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This page was generated on 2023-02-27 02:34:43 -0000 (Mon, 27 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4259
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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 1880/2169HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.9.0  (landing page)
Yichen Wang
Snapshot Date: 2023-02-23 09:40:21 -0000 (Thu, 23 Feb 2023)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: master
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/library --timings singleCellTK_2.9.0.tar.gz
StartedAt: 2023-02-24 18:40:54 -0000 (Fri, 24 Feb 2023)
EndedAt: 2023-02-24 20:40:54 -0000 (Fri, 24 Feb 2023)
EllapsedTime: 7200.0 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/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) (2023-01-14 r83615)
* 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 22.04.1 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 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/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
MitoGenes0.0030.0000.003
SEG0.0010.0020.003
calcEffectSizes0.2320.0090.241
combineSCE1.9990.0672.067
computeZScore0.3390.0200.360
convertSCEToSeurat4.0130.2204.233
convertSeuratToSCE0.5300.0000.531
dedupRowNames0.0730.0000.073
detectCellOutlier6.3310.1716.515
diffAbundanceFET0.0490.0080.057
discreteColorPalette0.0010.0080.009
distinctColors0.0000.0040.003
downSampleCells0.9940.0281.022
downSampleDepth0.7540.0040.758
expData-ANY-character-method0.4120.0400.452
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.4830.0200.503
expData-set0.4880.0080.496
expData0.4240.0000.424
expDataNames-ANY-method0.4540.0070.461
expDataNames0.4030.0000.403
expDeleteDataTag0.0490.0000.050
expSetDataTag0.0320.0000.031
expTaggedData0.0330.0000.033
exportSCE0.030.000.03
exportSCEtoAnnData0.0800.0160.096
exportSCEtoFlatFile0.0900.0040.095
featureIndex0.0460.0000.046
generateSimulatedData0.0500.0040.054
getBiomarker0.0600.0000.061
getDEGTopTable1.1340.0401.180
getDiffAbundanceResults0.1250.0080.133
getEnrichRResult0.3690.0248.771
getFindMarkerTopTable4.4650.2684.733
getMSigDBTable0.0040.0000.004
getPathwayResultNames0.0290.0000.029
getSampleSummaryStatsTable0.4370.0080.447
getSoupX0.4990.0520.551
getTSCANResults2.4430.0642.517
getTopHVG1.0370.0721.112
importAnnData0.0020.0000.001
importBUStools0.4110.0080.421
importCellRanger1.4440.0511.500
importCellRangerV2Sample0.3520.0000.353
importCellRangerV3Sample0.5630.0280.591
importDropEst0.4050.0430.450