##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ArrayExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ArrayExpress_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ArrayExpress.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.48.0'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
ArrayExpress 12.85   1.02   22.91
queryAE       5.10   0.61   11.24
getAE         4.54   0.53   11.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
ArrayExpress 11.15   0.99   27.52
queryAE       4.58   0.07    9.28
getAE         3.47   0.34    7.72
* 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-3.11-bioc/meat/ArrayExpress.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ArrayExpress_1.48.0.tar.gz && rm -rf ArrayExpress.buildbin-libdir && mkdir ArrayExpress.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ArrayExpress.buildbin-libdir ArrayExpress_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ArrayExpress_1.48.0.zip && rm ArrayExpress_1.48.0.tar.gz ArrayExpress_1.48.0.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
 39 41483   39 16384    0     0   128k      0 --:--:-- --:--:-- --:--:--  135k
100 41483  100 41483    0     0   323k      0 --:--:-- --:--:-- --:--:--  340k

install for i386

* installing *source* package 'ArrayExpress' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
** 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 from temporary location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
** testing if installed package can be loaded from final location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ArrayExpress' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
* MD5 sums
packaged installation of 'ArrayExpress' as ArrayExpress_1.48.0.zip
* DONE (ArrayExpress)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ArrayExpress' successfully unpacked and MD5 sums checked