Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:38 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the comapr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/comapr.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 382/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
comapr 1.3.0 (landing page) Ruqian Lyu
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: comapr |
Version: 1.3.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:comapr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings comapr_1.3.0.tar.gz |
StartedAt: 2023-02-28 00:06:32 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 00:15:24 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 531.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: comapr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:comapr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings comapr_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/comapr.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 ‘comapr/DESCRIPTION’ ... OK * this is package ‘comapr’ version ‘1.3.0’ * 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 ‘comapr’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘getStarted.Rmd’ using ‘UTF-8’... OK ‘single-sperm-co-analysis.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
comapr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL comapr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘comapr’ ... ** using staged installation ** R ** data ** 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 (comapr)
comapr.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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(comapr) > > test_check("comapr") [ FAIL 0 | WARN 3 | SKIP 0 | PASS 91 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 91 ] > > proc.time() user system elapsed 61.976 6.374 61.387
comapr.Rcheck/comapr-Ex.timings
name | user | system | elapsed | |
bootstrapDist | 4.600 | 0.204 | 4.804 | |
calGeneticDist | 0.182 | 0.251 | 0.206 | |
combineHapState | 2.193 | 0.336 | 2.533 | |
correctGT | 0.011 | 0.000 | 0.010 | |
countBinState | 0.441 | 0.068 | 0.912 | |
countCOs | 1.065 | 0.121 | 1.185 | |
countGT | 0.155 | 0.008 | 0.163 | |
filterGT | 0.119 | 0.012 | 0.132 | |
findDupSamples | 0.010 | 0.000 | 0.011 | |
getAFTracks | 1.583 | 0.096 | 1.680 | |
getCellAFTrack | 1.685 | 0.096 | 1.781 | |
getCellCORange | 0.78 | 0.04 | 0.82 | |
getCellDPTrack | 0.785 | 0.028 | 0.812 | |
getDistortedMarkers | 0.456 | 0.032 | 0.488 | |
getMeanDPTrack | 0.060 | 0.008 | 0.068 | |
getSNPDensityTrack | 0.063 | 0.000 | 0.063 | |
perCellChrQC | 0.058 | 0.004 | 0.061 | |
perSegChrQC | 0.085 | 0.008 | 0.092 | |
permuteDist | 0.028 | 0.004 | 0.032 | |
plotCount | 1.194 | 0.032 | 1.226 | |
plotGTFreq | 0.458 | 0.016 | 0.474 | |
plotGeneticDist | 0.442 | 0.012 | 0.453 | |
plotWholeGenome | 0.557 | 0.004 | 0.561 | |
readColMM | 0.011 | 0.000 | 0.011 | |
readHapState | 0.155 | 0.004 | 0.159 | |