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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Risa.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Risa_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Risa.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Risa/DESCRIPTION' ... OK
* this is package 'Risa' version '1.34.0'
* 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 'Risa' 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
getPackagesInBiocView: no visible global function definition for 'data'
readISAtabZip: no visible global function definition for 'unzip'
suggestBiocPackage: no visible global function definition for
  'read.csv'
write.assay.file: no visible global function definition for
  'write.table'
write.investigation.file: no visible global function definition for
  'write.table'
write.study.file: no visible global function definition for
  'write.table'
initialize,ISATab: no visible global function definition for
  'count.fields'
initialize,ISATab: no visible global function definition for
  'read.table'
initialize,ISATab : <anonymous>: no visible global function definition
  for 'read.table'
initialize,ISATab : <anonymous> : <anonymous>: no visible global
  function definition for 'read.table'
initialize,ISATab: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  count.fields data na.omit read.csv read.table unzip write.table
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "count.fields", "data", "read.csv", "read.table",
             "unzip", "write.table")
to your NAMESPACE file.
* 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
processAssayXcmsSet.1factor 1.28   0.03   30.33
processAssayXcmsSet         0.81   0.00   30.82
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
processAssayXcmsSet.1factor 1.64   0.02   29.96
processAssayXcmsSet         0.96   0.00   32.51
* 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-3.13-bioc/meat/Risa.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Risa_1.34.0.tar.gz && rm -rf Risa.buildbin-libdir && mkdir Risa.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Risa.buildbin-libdir Risa_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Risa_1.34.0.zip && rm Risa_1.34.0.tar.gz Risa_1.34.0.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
  4 2202k    4  101k    0     0   532k      0  0:00:04 --:--:--  0:00:04  531k
100 2202k  100 2202k    0     0  2461k      0 --:--:-- --:--:-- --:--:-- 2460k

install for i386

* installing *source* package 'Risa' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Risa'
    finding HTML links ... done
    AssayTab-class                          html  
    ISAtab-class                            html  
    Risa-package                            html  
    getAnnotatedDataFrameAssay              html  
    getAssayRawDataFilenames-methods        html  
    getExpressionSet                        html  
    getMIAMEMetadata                        html  
    getMSAssayFilenames                     html  
    getMicroarrayAssayFilenames             html  
    getRawDataFilenames-methods             html  
    getStudyFilename                        html  
    isMSAssay                               html  
    isMicroarrayAssay                       html  
    processAssayXcmsSet.1factor             html  
    processAssayXcmsSet                     html  
    readISAtab                              html  
    suggestBiocPackage                      html  
    updateAssayMetadata                     html  
    write.assay.file                        html  
    write.investigation.file                html  
    write.isatab                            html  
    write.study.file                        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 'Risa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Risa' as Risa_1.34.0.zip
* DONE (Risa)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'Risa' successfully unpacked and MD5 sums checked