############################################################################## ############################################################################## ### ### Running command: ### ### /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_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/RCSL.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RCSL/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RCSL’ version ‘1.12.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 PlotMST 28.553 0.320 28.912 PlotTrajectory 27.908 0.781 28.890 TrajectoryAnalysis 27.600 0.520 28.180 NeigRepresent 27.006 0.261 27.346 SimS 26.768 0.325 27.117 EstClusters 26.663 0.282 26.950 GenesFilter 26.351 0.575 27.007 PlotPseudoTime 26.495 0.130 26.636 BDSM 26.219 0.220 26.451 getLineage 24.801 0.260 25.238 RCSL 7.089 0.690 7.831 * 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-3.19-bioc/meat/RCSL.Rcheck/00check.log’ for details.