Package: hypeR

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hypeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings hypeR_1.0.0.tar.gz

StartedAt: 2019-10-16 04:29:05 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:31:41 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 155.7 seconds

RetCode: 0

Status:  OK

CheckDir: hypeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hypeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings hypeR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/hypeR.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 'hypeR/DESCRIPTION' ... OK
* this is package 'hypeR' version '1.0.0'
* 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 'hypeR' 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 ... NOTE
.hyper_enrichment: no visible global function definition for 'is'
.hyper_enrichment: no visible global function definition for 'p.adjust'
.hyper_enrichment: no visible global function definition for 'rjust'
.hyper_enrichment: no visible global function definition for 'quantile'
.hyper_enrichment: no visible global function definition for 'phyper'
download_gsets: no visible binding for global variable 'gs_name'
download_gsets: no visible binding for global variable 'gene_symbol'
download_gsets: no visible binding for global variable '.'
download_msigdb: no visible binding for global variable 'gs_cat'
download_msigdb: no visible binding for global variable 'gs_subcat'
download_msigdb: no visible global function definition for
  'packageVersion'
hyp_plot: no visible global function definition for 'head'
hyp_show : : no visible binding for global variable
  'symbols'
hyp_to_table: no visible global function definition for 'write.table'
hypeR: no visible global function definition for 'is'
hypeR: no visible global function definition for 'complete.cases'
Undefined global functions or variables:
  . complete.cases gene_symbol gs_cat gs_name gs_subcat head is
  p.adjust packageVersion phyper quantile rjust symbols write.table
Consider adding
  importFrom("graphics", "symbols")
  importFrom("methods", "is")
  importFrom("stats", "complete.cases", "p.adjust", "phyper", "quantile")
  importFrom("utils", "head", "packageVersion", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 or elapsed time > 5s
                 user system elapsed
db_get          21.75   2.10   23.86
download_msigdb 16.48   1.73   18.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
db_get          19.66   1.83   21.56
download_msigdb 18.22   0.71   18.94
* 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-3.9-bioc/meat/hypeR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/hypeR_1.0.0.tar.gz && rm -rf hypeR.buildbin-libdir && mkdir hypeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hypeR.buildbin-libdir hypeR_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL hypeR_1.0.0.zip && rm hypeR_1.0.0.tar.gz hypeR_1.0.0.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
100  202k  100  202k    0     0  3366k      0 --:--:-- --:--:-- --:--:-- 3828k

install for i386

* installing *source* package 'hypeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'hypeR'
    finding HTML links ... done
    db_get                                  html  
    db_info                                 html  
    dot-VERBOSE                             html  
    dot-hyper_enrichment                    html  
    download_gsets                          html  
    download_msigdb                         html  
    ex_get                                  html  
    hyp_plot                                html  
    hyp_show                                html  
    hyp_to_excel                            html  
    hyp_to_table                            html  
    hypeR                                   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 'hypeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hypeR' as hypeR_1.0.0.zip
* DONE (hypeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'hypeR' successfully unpacked and MD5 sums checked

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)
> library(hypeR)
> 
> test_check("hypeR")
Number of genes =  24 
Number of gene sets =  674 
Background population size =  2520 
P-Value cutoff =  1 
FDR cutoff =  0.05 
== testthat results  ===========================================================
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   2.04    0.20    2.95 

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)
> library(hypeR)
> 
> test_check("hypeR")
Number of genes =  24 
Number of gene sets =  674 
Background population size =  2520 
P-Value cutoff =  1 
FDR cutoff =  0.05 
== testthat results  ===========================================================
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   2.03    0.20    2.48