Multiple platform build/check report for BioC 3.9 - CHECK report for phemd on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phemd.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phemd_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/phemd.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phemd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phemd’ version ‘1.0.1’
* 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
Unexported objects imported by ':::' calls:
  ‘VGAM:::VGAM.weights.function’ ‘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
createDataObj: no visible global function definition for
  ‘packageVersion’
getSampleHistsByCluster: no visible global function definition for
  ‘GetIdent’
Undefined global functions or variables:
  GetIdent packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
compareSamples           16.688  0.470  17.237
clusterIndividualSamples 16.328  0.637  17.125
plotCellYield            16.259  0.598  16.858
getSampleHistsByCluster  15.988  0.440  16.495
printClusterAssignments  15.784  0.473  16.260
getSampleCelltypeFreqs   15.835  0.418  16.352
generateGDM              15.706  0.508  16.213
groupSamples             15.541  0.411  15.989
plotGroupedSamplesDmap   15.408  0.430  15.840
getCellYield             15.020  0.452  15.504
plotHeatmaps             13.852  0.354  14.212
plotEmbeddings           13.435  0.446  14.430
Phemd-methods            12.896  0.272  13.208
orderCellsMonocle        12.215  0.389  12.604
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/phemd.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL phemd
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

Tests output

Example timings

name	user	system	elapsed
GDM	0.889	0.083	0.972
Phemd-methods	12.896	0.272	13.208
aggregateSamples	3.096	0.013	3.161
assignCellClusterNearestNode	0	0	0
batchIDs	0.618	0.002	0.620
bindSeuratObj	1.727	0.041	1.776
celltypeFreqs	0.673	0.001	0.674
clusterIndividualSamples	16.328	0.637	17.125
compareSamples	16.688	0.470	17.237
createDataObj	0.710	0.002	0.712
drawColnames45	0.001	0.001	0.001
embedCells	4.842	0.031	4.878
generateGDM	15.706	0.508	16.213
getArithmeticCentroids	0.000	0.000	0.001
getCellYield	15.020	0.452	15.504
getSampleCelltypeFreqs	15.835	0.418	16.352
getSampleHistsByCluster	15.988	0.440	16.495
getSampleSizes	0.001	0.000	0.000
groupSamples	15.541	0.411	15.989
identifyCentroids	0	0	0
monocleInfo	0.633	0.023	0.656
orderCellsMonocle	12.215	0.389	12.604
plotCellYield	16.259	0.598	16.858
plotEmbeddings	13.435	0.446	14.430
plotGroupedSamplesDmap	15.408	0.430	15.840
plotHeatmaps	13.852	0.354	14.212
pooledCells	0.644	0.006	0.649
printClusterAssignments	15.784	0.473	16.260
rawExpn	0.687	0.001	0.688
removeTinySamples	1.277	0.003	1.282
retrieveRefClusters	0.000	0.000	0.001
sNames	0.542	0.001	0.544
selectFeatures	3.697	0.009	3.706
selectMarkers	0.582	0.002	0.584
seuratInfo	0.632	0.002	0.634
subsampledBool	0.683	0.002	0.684
subsampledIdx	0.590	0.002	0.591

CHECK report for phemd on celaya2

Summary

Command output

Installation output

Tests output

Example timings