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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SNAGEE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SNAGEE_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SNAGEE.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SNAGEE/DESCRIPTION' ... OK
* this is package 'SNAGEE' 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 'SNAGEE' 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
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
qualSample: no visible global function definition for 'sd'
qualSample: no visible global function definition for 'cor'
qualSample: no visible global function definition for 'mclapply'
qualSample: no visible global function definition for 'median'
qualSample: no visible global function definition for 'mad'
qualStudy: no visible global function definition for 'cor'
qualStudy: no visible global function definition for 'sd'
toSnageeFormat: no visible global function definition for 'is'
toSnageeFormat: no visible global function definition for 'annotation'
toSnageeFormat: no visible global function definition for 'exprs'
toSnageeFormat: no visible global function definition for
  'selectMethod'
toSnageeFormat: no visible global function definition for 'medpolish'
Undefined global functions or variables:
  annotation cor exprs is mad mclapply median medpolish sd selectMethod
Consider adding
  importFrom("methods", "is", "selectMethod")
  importFrom("stats", "cor", "mad", "median", "medpolish", "sd")
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
SNAGEE-package 7.61   3.91   15.98
qualSample     6.26   3.48    9.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
SNAGEE-package 7.80   3.53   11.33
qualSample     5.81   3.47    9.30
* 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-3.14-bioc/meat/SNAGEE.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SNAGEE_1.34.0.tar.gz && rm -rf SNAGEE.buildbin-libdir && mkdir SNAGEE.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SNAGEE.buildbin-libdir SNAGEE_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SNAGEE_1.34.0.zip && rm SNAGEE_1.34.0.tar.gz SNAGEE_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
100  6253  100  6253    0     0  14590      0 --:--:-- --:--:-- --:--:-- 14575
100  6253  100  6253    0     0  14580      0 --:--:-- --:--:-- --:--:-- 14575

install for i386

* installing *source* package 'SNAGEE' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SNAGEE'
    finding HTML links ... done
    SNAGEE-package                          html  
    qualSample                              html  
    qualStudy                               html  
    toSnageeFormat                          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 'SNAGEE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SNAGEE' as SNAGEE_1.34.0.zip
* DONE (SNAGEE)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SNAGEE' successfully unpacked and MD5 sums checked