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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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/phemd.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phemd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phemd’ version ‘1.16.0’
* 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            18.534  0.236  25.048
compareSamples           18.191  0.289  24.519
printClusterAssignments  17.595  0.164  24.015
getCellYield             17.430  0.213  23.620
groupSamples             17.302  0.209  23.683
plotCellYield            17.293  0.198  23.890
plotGroupedSamplesDmap   16.847  0.178  23.210
getSampleHistsByCluster  16.736  0.164  23.327
getSampleCelltypeFreqs   16.549  0.158  23.275
clusterIndividualSamples 16.318  0.289  21.948
generateGDM              16.013  0.196  21.125
plotEmbeddings           15.364  0.155  20.813
plotHeatmaps             14.890  0.146  20.209
orderCellsMonocle        13.666  0.129  18.845
embedCells                5.756  0.039   7.600
selectFeatures            4.289  0.017   5.806
* 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-3.17-bioc/meat/phemd.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL phemd
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘phemd’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (phemd)