Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
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 411/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
comapr 1.8.0 (landing page) Ruqian Lyu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the comapr package: - 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 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. |
Package: comapr |
Version: 1.8.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:comapr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings comapr_1.8.0.tar.gz |
StartedAt: 2024-06-12 21:51:08 -0400 (Wed, 12 Jun 2024) |
EndedAt: 2024-06-12 21:58:38 -0400 (Wed, 12 Jun 2024) |
EllapsedTime: 450.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: comapr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:comapr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings comapr_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/comapr.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘comapr/DESCRIPTION’ ... OK * this is package ‘comapr’ version ‘1.8.0’ * 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 ‘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 code 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 ... NOTE checkRd: (-1) perCellChrQC.Rd:22: Lost braces; missing escapes or markup? 22 | \item{path, }{the path to the files, with name patterns *{chrom}_vi.mtx, | ^ checkRd: (-1) perCellChrQC.Rd:23: Lost braces; missing escapes or markup? 23 | *{chrom}_viSegInfo.txt, end with slash} | ^ checkRd: (-1) perSegChrQC.Rd:21: Lost braces; missing escapes or markup? 21 | \item{path, }{the path to the files, with name patterns *{chrom}_vi.mtx, | ^ checkRd: (-1) perSegChrQC.Rd:22: Lost braces; missing escapes or markup? 22 | *{chrom}_viSegInfo.txt, end with slash} | ^ checkRd: (-1) readHapState.Rd:28: Lost braces; missing escapes or markup? 28 | \item{path, }{the path to the files, with name patterns *{chrom}_vi.mtx, | ^ checkRd: (-1) readHapState.Rd:29: Lost braces; missing escapes or markup? 29 | *{chrom}_viSegInfo.txt, end with slash} | ^ * 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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/comapr.Rcheck/00check.log’ for details.
comapr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL comapr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 41.119 5.144 41.852
comapr.Rcheck/comapr-Ex.timings
name | user | system | elapsed | |
bootstrapDist | 4.359 | 0.312 | 4.672 | |
calGeneticDist | 0.126 | 0.004 | 0.130 | |
combineHapState | 1.578 | 0.204 | 1.783 | |
correctGT | 0.004 | 0.004 | 0.008 | |
countBinState | 0.346 | 0.060 | 0.776 | |
countCOs | 0.552 | 0.080 | 0.632 | |
countGT | 0.118 | 0.004 | 0.122 | |
filterGT | 0.078 | 0.000 | 0.078 | |
findDupSamples | 0.007 | 0.000 | 0.008 | |
getAFTracks | 1.071 | 0.088 | 1.160 | |
getCellAFTrack | 0.901 | 0.059 | 0.959 | |
getCellCORange | 0.356 | 0.032 | 0.388 | |
getCellDPTrack | 0.400 | 0.024 | 0.424 | |
getDistortedMarkers | 0.288 | 0.032 | 0.319 | |
getMeanDPTrack | 0.044 | 0.008 | 0.051 | |
getSNPDensityTrack | 0.046 | 0.000 | 0.045 | |
perCellChrQC | 0.041 | 0.008 | 0.048 | |
perSegChrQC | 0.049 | 0.012 | 0.062 | |
permuteDist | 0.024 | 0.004 | 0.029 | |
plotCount | 0.664 | 0.076 | 0.740 | |
plotGTFreq | 0.389 | 0.012 | 0.401 | |
plotGeneticDist | 0.257 | 0.004 | 0.262 | |
plotWholeGenome | 0.334 | 0.020 | 0.355 | |
readColMM | 0.006 | 0.004 | 0.010 | |
readHapState | 0.079 | 0.024 | 0.102 | |