Package: phemd

Version: 0.99.37

Command: /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_0.99.37.tar.gz

StartedAt: 2019-04-09 04:21:02 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:30:47 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 584.8 seconds

RetCode: 0

Status:  OK

CheckDir: phemd.Rcheck

Warnings: 0

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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_0.99.37.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/phemd.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘0.99.37’
* 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 or elapsed time > 5s
                           user system elapsed
getSampleCelltypeFreqs   16.317  0.528  16.906
groupSamples             15.550  0.349  15.927
compareSamples           14.792  0.454  15.279
printClusterAssignments  14.808  0.425  15.235
getSampleHistsByCluster  14.574  0.431  15.050
plotGroupedSamplesDmap   14.379  0.610  14.989
getCellYield             14.319  0.503  14.884
clusterIndividualSamples 14.300  0.491  14.824
generateGDM              14.245  0.412  14.698
plotCellYield            14.095  0.437  14.534
Phemd-methods            13.660  0.309  13.969
orderCellsMonocle        12.891  0.390  13.335
plotEmbeddings           12.112  0.344  12.456
plotHeatmaps             11.966  0.391  12.405
* 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-3.9-bioc/meat/phemd.Rcheck/00check.log’
for details.

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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)

name	user	system	elapsed
GDM	0.748	0.057	0.805
Phemd-methods	13.660	0.309	13.969
aggregateSamples	2.868	0.010	2.878
assignCellClusterNearestNode	0.001	0.000	0.000
batchIDs	0.684	0.001	0.686
bindSeuratObj	4.682	0.068	4.755
celltypeFreqs	0.666	0.022	0.688
clusterIndividualSamples	14.300	0.491	14.824
compareSamples	14.792	0.454	15.279
createDataObj	0.674	0.018	0.692
drawColnames45	0.000	0.001	0.000
embedCells	4.164	0.030	4.222
generateGDM	14.245	0.412	14.698
getArithmeticCentroids	0	0	0
getCellYield	14.319	0.503	14.884
getSampleCelltypeFreqs	16.317	0.528	16.906
getSampleHistsByCluster	14.574	0.431	15.050
getSampleSizes	0.000	0.001	0.001
groupSamples	15.550	0.349	15.927
identifyCentroids	0	0	0
monocleInfo	0.756	0.010	0.766
orderCellsMonocle	12.891	0.390	13.335
plotCellYield	14.095	0.437	14.534
plotEmbeddings	12.112	0.344	12.456
plotGroupedSamplesDmap	14.379	0.610	14.989
plotHeatmaps	11.966	0.391	12.405
pooledCells	0.667	0.007	0.672
printClusterAssignments	14.808	0.425	15.235
rawExpn	0.491	0.026	0.517
removeTinySamples	1.047	0.002	1.049
retrieveRefClusters	0.000	0.001	0.000
sNames	0.725	0.001	0.726
selectFeatures	3.502	0.010	3.512
selectMarkers	0.539	0.000	0.540
seuratInfo	0.561	0.001	0.561
subsampledBool	0.721	0.036	0.757
subsampledIdx	0.522	0.003	0.524