| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:41:17 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 | ||||
| Package 1971/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| singleCellTK 2.12.0 (landing page) Yichen Wang
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
To the developers/maintainers of the singleCellTK package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: singleCellTK |
| Version: 2.12.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings singleCellTK_2.12.0.tar.gz |
| StartedAt: 2023-11-02 14:26:36 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 15:06:37 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 2400.4 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: singleCellTK.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings singleCellTK_2.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/singleCellTK.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.12.0’
* 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 6.9Mb
sub-directories of 1Mb or more:
extdata 1.6Mb
shiny 3.0Mb
* 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 ...
singleCellTK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL singleCellTK ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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)
singleCellTK.Rcheck/singleCellTK-Ex.timings
| name | user | system | elapsed | |
| MitoGenes | 0.003 | 0.000 | 0.003 | |
| SEG | 0.001 | 0.002 | 0.003 | |
| calcEffectSizes | 0.279 | 0.004 | 0.284 | |
| combineSCE | 2.112 | 0.111 | 2.228 | |
| computeZScore | 1.121 | 0.092 | 1.217 | |
| convertSCEToSeurat | 3.201 | 0.084 | 3.292 | |
| convertSeuratToSCE | 0.544 | 0.000 | 0.545 | |
| dedupRowNames | 0.104 | 0.008 | 0.113 | |
| detectCellOutlier | 7.691 | 0.200 | 7.941 | |
| diffAbundanceFET | 0.056 | 0.008 | 0.065 | |
| discreteColorPalette | 0.004 | 0.004 | 0.008 | |
| distinctColors | 0.003 | 0.000 | 0.002 | |
| downSampleCells | 0.965 | 0.067 | 1.036 | |
| downSampleDepth | 0.813 | 0.011 | 0.827 | |
| expData-ANY-character-method | 0.439 | 0.004 | 0.444 | |
| expData-set-ANY-character-CharacterOrNullOrMissing-logical-method | 0.482 | 0.016 | 0.499 | |
| expData-set | 0.457 | 0.032 | 0.489 | |
| expData | 0.420 | 0.024 | 0.444 | |
| expDataNames-ANY-method | 0.446 | 0.008 | 0.455 | |
| expDataNames | 0.412 | 0.004 | 0.417 | |
| expDeleteDataTag | 0.040 | 0.003 | 0.043 | |
| expSetDataTag | 0.03 | 0.00 | 0.03 | |
| expTaggedData | 0.031 | 0.000 | 0.031 | |
| exportSCE | 0.028 | 0.000 | 0.027 | |
| exportSCEtoAnnData | 0.089 | 0.000 | 0.090 | |
| exportSCEtoFlatFile | 0.072 | 0.020 | 0.091 | |
| featureIndex | 0.048 | 0.000 | 0.048 | |
| generateSimulatedData | 0.062 | 0.004 | 0.066 | |
| getBiomarker | 0.073 | 0.000 | 0.073 | |
| getDEGTopTable | 1.105 | 0.023 | 1.133 | |
| getDiffAbundanceResults | 0.060 | 0.004 | 0.064 | |
| getEnrichRResult | 0.431 | 0.048 | 18.134 | |
| getFindMarkerTopTable | 4.781 | 0.087 | 4.895 | |
| getMSigDBTable | 0.004 | 0.000 | 0.004 | |
| getPathwayResultNames | 0.029 | 0.000 | 0.029 | |
| getSampleSummaryStatsTable | 0.435 | 0.004 | 0.443 | |
| getSoupX | 0.001 | 0.000 | 0.000 | |
| getTSCANResults | 2.601 | 0.052 | 2.670 | |
| getTopHVG | 1.199 | 0.012 | 1.220 | |
| importAnnData | 0.002 | 0.000 | 0.001 | |
| importBUStools | 0.386 | 0.000 | 0.388 | |
| importCellRanger | 1.547 | 0.036 | 1.595 | |
| importCellRangerV2Sample | 0.361 | 0.007 | 0.372 | |
| importCellRangerV3Sample | 0.598 | 0.012 | 0.614 | |
| importDropEst | 0.441 | 0.004 | 0.448 | |