Package: affyContam

Version: 1.38.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affyContam.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings affyContam_1.38.0.tar.gz

StartedAt: 2018-10-17 00:25:43 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:27:23 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 100.4 seconds

RetCode: 0

Status:  OK

CheckDir: affyContam.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affyContam.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings affyContam_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/affyContam.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyContam/DESCRIPTION' ... OK
* this is package 'affyContam' 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 'affyContam' 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 ... NOTE
Packages in Depends field not imported from:
  'Biobase' 'affy' 'affydata'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getCircRegion: no visible global function definition for 'annotation'
getCircRegion : <anonymous>: no visible global function definition for
  'xy2indices'
getCircRegion: no visible global function definition for 'exprs'
getRectRegion: no visible global function definition for 'annotation'
getRectRegion : <anonymous>: no visible global function definition for
  'xy2indices'
getRectRegion: no visible global function definition for 'exprs'
setCircRegion: no visible global function definition for 'annotation'
setCircRegion : <anonymous>: no visible global function definition for
  'xy2indices'
setCircRegion: no visible global function definition for 'exprs'
setCircRegion: no visible global function definition for 'exprs<-'
setRectRegion: no visible global function definition for 'annotation'
setRectRegion : <anonymous>: no visible global function definition for
  'xy2indices'
setRectRegion: no visible global function definition for 'exprs'
setRectRegion: no visible global function definition for 'exprs<-'
Undefined global functions or variables:
  annotation exprs exprs<- xy2indices
* 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 or elapsed time > 5s
               user system elapsed
setRectRegion 20.04   0.59   21.85
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
setRectRegion 17.42   0.38    17.8
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/affyContam.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/affyContam_1.38.0.tar.gz && rm -rf affyContam.buildbin-libdir && mkdir affyContam.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affyContam.buildbin-libdir affyContam_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL affyContam_1.38.0.zip && rm affyContam_1.38.0.tar.gz affyContam_1.38.0.zip
###
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100  219k  100  219k    0     0  4135k      0 --:--:-- --:--:-- --:--:-- 4775k

install for i386

* installing *source* package 'affyContam' ...
** R
** byte-compile and prepare package for lazy loading
     Package    LibPath                                     Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.7-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
** help
*** installing help indices
  converting help for package 'affyContam'
    finding HTML links ... done
    setRectRegion                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
     Package    LibPath                                     Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.7-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
In R CMD INSTALL

install for x64

* installing *source* package 'affyContam' ...
** testing if installed package can be loaded
     Package    LibPath                                     Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.7-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
* MD5 sums
packaged installation of 'affyContam' as affyContam_1.38.0.zip
* DONE (affyContam)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'affyContam' successfully unpacked and MD5 sums checked
In R CMD INSTALL