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 02:50:18 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:58:23 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 484.8 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) (2018-11-27 r75683)
* 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
generateGDM              14.164  0.256  14.651
getCellYield             13.820  0.219  14.159
clusterIndividualSamples 13.439  0.257  13.813
plotEmbeddings           13.356  0.199  13.709
getSampleHistsByCluster  13.337  0.200  13.583
printClusterAssignments  13.222  0.207  13.496
plotCellYield            13.186  0.202  13.492
compareSamples           13.054  0.203  13.338
getSampleCelltypeFreqs   13.043  0.210  13.334
groupSamples             12.706  0.233  12.977
plotGroupedSamplesDmap   12.168  0.213  12.462
Phemd-methods            11.766  0.227  12.070
plotHeatmaps             11.525  0.216  11.798
orderCellsMonocle        10.821  0.221  11.104
* 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’ ...
** 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
* DONE (phemd)

name	user	system	elapsed
GDM	0.793	0.034	0.829
Phemd-methods	11.766	0.227	12.070
aggregateSamples	2.309	0.007	2.319
assignCellClusterNearestNode	0	0	0
batchIDs	0.507	0.002	0.511
bindSeuratObj	3.800	0.025	3.869
celltypeFreqs	0.588	0.006	0.614
clusterIndividualSamples	13.439	0.257	13.813
compareSamples	13.054	0.203	13.338
createDataObj	0.568	0.002	0.570
drawColnames45	0.001	0.000	0.000
embedCells	3.997	0.027	4.039
generateGDM	14.164	0.256	14.651
getArithmeticCentroids	0.001	0.000	0.001
getCellYield	13.820	0.219	14.159
getSampleCelltypeFreqs	13.043	0.210	13.334
getSampleHistsByCluster	13.337	0.200	13.583
getSampleSizes	0.001	0.000	0.000
groupSamples	12.706	0.233	12.977
identifyCentroids	0	0	0
monocleInfo	0.463	0.001	0.465
orderCellsMonocle	10.821	0.221	11.104
plotCellYield	13.186	0.202	13.492
plotEmbeddings	13.356	0.199	13.709
plotGroupedSamplesDmap	12.168	0.213	12.462
plotHeatmaps	11.525	0.216	11.798
pooledCells	0.525	0.001	0.531
printClusterAssignments	13.222	0.207	13.496
rawExpn	0.530	0.001	0.531
removeTinySamples	0.788	0.002	0.791
retrieveRefClusters	0.000	0.000	0.001
sNames	0.446	0.001	0.448
selectFeatures	2.908	0.007	2.927
selectMarkers	0.454	0.001	0.456
seuratInfo	0.450	0.001	0.452
subsampledBool	0.416	0.001	0.417
subsampledIdx	0.408	0.001	0.410