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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:corral.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings corral_1.5.7.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/corral.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'corral/DESCRIPTION' ... OK
* this is package 'corral' version '1.5.7'
* 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 'corral' 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
* 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
Unexported object imported by a ':::' call: 'ggthemes:::check_pal_n'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biplot_corral: no visible binding for global variable 'Name'
plot_embedding: no visible binding for global variable 'Xdim'
plot_embedding: no visible binding for global variable 'Ydim'
scal_var: no visible binding for global variable 'PC_ind'
scal_var: no visible binding for global variable 'sv'
scal_var: no visible binding for global variable 'Batch'
Undefined global functions or variables:
  Batch Name PC_ind Xdim Ydim sv
* checking Rd files ... NOTE
prepare_Rd: corral_preproc.Rd:41-43: Dropping empty section \details
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
biplot_corral          65.73  12.08   78.20
add_embeddings2scelist 16.60   2.60   20.32
corralm                11.45   3.66   15.71
corral                 10.36   3.39   14.34
sce2matlist             5.55   1.69    7.57
plot_embedding_sce      5.64   1.41    7.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/corral.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL corral
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'corral' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'corral'
    finding HTML links ... done
    add_embeddings2scelist                  html  
    all_are                                 html  
    biplot_corral                           html  
    compsvd                                 html  
    corral                                  html  
    finding level-2 HTML links ... done

    corral_preproc                          html  
    corralm                                 html  
    earthmover_dist                         html  
    get_pct_var_exp_svd                     html  
    get_weights                             html  
    list2mat                                html  
    na2zero                                 html  
    obs2probs                               html  
    pairwise_rv                             html  
    plot_embedding                          html  
    plot_embedding_sce                      html  
    rv                                      html  
    scal_var                                html  
    scal_var_mat                            html  
    sce2matlist                             html  
    trim_matdist                            html  
    var_stabilize                           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
* DONE (corral)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'AMARETTO' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> proc.time()
   user  system elapsed 
   0.10    0.09    0.17