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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ctgGEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ctgGEM_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ctgGEM.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ctgGEM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ctgGEM' version '1.2.0'
* 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 'ctgGEM' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'SummarizedExperiment::distance' by 'destiny::distance' when loading 'ctgGEM'
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ctgGEM.Rcheck/00install.out' for details.
* 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 ... WARNING
'::' or ':::' imports not declared from:
  'Matrix' 'ggplot2'
Namespace in Imports field not imported from: 'HSMMSingleCell'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
generate_tree    8.94   0.69    9.64
plotOriginalTree 7.70   0.72    8.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
generate_tree    7.44   0.64    8.11
plotOriginalTree 6.20   0.31    6.52
* 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 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ctgGEM.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ctgGEM_1.2.0.tar.gz && rm -rf ctgGEM.buildbin-libdir && mkdir ctgGEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ctgGEM.buildbin-libdir ctgGEM_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ctgGEM_1.2.0.zip && rm ctgGEM_1.2.0.tar.gz ctgGEM_1.2.0.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 18628  100 18628    0     0   323k      0 --:--:-- --:--:-- --:--:--  330k

install for i386

* installing *source* package 'ctgGEM' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'SummarizedExperiment::distance' by 'destiny::distance' when loading 'ctgGEM'
** help
*** installing help indices
  converting help for package 'ctgGEM'
    finding HTML links ... done
    ctgGEMset-methods                       html  
    ctgGEMset                               html  
    generate_tree                           html  
    makeDestiny                             html  
    makeMonocle                             html  
    makeSincell                             html  
    makeTSCAN                               html  
    plotOriginalTree                        html  
    tree2igraph                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'SummarizedExperiment::distance' by 'destiny::distance' when loading 'ctgGEM'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'SummarizedExperiment::distance' by 'destiny::distance' when loading 'ctgGEM'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ctgGEM' ...
** testing if installed package can be loaded
Warning: replacing previous import 'SummarizedExperiment::distance' by 'destiny::distance' when loading 'ctgGEM'
* MD5 sums
packaged installation of 'ctgGEM' as ctgGEM_1.2.0.zip
* DONE (ctgGEM)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ctgGEM' successfully unpacked and MD5 sums checked