Package: ArrayExpress

Version: 1.38.0

Command: rm -rf ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && mkdir ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayExpress.buildbin-libdir ArrayExpress_1.38.0.tar.gz >ArrayExpress.Rcheck\00install.out 2>&1 && cp ArrayExpress.Rcheck\00install.out ArrayExpress-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ArrayExpress.buildbin-libdir --install="check:ArrayExpress-install.out" --force-multiarch --no-vignettes --timings ArrayExpress_1.38.0.tar.gz

StartedAt: 2018-04-11 22:14:21 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:20:07 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 346.7 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayExpress.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && mkdir ArrayExpress.buildbin-libdir ArrayExpress.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayExpress.buildbin-libdir ArrayExpress_1.38.0.tar.gz >ArrayExpress.Rcheck\00install.out 2>&1 && cp ArrayExpress.Rcheck\00install.out ArrayExpress-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ArrayExpress.buildbin-libdir --install="check:ArrayExpress-install.out" --force-multiarch --no-vignettes --timings ArrayExpress_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ArrayExpress.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ArrayExpress/DESCRIPTION' ... OK
* this is package 'ArrayExpress' version '1.38.0'
* 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 'ArrayExpress' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
ae2bioc: no visible global function definition for 'new'
extract.zip : <anonymous>: no visible global function definition for
  'unzip'
getAE : <anonymous>: no visible global function definition for
  'download.file'
getAE: no visible global function definition for 'download.file'
getDataColsForAE1: no visible global function definition for
  'read.table'
preparePhenoDataFor2channel: no visible global function definition for
  'new'
queryAE: no visible global function definition for 'download.file'
readDerivedDataFiles: no visible global function definition for
  'read.table'
readDerivedDataFiles: no visible global function definition for 'new'
readDerivedDataMatrixFile: no visible global function definition for
  'read.table'
readDerivedDataMatrixFile: no visible global function definition for
  'new'
readExperimentData: no visible global function definition for 'new'
readFeatures: no visible global function definition for 'read.table'
readFeatures: no visible global function definition for 'new'
readPhenoData: no visible global function definition for 'new'
Undefined global functions or variables:
  download.file new read.table unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "read.table", "unzip")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
ArrayExpress 8.03   0.71   48.06
getAE        6.97   0.78   46.25
queryAE      3.10   0.06   10.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
ArrayExpress 8.28   0.64   17.47
getAE        3.28   0.25    7.43
queryAE      2.39   0.03    8.14
* 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-3.6-bioc/meat/ArrayExpress.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ArrayExpress' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ArrayExpress'
    finding HTML links ... done
    ArrayExpress                            html  
    ae2bioc                                 html  
    extract.zip                             html  
    getAE                                   html  
    getcolproc                              html  
    getcolraw                               html  
    procset                                 html  
    queryAE                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ArrayExpress' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ArrayExpress' as ArrayExpress_1.38.0.zip
* DONE (ArrayExpress)
In R CMD INSTALL
In R CMD INSTALL