##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RCSL.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RCSL_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RCSL.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RCSL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCSL' version '1.14.0'
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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
Namespaces in Imports field not imported from:
  'MatrixGenerics' 'Rcpp' 'SingleCellExperiment'
  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 ... 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 ... NOTE
checkRd: (-1) BDSM.Rd:6: Lost braces; missing escapes or markup?
     6 | min_{B>=0, B*1=1, F'*F=I}  ||B - A||_1 + r*||B||^2 + 2*lambda*trace(F'*L*F)}
       |     ^
checkRd: (-1) BDSM.Rd:22: Lost braces; missing escapes or markup?
    22 | min_{B>=0, B*1=1, F'*F=I}  ||B - A||_1 + r*||B||^2 + 2*lambda*trace(F'*L*F)
       |     ^
* 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
BDSM               46.75   0.44   47.24
SimS               43.82   0.50   44.34
TrajectoryAnalysis 43.14   0.48   43.62
EstClusters        43.09   0.40   43.53
getLineage         42.74   0.31   43.05
GenesFilter        42.42   0.49   42.90
PlotMST            42.23   0.53   42.77
PlotTrajectory     41.68   0.56   42.25
PlotPseudoTime     41.08   0.19   41.28
NeigRepresent      39.24   0.34   39.58
RCSL               10.79   0.46   11.25
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.20-bioc/meat/RCSL.Rcheck/00check.log'
for details.