############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phemd.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phemd_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/phemd.Rcheck’ * using R version 4.3.1 Patched (2023-06-17 r84564) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘phemd/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘phemd’ version ‘1.18.0’ * 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 ‘phemd’ 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 ':::' call which should be '::': ‘monocle:::reducedDimA<-’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘VGAM:::VGAM.weights.function’ ‘monocle:::extract_ddrtree_ordering’ ‘monocle:::extract_good_branched_ordering’ ‘monocle:::findNearestPointOnMST’ ‘monocle:::projPointOnLine’ ‘monocle:::project_point_to_line_segment’ ‘monocle:::reducedDimK<-’ ‘monocle:::reducedDimW<-’ ‘monocle:::select_root_cell’ ‘pheatmap:::find_coordinates’ 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 newCellDataSetUpdated: no visible global function definition for ‘isSparseMatrix’ orderCellsUpdated: no visible binding for '<<-' assignment to ‘next_node’ orderCellsUpdated: no visible global function definition for ‘pq_helper’ orderCellsUpdated: no visible global function definition for ‘select_root_cell’ project2MSTUpdated: no visible global function definition for ‘nei’ Undefined global functions or variables: isSparseMatrix nei pq_helper select_root_cell * 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 ... WARNING Found the following significant warnings: Warning: 'as(, "dsTMatrix")' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed Phemd-methods 9.690 0.202 9.974 compareSamples 9.317 0.295 9.702 groupSamples 8.728 0.201 8.986 getCellYield 8.611 0.230 8.888 plotGroupedSamplesDmap 8.538 0.265 8.987 plotEmbeddings 8.461 0.221 8.745 plotHeatmaps 8.279 0.253 8.594 plotCellYield 8.247 0.214 8.529 clusterIndividualSamples 8.161 0.263 8.540 getSampleHistsByCluster 8.182 0.197 8.424 printClusterAssignments 8.092 0.180 8.331 getSampleCelltypeFreqs 7.999 0.182 8.226 orderCellsMonocle 7.873 0.207 8.141 generateGDM 7.695 0.192 7.931 * 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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/phemd.Rcheck/00check.log’ for details.