##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeomxTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeomxTools_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GeomxTools.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 'GeomxTools/DESCRIPTION' ... OK
* this is package 'GeomxTools' version '1.0.0'
* 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 'GeomxTools' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    extdata  10.6Mb
* 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
setSignatureFuncs<-,NanoStringGeomxSet-character: no visible global
  function definition for 'setSigFuncs<-'
setSignatureGroups<-,NanoStringGeomxSet-character: no visible global
  function definition for 'groups<-'
setSignatureGroups<-,NanoStringGeomxSet-factor: no visible global
  function definition for 'groups<-'
signatureFuncs,NanoStringGeomxSet: no visible global function
  definition for 'getSigFuncs'
signatureGroups,NanoStringGeomxSet: no visible global function
  definition for 'groups'
Undefined global functions or variables:
  getSigFuncs groups groups<- setSigFuncs<-
* 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
readNanoStringGeomxSet   40.29   0.74   41.01
NanoStringGeomxSet-class 15.56   0.65   19.78
readPKCFile               5.65   0.00    5.66
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
readNanoStringGeomxSet   42.44   0.78   43.22
NanoStringGeomxSet-class 20.18   0.47   20.64
readPKCFile               8.35   0.01    8.38
* 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-3.13-bioc/meat/GeomxTools.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GeomxTools_1.0.0.tar.gz && rm -rf GeomxTools.buildbin-libdir && mkdir GeomxTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeomxTools.buildbin-libdir GeomxTools_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GeomxTools_1.0.0.zip && rm GeomxTools_1.0.0.tar.gz GeomxTools_1.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 19 3220k   19  619k    0     0  1273k      0  0:00:02 --:--:--  0:00:02 1272k
 92 3220k   92 2991k    0     0  2016k      0  0:00:01  0:00:01 --:--:-- 2017k
100 3220k  100 3220k    0     0  2067k      0  0:00:01  0:00:01 --:--:-- 2067k

install for i386

* installing *source* package 'GeomxTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GeomxTools'
    finding HTML links ... done
    NanoStringGeomxSet-class                html  
    finding level-2 HTML links ... done

    readDccFile                             html  
    readNanoStringGeomxSet                  html  
    readPKCFile                             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 'GeomxTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeomxTools' as GeomxTools_1.0.0.zip
* DONE (GeomxTools)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GeomxTools' successfully unpacked and MD5 sums checked