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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RCSL.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RCSL_1.3.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/RCSL.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 'RCSL/DESCRIPTION' ... OK
* this is package 'RCSL' version '1.3.0'
* 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 'RCSL' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'RcppAnnoy'
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PlotMST: no visible binding for global variable 'X1'
PlotMST: no visible binding for global variable 'X2'
PlotMST: no visible binding for global variable 'label'
PlotMST: no visible binding for global variable 'from.x'
PlotMST: no visible binding for global variable 'to.x'
PlotMST: no visible binding for global variable 'from.y'
PlotMST: no visible binding for global variable 'to.y'
PlotMST: no visible binding for global variable 'V1'
PlotMST: no visible binding for global variable 'V2'
PlotPseudoTime: no visible binding for global variable 'x'
PlotPseudoTime: no visible binding for global variable 'y'
PlotPseudoTime: no visible binding for global variable 'Timepoint'
PlotTrajectory: no visible binding for global variable 'X1'
PlotTrajectory: no visible binding for global variable 'X2'
PlotTrajectory: no visible binding for global variable 'label'
PlotTrajectory: no visible binding for global variable 'x'
PlotTrajectory: no visible binding for global variable 'y'
Undefined global functions or variables:
  Timepoint V1 V2 X1 X2 from.x from.y label to.x to.y x y
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
TrajectoryAnalysis 34.81   0.56   35.38
EstClusters        34.60   0.25   34.84
PlotTrajectory     33.35   0.47   33.81
BDSM               32.71   0.47   33.34
GenesFilter        32.63   0.34   32.97
PlotMST            31.44   0.39   31.90
NeigRepresent      30.53   0.33   30.86
getLineage         27.42   0.17   27.59
PlotPseudoTime     26.40   0.19   26.60
SimS               25.56   0.23   25.79
RCSL                8.64   0.30    8.94
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/RCSL.Rcheck/00check.log'
for details.

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### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RCSL
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'RCSL' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RCSL'
    finding HTML links ... done
    BDSM                                    html  
    EProjSimplexdiag                        html  
    EstClusters                             html  
    EucDist                                 html  
    GenesFilter                             html  
    NeigRepresent                           html  
    PlotMST                                 html  
    PlotPseudoTime                          html  
    PlotTrajectory                          html  
    RCSL                                    html  
    SimS                                    html  
    TrajectoryAnalysis                      html  
    ann                                     html  
    getLineage                              html  
    yan                                     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 (RCSL)
Making 'packages.html' ... done