Package: phemd

Version: 1.0.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:phemd.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings phemd_1.0.1.tar.gz

StartedAt: 2019-10-16 03:53:34 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:00:43 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 429.0 seconds

RetCode: 0

Status:  OK

CheckDir: phemd.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:phemd.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings phemd_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/phemd.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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
plotGroupedSamplesDmap   11.920  0.024  11.957
groupSamples             11.440  0.020  11.460
getCellYield             11.303  0.003  11.364
getSampleCelltypeFreqs   11.269  0.032  11.303
printClusterAssignments  11.123  0.004  11.128
compareSamples           10.955  0.031  11.031
generateGDM              10.900  0.000  10.919
getSampleHistsByCluster  10.516  0.020  10.535
clusterIndividualSamples 10.033  0.076  10.113
Phemd-methods             9.615  0.088   9.705
plotHeatmaps              9.679  0.000   9.684
plotCellYield             9.382  0.008   9.389
orderCellsMonocle         8.332  0.004   8.336
plotEmbeddings            7.778  0.000   7.778
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/phemd.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL phemd
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

name	user	system	elapsed
GDM	0.485	0.024	0.509
Phemd-methods	9.615	0.088	9.705
aggregateSamples	2.464	0.002	2.492
assignCellClusterNearestNode	0	0	0
batchIDs	0.476	0.000	0.476
bindSeuratObj	1.068	0.004	1.073
celltypeFreqs	0.361	0.000	0.362
clusterIndividualSamples	10.033	0.076	10.113
compareSamples	10.955	0.031	11.031
createDataObj	0.558	0.004	0.562
drawColnames45	0	0	0
embedCells	4.252	0.000	4.264
generateGDM	10.900	0.000	10.919
getArithmeticCentroids	0	0	0
getCellYield	11.303	0.003	11.364
getSampleCelltypeFreqs	11.269	0.032	11.303
getSampleHistsByCluster	10.516	0.020	10.535
getSampleSizes	0.001	0.000	0.001
groupSamples	11.44	0.02	11.46
identifyCentroids	0	0	0
monocleInfo	0.619	0.000	0.619
orderCellsMonocle	8.332	0.004	8.336
plotCellYield	9.382	0.008	9.389
plotEmbeddings	7.778	0.000	7.778
plotGroupedSamplesDmap	11.920	0.024	11.957
plotHeatmaps	9.679	0.000	9.684
pooledCells	0.472	0.004	0.476
printClusterAssignments	11.123	0.004	11.128
rawExpn	0.323	0.000	0.323
removeTinySamples	0.845	0.000	0.845
retrieveRefClusters	0	0	0
sNames	0.344	0.000	0.343
selectFeatures	2.405	0.000	2.405
selectMarkers	0.531	0.000	0.533
seuratInfo	0.431	0.000	0.430
subsampledBool	0.421	0.000	0.421
subsampledIdx	0.326	0.000	0.325