getOMAGroup1.810.026.50
getObjectAttributes0.080.000.33
getProtein0.230.001.17
getTaxonomy0.070.000.90
getTopGO1.440.112.10
getTree0.000.000.18
getVersion0.020.000.13
mapSequence0.910.018.90
resolveURL0.060.000.39
searchProtein4.220.027.58