Multiple platform build/check report for BioC 3.11 - 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/phemd.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.3.0’
* 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
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 ... OK
* 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 (user + system) or elapsed time > 5s
                           user system elapsed
getSampleCelltypeFreqs   16.655  0.402  17.068
getCellYield             16.598  0.387  16.989
compareSamples           16.540  0.395  16.946
clusterIndividualSamples 16.357  0.506  16.875
groupSamples             16.190  0.304  16.503
plotGroupedSamplesDmap   16.045  0.402  16.454
plotCellYield            16.060  0.367  16.429
generateGDM              15.967  0.359  16.331
getSampleHistsByCluster  15.864  0.398  16.269
printClusterAssignments  15.725  0.467  16.199
Phemd-methods            15.935  0.053  15.992
plotEmbeddings           15.258  0.351  15.614
plotHeatmaps             14.765  0.247  15.034
orderCellsMonocle        14.637  0.346  14.986
embedCells                5.256  0.046   5.303
selectFeatures            4.983  0.022   5.005
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/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	1.002	0.082	1.084
Phemd-methods	15.935	0.053	15.992
aggregateSamples	3.358	0.014	3.374
assignCellClusterNearestNode	0.000	0.001	0.000
batchIDs	0.672	0.002	0.674
bindSeuratObj	2.024	0.042	2.074
celltypeFreqs	0.688	0.002	0.690
clusterIndividualSamples	16.357	0.506	16.875
compareSamples	16.540	0.395	16.946
createDataObj	0.647	0.002	0.650
drawColnames45	0.000	0.000	0.001
embedCells	5.256	0.046	5.303
generateGDM	15.967	0.359	16.331
getArithmeticCentroids	0.000	0.001	0.001
getCellYield	16.598	0.387	16.989
getSampleCelltypeFreqs	16.655	0.402	17.068
getSampleHistsByCluster	15.864	0.398	16.269
getSampleSizes	0	0	0
groupSamples	16.190	0.304	16.503
identifyCentroids	0	0	0
monocleInfo	0.698	0.002	0.699
orderCellsMonocle	14.637	0.346	14.986
phateInfo	0.630	0.002	0.632
plotCellYield	16.060	0.367	16.429
plotEmbeddings	15.258	0.351	15.614
plotGroupedSamplesDmap	16.045	0.402	16.454
plotHeatmaps	14.765	0.247	15.034
pooledCells	0.785	0.051	0.837
printClusterAssignments	15.725	0.467	16.199
rawExpn	0.722	0.021	0.742
removeTinySamples	1.295	0.003	1.298
retrieveRefClusters	0.001	0.000	0.001
sNames	0.618	0.001	0.619
selectFeatures	4.983	0.022	5.005
selectMarkers	0.722	0.002	0.724
seuratInfo	0.673	0.002	0.675
subsampledBool	0.678	0.002	0.679
subsampledIdx	0.697	0.002	0.699

CHECK report for phemd on celaya2

Summary

Command output

Installation output

Tests output

Example timings