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This page was generated on 2021-10-15 15:05:48 -0400 (Fri, 15 Oct 2021).

CHECK results for phemd on nebbiolo1

To the developers/maintainers of the phemd package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/phemd.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1379/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phemd 1.8.0  (landing page)
William S Chen
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/phemd
git_branch: RELEASE_3_13
git_last_commit: 6c77cb3
git_last_commit_date: 2021-05-19 12:40:57 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: phemd
Version: 1.8.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:phemd.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings phemd_1.8.0.tar.gz
StartedAt: 2021-10-14 11:00:42 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:06:44 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 361.7 seconds
RetCode: 0
Status:   OK  
CheckDir: phemd.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:phemd.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings phemd_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/phemd.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.8.0’
* 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 LazyData ... 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
printClusterAssignments  8.756  1.157   9.913
compareSamples           9.258  0.164   9.423
clusterIndividualSamples 8.746  0.199   8.947
plotGroupedSamplesDmap   8.349  0.136   8.486
getCellYield             8.209  0.129   8.337
getSampleHistsByCluster  8.035  0.131   8.166
Phemd-methods            7.679  0.115   7.795
plotCellYield            7.647  0.120   7.768
groupSamples             7.384  0.156   7.541
plotEmbeddings           7.309  0.140   7.449
getSampleCelltypeFreqs   7.132  0.100   7.231
generateGDM              7.063  0.116   7.180
orderCellsMonocle        6.890  0.163   7.054
plotHeatmaps             6.462  0.128   6.589
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/phemd.Rcheck/00check.log’
for details.



Installation output

phemd.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL phemd
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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)

Tests output


Example timings

phemd.Rcheck/phemd-Ex.timings

nameusersystemelapsed
GDM1.3300.0131.342
Phemd-methods7.6790.1157.795
aggregateSamples1.6100.0121.621
assignCellClusterNearestNode000
batchIDs0.3410.0000.342
bindSeuratObj1.3360.0411.376
celltypeFreqs0.4160.0120.428
clusterIndividualSamples8.7460.1998.947
compareSamples9.2580.1649.423
createDataObj0.3280.0110.339
drawColnames450.0010.0010.000
embedCells2.7850.0272.812
generateGDM7.0630.1167.180
getArithmeticCentroids0.0010.0000.000
getCellYield8.2090.1298.337
getSampleCelltypeFreqs7.1320.1007.231
getSampleHistsByCluster8.0350.1318.166
getSampleSizes0.0000.0000.001
groupSamples7.3840.1567.541
identifyCentroids000
monocleInfo0.3200.0010.320
orderCellsMonocle6.8900.1637.054
phateInfo0.3110.0000.312
plotCellYield7.6470.1207.768
plotEmbeddings7.3090.1407.449
plotGroupedSamplesDmap8.3490.1368.486
plotHeatmaps6.4620.1286.589
pooledCells0.3600.0200.381
printClusterAssignments8.7561.1579.913
rawExpn0.3160.0000.316
removeTinySamples0.6500.0000.649
retrieveRefClusters000
sNames0.3270.0000.326
selectFeatures1.9510.0201.971
selectMarkers0.3240.0000.323
seuratInfo0.3740.0000.374
subsampledBool0.3600.0000.361
subsampledIdx0.2980.0030.301