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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AffiXcan.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings AffiXcan_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/AffiXcan.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 'AffiXcan/DESCRIPTION' ... OK
* this is package 'AffiXcan' version '1.6.0'
* 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 'AffiXcan' 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
affiXcanBs: no visible global function definition for 'p.adjust'
affiXcanPcs: no visible global function definition for 'setNames'
computeBs: no visible binding for global variable 'V1'
computeBs: no visible global function definition for 'lm'
computeBs: no visible global function definition for 'anova'
computeBs: no visible global function definition for 'pf'
computeCorrelation: no visible global function definition for 'cor'
computeCorrelation: no visible global function definition for
  'cor.test'
computePca: no visible global function definition for 'var'
computePca: no visible global function definition for 'prcomp'
computeRSquared: no visible binding for global variable 'exprMatrix'
Undefined global functions or variables:
  V1 anova cor cor.test exprMatrix lm p.adjust pf prcomp setNames var
Consider adding
  importFrom("stats", "anova", "cor", "cor.test", "lm", "p.adjust", "pf",
             "prcomp", "setNames", "var")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
AffiXcan-package 4.06   0.22   80.64
affiXcanImpute   3.06   0.10   73.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
AffiXcan-package 4.42   0.22   75.78
affiXcanImpute   3.75   0.14   80.56
* 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-3.11-bioc/meat/AffiXcan.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/AffiXcan_1.6.0.tar.gz && rm -rf AffiXcan.buildbin-libdir && mkdir AffiXcan.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AffiXcan.buildbin-libdir AffiXcan_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL AffiXcan_1.6.0.zip && rm AffiXcan_1.6.0.tar.gz AffiXcan_1.6.0.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
100 1710k  100 1710k    0     0  22.3M      0 --:--:-- --:--:-- --:--:-- 24.5M

install for i386

* installing *source* package 'AffiXcan' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AffiXcan'
    finding HTML links ... done
    AffiXcan-package                        html  
    affiXcanBs                              html  
    affiXcanGReX                            html  
    affiXcanImpute                          html  
    affiXcanPca                             html  
    affiXcanPcs                             html  
    affiXcanTrain                           html  
    assoc2list                              html  
    computeBs                               html  
    computeCorrelation                      html  
    computeExpr                             html  
    computePca                              html  
    computePcs                              html  
    computeRSquared                         html  
    exprMatrix                              html  
    overlookRegions                         html  
    regionAssoc                             html  
    subsetKFold                             html  
    trainingCovariates                      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 'AffiXcan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AffiXcan' as AffiXcan_1.6.0.zip
* DONE (AffiXcan)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'AffiXcan' successfully unpacked and MD5 sums checked