Package: a4Preproc

Version: 1.30.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:a4Preproc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings a4Preproc_1.30.0.tar.gz

StartedAt: 2019-04-13 00:23:52 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 00:26:30 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 157.7 seconds

RetCode: 0

Status:  OK

CheckDir: a4Preproc.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:a4Preproc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings a4Preproc_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/a4Preproc.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'a4Preproc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Preproc' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'a4Preproc' can be installed ... OK
* checking installed package size ... OK
* checking package 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
Package in Depends field not imported from: 'methods'
  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
addGeneInfo: no visible global function definition for 'annotation'
addGeneInfo: no visible global function definition for 'featureNames'
addGeneInfo: no visible global function definition for 'featureData'
addGeneInfo: no visible global function definition for 'pData'
addGeneInfo: no visible global function definition for 'pData<-'
addGeneInfo: no visible global function definition for 'featureData<-'
addGeneInfo: no visible global function definition for 'fvarMetadata'
addGeneInfo: no visible global function definition for 'fvarMetadata<-'
Undefined global functions or variables:
  annotation featureData featureData<- featureNames fvarMetadata
  fvarMetadata<- pData pData<-
* 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/a4Preproc.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/a4Preproc_1.30.0.tar.gz && rm -rf a4Preproc.buildbin-libdir && mkdir a4Preproc.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=a4Preproc.buildbin-libdir a4Preproc_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL a4Preproc_1.30.0.zip && rm a4Preproc_1.30.0.tar.gz a4Preproc_1.30.0.zip
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install for i386

* installing *source* package 'a4Preproc' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'a4Preproc'
    finding HTML links ... done
    addGeneInfo                             html  
** building package indices
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'a4Preproc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'a4Preproc' as a4Preproc_1.30.0.zip
* DONE (a4Preproc)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'a4Preproc' successfully unpacked and MD5 sums checked
In R CMD INSTALL