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This page was generated on 2023-04-12 11:05:19 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for singleCellTK on nebbiolo2


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 1889/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.8.0  (landing page)
Yichen Wang
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: RELEASE_3_16
git_last_commit: 711d2ed
git_last_commit_date: 2022-11-01 11:17:41 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    TIMEOUT  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: singleCellTK
Version: 2.8.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings singleCellTK_2.8.0.tar.gz
StartedAt: 2023-04-11 00:04:29 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 00:44:30 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 2401.3 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: singleCellTK.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings singleCellTK_2.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/singleCellTK.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.8.0’
* 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 ‘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 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-3.16-bioc/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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
MitoGenes0.0040.0000.003
SEG0.0030.0000.003
calcEffectSizes0.160.000.16
combineSCE1.7620.0631.826
computeZScore0.3250.0610.384
convertSCEToSeurat3.7240.7404.464
convertSeuratToSCE0.4570.0000.457
dedupRowNames0.0510.0040.054
detectCellOutlier6.2940.2556.550
diffAbundanceFET0.0470.0040.051
discreteColorPalette0.0080.0000.008
distinctColors0.0020.0000.003
downSampleCells0.6970.0360.733
downSampleDepth0.5740.0000.574
expData-ANY-character-method0.3460.0070.354
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.3770.0280.405
expData-set0.3750.0000.375
expData0.3320.0040.336
expDataNames-ANY-method0.320.000.32
expDataNames0.3130.0030.317
expDeleteDataTag0.0310.0090.039
expSetDataTag0.0250.0000.025
expTaggedData0.0260.0000.026
exportSCE0.0230.0000.023
exportSCEtoAnnData0.0980.0000.098
exportSCEtoFlatFile0.0950.0000.095
featureIndex0.0370.0000.037
generateSimulatedData0.0300.0150.046
getBiomarker0.0530.0000.053
getDEGTopTable0.9200.0280.949
getDiffAbundanceResults0.040.000.04