Package: mygene

Version: 1.16.2

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mygene.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings mygene_1.16.2.tar.gz

StartedAt: 2018-10-17 03:35:44 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 03:40:21 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 276.7 seconds

RetCode: 0

Status:  OK

CheckDir: mygene.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mygene.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings mygene_1.16.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/mygene.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 'mygene/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mygene' version '1.16.2'
* 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 'mygene' 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
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.df2DF: no visible binding for global variable 'as'
.unnest.df : <anonymous>: no visible global function definition for
  'is'
.unnest.df : <anonymous>: no visible global function definition for
  'setNames'
MyGene: no visible global function definition for 'new'
index.tx.id: no visible global function definition for
  'installed.packages'
validMyGeneObject: no visible global function definition for 'slot'
.request.get,MyGene: no visible global function definition for
  'capture.output'
.request.post,MyGene: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  as capture.output installed.packages is new setNames slot
Consider adding
  importFrom("methods", "as", "is", "new", "slot")
  importFrom("stats", "setNames")
  importFrom("utils", "capture.output", "installed.packages")
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
** running examples for arch 'x64' ... 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/mygene.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/mygene_1.16.2.tar.gz && rm -rf mygene.buildbin-libdir && mkdir mygene.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mygene.buildbin-libdir mygene_1.16.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL mygene_1.16.2.zip && rm mygene_1.16.2.tar.gz mygene_1.16.2.zip
###
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install for i386

* installing *source* package 'mygene' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mygene'
    finding HTML links ... done
    MyGene-class                            html  
    MyGene                                  html  
    getGene                                 html  
    getGenes                                html  
    makeTxDbFromMyGene                      html  
    metadata                                html  
    mygene-package                          html  
    query                                   html  
    queryMany                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'mygene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mygene' as mygene_1.16.2.zip
* DONE (mygene)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'mygene' successfully unpacked and MD5 sums checked
In R CMD INSTALL