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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCSL.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCSL_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RCSL.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 for sufficient/correct file permissions ... 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               130.571  1.486 141.131
PlotMST            130.417  1.080 138.133
TrajectoryAnalysis 128.449  0.983 139.833
getLineage         127.696  0.909 135.022
EstClusters        127.145  1.154 140.248
PlotTrajectory     126.706  1.175 134.531
GenesFilter        124.536  2.941 134.473
NeigRepresent      125.038  1.379 132.085
PlotPseudoTime     125.267  1.012 134.338
SimS               124.061  1.391 140.101
RCSL                31.664  2.565  36.893
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/RCSL.Rcheck/00check.log’
for details.