Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:43 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1479/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
packFinder 1.19.0 (landing page) Jack Gisby
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the packFinder package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/packFinder.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: packFinder |
Version: 1.19.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:packFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings packFinder_1.19.0.tar.gz |
StartedAt: 2024-12-23 22:07:48 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:08:58 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 70.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: packFinder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:packFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings packFinder_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/packFinder.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘packFinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘packFinder’ version ‘1.19.0’ * 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 ‘packFinder’ 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 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) readBlast.Rd:100: Lost braces 100 | code{\link{blastAnalysis}}, code{\link{blastAnnotate}}, | ^ checkRd: (-1) readBlast.Rd:100: Lost braces 100 | code{\link{blastAnalysis}}, code{\link{blastAnnotate}}, | ^ checkRd: (-1) readBlast.Rd:101: Lost braces 101 | code{\link{packAlign}}, | ^ checkRd: (-1) readBlast.Rd:102: Lost braces 102 | code{\link{readUc}}, code{\link{packClust}} | ^ checkRd: (-1) readBlast.Rd:102: Lost braces 102 | code{\link{readUc}}, code{\link{packClust}} | ^ checkRd: (-1) readUc.Rd:98: Lost braces 98 | code{\link{tirClust}}, code{\link{packAlign}}, | ^ checkRd: (-1) readUc.Rd:98: Lost braces 98 | code{\link{tirClust}}, code{\link{packAlign}}, | ^ checkRd: (-1) readUc.Rd:99: Lost braces 99 | code{\link{readBlast}}, code{\link{packClust}} | ^ checkRd: (-1) readUc.Rd:99: Lost braces 99 | code{\link{readBlast}}, code{\link{packClust}} | ^ checkRd: (-1) tirClust.Rd:86: Lost braces 86 | code{\link{packClust}}, code{\link{packAlign}}, | ^ checkRd: (-1) tirClust.Rd:86: Lost braces 86 | code{\link{packClust}}, code{\link{packAlign}}, | ^ * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/packFinder.Rcheck/00check.log’ for details.
packFinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL packFinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘packFinder’ ... ** 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 (packFinder)
packFinder.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(packFinder) > > test_check("packFinder") DNAStringSet object of length 1: width seq names [1] 3800001 GGTGTTAAAAGGTTCTTGAGTG...TAGTCAGGTTTCTAACAGAAAA Chr3 [1] "File successfully written to tempTestOutput/packMatches.csv" [1] "FASTA written to tempTestOutput/packMatches.fasta" 2024-12-23 22:08:32.928 R[94602:738808795] XType: com.apple.fonts is not accessible. 2024-12-23 22:08:32.929 R[94602:738808795] XType: XTFontStaticRegistry is enabled. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ] > > proc.time() user system elapsed 5.977 0.359 6.356
packFinder.Rcheck/packFinder-Ex.timings
name | user | system | elapsed | |
arabidopsisThalianaRefseq | 4.162 | 0.199 | 4.383 | |
blastAnalysis | 0 | 0 | 0 | |
blastAnnotate | 0.005 | 0.002 | 0.007 | |
collapseSeqs | 0.494 | 0.008 | 0.506 | |
filterWildcards | 0.090 | 0.006 | 0.098 | |
getPackSeqs | 1.053 | 0.014 | 1.075 | |
getPacksFromCsv | 0.003 | 0.002 | 0.005 | |
getPacksFromFasta | 0.073 | 0.006 | 0.080 | |
getPacksFromGRanges | 0.061 | 0.001 | 0.063 | |
getTsds | 0.091 | 0.006 | 0.099 | |
identifyPotentialPackElements | 0.461 | 0.008 | 0.471 | |
identifyTirMatches | 0.079 | 0.004 | 0.083 | |
makeBlastDb | 0 | 0 | 0 | |
packAlign | 0.060 | 0.004 | 0.066 | |
packBlast | 0 | 0 | 0 | |
packClust | 0.062 | 0.005 | 0.068 | |
packMatches | 0.913 | 0.010 | 0.928 | |
packSearch | 0.936 | 0.008 | 0.950 | |
packsToCsv | 0.003 | 0.002 | 0.005 | |
packsToFasta | 0.084 | 0.007 | 0.092 | |
packsToGRanges | 0.015 | 0.001 | 0.017 | |
readBlast | 0.004 | 0.001 | 0.006 | |
readUc | 0.004 | 0.001 | 0.005 | |
tirClust | 0.500 | 0.025 | 0.528 | |