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CHECK report for OmaDB on tokay2

This page was generated on 2018-10-17 08:45:00 -0400 (Wed, 17 Oct 2018).

Package 1016/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmaDB 1.0.1
Klara Kaleb , Adrian Altenhoff
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/OmaDB
Branch: RELEASE_3_7
Last Commit: e902bdf
Last Changed Date: 2018-06-29 07:06:48 -0400 (Fri, 29 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OmaDB
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmaDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings OmaDB_1.0.1.tar.gz
StartedAt: 2018-10-17 03:43:09 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:50:06 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 417.3 seconds
RetCode: 0
Status:  OK  
CheckDir: OmaDB.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmaDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings OmaDB_1.0.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/OmaDB.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.0.1'
* 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 ... NOTE
Missing or unexported object: 'topGO::annFUN.GO2gene'
* 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
getOntologies 7.15   0.05   56.46
getSequences  4.03   0.01   29.86
getXref       3.68   0.01    8.28
mapSequence   0.74   0.03   10.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOntologies 8.74   0.14   56.15
getSequences  4.89   0.06   30.43
getXref       3.41   0.05    8.01
mapSequence   0.70   0.03    9.30
resolveURL    0.00   0.00    5.49
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/OmaDB.Rcheck/00check.log'
for details.

Installation output

OmaDB.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/OmaDB_1.0.1.tar.gz && rm -rf OmaDB.buildbin-libdir && mkdir OmaDB.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmaDB.buildbin-libdir OmaDB_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL OmaDB_1.0.1.zip && rm OmaDB_1.0.1.tar.gz OmaDB_1.0.1.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
100  100k  100  100k    0     0  1779k      0 --:--:-- --:--:-- --:--:-- 2003k

install for i386

* installing *source* package 'OmaDB' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OmaDB'
    finding HTML links ... done
    OmaDB-package                           html  
    formatTopGO                             html  
    getAnnotation                           html  
    getAttribute                            html  
    getData                                 html  
    getGRanges                              html  
    getGenomeAlignment                      html  
    getHOG                                  html  
    getObjectAttributes                     html  
    getOntologies                           html  
    getSequences                            html  
    getTaxonomy                             html  
    getTopGO                                html  
    getXref                                 html  
    group                                   html  
    hog                                     html  
    mapSequence                             html  
    orthologs                               html  
    pairs                                   html  
    protein                                 html  
    resolveURL                              html  
    sequence_annotation                     html  
    sequence_map                            html  
    taxonomy                                html  
    xref                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'OmaDB' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmaDB' as OmaDB_1.0.1.zip
* DONE (OmaDB)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'OmaDB' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

OmaDB.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 
   0.37    0.01    1.93

OmaDB.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 
   0.31    0.03    1.93

Example timings

OmaDB.Rcheck/examples_i386/OmaDB-Ex.timings

nameusersystemelapsed
formatTopGO0.360.111.89
getAnnotation0.060.000.43
getAttribute0.610.001.69
getData0.030.000.28
getGRanges0.400.051.49
getGenomeAlignment0.910.062.93
getHOG0.110.000.52
getObjectAttributes0.300.001.37
getOntologies 7.15 0.0556.46
getSequences 4.03 0.0129.86
getTaxonomy0.130.001.64
getTopGO1.000.061.61
getXref3.680.018.28
mapSequence 0.74 0.0310.52
resolveURL0.090.053.36

OmaDB.Rcheck/examples_x64/OmaDB-Ex.timings

nameusersystemelapsed
formatTopGO0.430.001.83
getAnnotation0.460.000.90
getAttribute0.280.031.47
getData0.040.000.32
getGRanges0.390.011.54
getGenomeAlignment0.910.053.30
getHOG0.150.000.60
getObjectAttributes0.330.001.46
getOntologies 8.74 0.1456.15
getSequences 4.89 0.0630.43
getTaxonomy0.070.021.79
getTopGO0.990.051.63
getXref3.410.058.01
mapSequence0.700.039.30
resolveURL0.000.005.49