Multiple platform build/check report for BioC 3.12 - CHECK report for biomaRt on tokay1

Package: biomaRt

Version: 2.46.3

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomaRt.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biomaRt_2.46.3.tar.gz

StartedAt: 2021-05-06 00:53:49 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 00:59:32 -0400 (Thu, 06 May 2021)

EllapsedTime: 342.7 seconds

RetCode: 0

Status: OK

CheckDir: biomaRt.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomaRt.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biomaRt_2.46.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/biomaRt.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biomaRt/DESCRIPTION' ... OK
* this is package 'biomaRt' version '2.46.3'
* 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 'biomaRt' 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
Unexported object imported by a ':::' call: 'AnnotationDbi:::smartKeys'
  See the note in ?`:::` about the use of this operator.
* 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
select 14.89   0.03   23.32
getBM  13.83   0.05   31.69
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
getBM  9.92   0.04   16.89
select 6.37   0.04   14.61
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/biomaRt.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/biomaRt_2.46.3.tar.gz && rm -rf biomaRt.buildbin-libdir && mkdir biomaRt.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biomaRt.buildbin-libdir biomaRt_2.46.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL biomaRt_2.46.3.zip && rm biomaRt_2.46.3.tar.gz biomaRt_2.46.3.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  118k  100  118k    0     0  5444k      0 --:--:-- --:--:-- --:--:-- 5658k

install for i386

* installing *source* package 'biomaRt' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biomaRt'
    finding HTML links ... done
    Mart-class                              html  
    NP2009code                              html  
    attributePages                          html  
    biomartCache                            html  
    exportFASTA                             html  
    filterOptions                           html  
    filterType                              html  
    getBM                                   html  
    getBMlist                               html  
    getGene                                 html  
    getLDS                                  html  
    getSequence                             html  
    listAttributes                          html  
    listDatasets                            html  
    listEnsembl                             html  
    listEnsemblArchives                     html  
    listFilterValues                        html  
    listFilters                             html  
    listMarts                               html  
    select                                  html  
    useDataset                              html  
    useEnsembl                              html  
    useMart                                 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 'biomaRt' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biomaRt' as biomaRt_2.46.3.zip
* DONE (biomaRt)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'biomaRt' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
> library(mockery)
> library(biomaRt)
> 
> #biomartCacheClear()
> 
> #test_check("biomaRt", encoding = "UTF-8")
> 
> proc.time()
   user  system elapsed 
   3.92    0.25    5.84


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
> library(mockery)
> library(biomaRt)
> 
> #biomartCacheClear()
> 
> #test_check("biomaRt", encoding = "UTF-8")
> 
> proc.time()
   user  system elapsed 
   4.62    0.26    6.40

name	user	system	elapsed
NP2009code	0	0	0
attributePages	0	0	0
exportFASTA	0	0	0
filterOptions	0	0	0
filterType	0	0	0
getBM	13.83	0.05	31.69
getBMlist	0	0	0
getGene	0	0	0
getLDS	0	0	0
getSequence	0	0	0
listAttributes	0	0	0
listDatasets	0	0	0
listEnsembl	0	0	0
listEnsemblArchives	0.02	0.00	0.55
listFilterValues	0	0	0
listFilters	0	0	0
listMarts	0	0	0
select	14.89	0.03	23.32
useDataset	0	0	0
useEnsembl	0	0	0
useMart	0	0	0

name	user	system	elapsed
NP2009code	0	0	0
attributePages	0	0	0
exportFASTA	0.02	0.00	0.02
filterOptions	0	0	0
filterType	0	0	0
getBM	9.92	0.04	16.89
getBMlist	0	0	0
getGene	0.02	0.00	0.01
getLDS	0	0	0
getSequence	0	0	0
listAttributes	0	0	0
listDatasets	0	0	0
listEnsembl	0	0	0
listEnsemblArchives	0.06	0.00	0.39
listFilterValues	0	0	0
listFilters	0	0	0
listMarts	0	0	0
select	6.37	0.04	14.61
useDataset	0	0	0
useEnsembl	0	0	0
useMart	0	0	0

CHECK report for biomaRt on tokay1

Summary

Command output

Installation output

Tests output

Example timings