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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:phemd.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings phemd_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/phemd.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘phemd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phemd’ version ‘1.17.0’
* 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 loading without being on the library search path ... 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
plotGroupedSamplesDmap   11.482  0.136  11.618
clusterIndividualSamples 11.220  0.248  11.471
Phemd-methods            10.952  0.368  11.320
generateGDM              10.943  0.168  11.111
groupSamples             10.839  0.188  11.028
printClusterAssignments  10.884  0.033  10.918
getCellYield             10.586  0.088  10.674
getSampleCelltypeFreqs   10.591  0.048  10.639
getSampleHistsByCluster  10.489  0.120  10.609
compareSamples           10.472  0.100  10.572
plotCellYield            10.184  0.048  10.233
plotHeatmaps              9.387  0.032   9.420
plotEmbeddings            9.246  0.048   9.294
orderCellsMonocle         8.296  0.048   8.345
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘phemd.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘phemd.Rmd’ using rmarkdown
Error: processing vignette 'phemd.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘phemd.Rmd’

SUMMARY: processing the following file failed:
  ‘phemd.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/phemd.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL phemd
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-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)