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This page was generated on 2023-03-27 05:50:44 -0000 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6083
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CHECK results for singleCellTK on kunpeng1


To the developers/maintainers of the singleCellTK package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singleCellTK.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1906/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.9.0  (landing page)
Yichen Wang
Snapshot Date: 2023-03-24 01:40:07 -0000 (Fri, 24 Mar 2023)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: devel
git_last_commit: 4468720
git_last_commit_date: 2022-11-01 15:17:41 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    TIMEOUT  

Summary

Package: singleCellTK
Version: 2.9.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings singleCellTK_2.9.0.tar.gz
StartedAt: 2023-03-25 12:42:18 -0000 (Sat, 25 Mar 2023)
EndedAt: 2023-03-25 13:22:18 -0000 (Sat, 25 Mar 2023)
EllapsedTime: 2400.1 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: singleCellTK.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings singleCellTK_2.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/singleCellTK.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.9.0’
* 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 ‘singleCellTK’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    shiny     2.9Mb
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...

Installation output

singleCellTK.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘singleCellTK’ ...
** using staged installation
** R
** data
** exec
** inst
** 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 (singleCellTK)

Tests output


Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0030.0000.004
SEG0.0030.0000.003
calcEffectSizes0.2450.0160.262
combineSCE1.8860.0201.907
computeZScore0.3020.0200.322
convertSCEToSeurat3.7290.1513.882
convertSeuratToSCE0.5630.0110.576
dedupRowNames0.0720.0000.071
detectCellOutlier6.2200.0806.312
diffAbundanceFET0.0550.0000.055
discreteColorPalette0.0090.0000.009
distinctColors0.0030.0000.003
downSampleCells0.8690.0960.965
downSampleDepth0.7080.0040.712
expData-ANY-character-method0.3910.0040.395
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.4420.0040.446
expData-set0.4400.0120.452
expData0.4250.0040.429
expDataNames-ANY-method0.3880.0000.389
expDataNames0.3900.0040.394
expDeleteDataTag0.0440.0000.044
expSetDataTag0.0330.0020.034
expTaggedData0.0340.0020.036
exportSCE0.0350.0000.036
exportSCEtoAnnData0.0920.0040.095
exportSCEtoFlatFile0.0870.0080.095
featureIndex0.0450.0000.045
generateSimulatedData0.0520.0000.052
getBiomarker0.0580.0000.058
getDEGTopTable1.0620.0441.108
getDiffAbundanceResults0.0440.0000.043
getEnrichRResult0.5190.1288.607
getFindMarkerTopTable4.2150.3964.611
getMSigDBTable0.0050.0000.005
getPathwayResultNames0.0260.0040.030
getSampleSummaryStatsTable0.4630.0320.496
getSoupX0.4370.0440.482
getTSCANResults2.4370.0882.530
getTopHVG1.0170.0521.071
importAnnData0.0010.0000.001
importBUStools0.3470.0120.360
importCellRanger1.4060.0481.457
importCellRangerV2Sample0.3470.0120.359
importCellRangerV3Sample0.5740.0200.594
importDropEst0.4180.0160.435