Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-11 12:04:56 -0400 (Mon, 11 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4323 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4136 |
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 |
To the developers/maintainers of the conclus package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/conclus.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. |
Package 382/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
conclus 1.2.4 (landing page) Ilyess Rachedi
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: conclus |
Version: 1.2.4 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:conclus.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings conclus_1.2.4.tar.gz |
StartedAt: 2022-04-10 06:46:32 -0400 (Sun, 10 Apr 2022) |
EndedAt: 2022-04-10 06:57:15 -0400 (Sun, 10 Apr 2022) |
EllapsedTime: 642.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: conclus.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:conclus.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings conclus_1.2.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/conclus.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘conclus/DESCRIPTION’ ... OK * this is package ‘conclus’ version ‘1.2.4’ * 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 ‘conclus’ 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed retrieveFromGEO 10.071 0.936 11.010 runCONCLUS 9.807 0.801 83.770 retrieveGenesInfo-scRNAseq 4.960 0.449 62.876 addClustering-scRNAseq 4.775 0.317 46.825 normaliseCountMatrix-scRNAseq 2.960 0.220 14.826 testClustering-scRNAseq 0.666 0.020 14.911 runDBSCAN-scRNAseq 0.269 0.035 13.730 clusterCellsInternal-scRNAseq 0.240 0.049 13.364 generateTSNECoordinates-scRNAseq 0.195 0.028 18.301 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.R’ OK * 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: OK
conclus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL conclus ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘conclus’ ... ** using staged installation ** R ** 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 (conclus)
conclus.Rcheck/tests/test-all.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("testthat") > library("conclus") Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > test_check("conclus") Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 The following matrix shows how many times a number of clusters 'k' has been found among the dbscan solutions : 1 2 3 4 Number of clusters k : 1 4 2 3 Count : 58 12 8 6 Statistics about number of clusters 'k' among dbscan solutions: Min. 1st Qu. Median Mean 3rd Qu. Max. 1.000 1.000 1.000 1.667 2.000 4.000 Suggested clusters number to use in clusterCellsInternal() : clusterNumber=1.[ FAIL 0 | WARN 0 | SKIP 0 | PASS 278 ] > > proc.time() user system elapsed 30.439 2.143 104.661
conclus.Rcheck/conclus-Ex.timings
name | user | system | elapsed | |
addClustering-scRNAseq | 4.775 | 0.317 | 46.825 | |
calculateClustersSimilarity-scRNAseq | 0.040 | 0.012 | 0.052 | |
clusterCellsInternal-scRNAseq | 0.240 | 0.049 | 13.364 | |
conclusCacheClear | 0.000 | 0.000 | 0.001 | |
constructors | 0.014 | 0.000 | 0.015 | |
exportResults-scRNAseq | 0.109 | 0.008 | 0.117 | |
generateTSNECoordinates-scRNAseq | 0.195 | 0.028 | 18.301 | |
getters | 0.012 | 0.000 | 0.012 | |
loadDataOrMatrix | 0.009 | 0.005 | 0.013 | |
normaliseCountMatrix-scRNAseq | 2.960 | 0.220 | 14.826 | |
plotCellHeatmap | 0.167 | 0.020 | 0.187 | |
plotCellSimilarity-scRNAseq | 0.081 | 0.000 | 0.081 | |
plotClusteredTSNE-scRNAseq | 0.381 | 0.007 | 0.389 | |
plotClustersSimilarity | 0.048 | 0.008 | 0.056 | |
plotGeneExpression-scRNAseq | 0.176 | 0.016 | 0.192 | |
rankGenes-scRNAseq | 0.173 | 0.000 | 0.172 | |
retrieveFromGEO | 10.071 | 0.936 | 11.010 | |
retrieveGenesInfo-scRNAseq | 4.960 | 0.449 | 62.876 | |
retrieveTableClustersCells-scRNAseq | 0.019 | 0.000 | 0.020 | |
retrieveTopClustersMarkers-scRNAseq | 0.023 | 0.000 | 0.023 | |
runCONCLUS | 9.807 | 0.801 | 83.770 | |
runDBSCAN-scRNAseq | 0.269 | 0.035 | 13.730 | |
setters | 0.017 | 0.006 | 0.022 | |
testClustering-scRNAseq | 0.666 | 0.020 | 14.911 | |