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### Running command:
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###   /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
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* 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(<dsCMatrix>, "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.