Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-02 12:04 -0500 (Mon, 02 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4739 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4482 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4510 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4462 |
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 1839/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sangerseqR 1.42.0 (landing page) Jonathon Hill
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the sangerseqR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sangerseqR.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: sangerseqR |
Version: 1.42.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sangerseqR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings sangerseqR_1.42.0.tar.gz |
StartedAt: 2024-11-29 05:58:43 -0500 (Fri, 29 Nov 2024) |
EndedAt: 2024-11-29 06:04:24 -0500 (Fri, 29 Nov 2024) |
EllapsedTime: 340.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sangerseqR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sangerseqR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings sangerseqR_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sangerseqR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘sangerseqR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sangerseqR’ version ‘1.42.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘sangerseqR’ 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 ... 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 setAllelePhase 9.340 0.120 9.459 chromatogram 8.629 0.065 8.695 makeBaseCalls 8.370 0.070 8.441 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: OK
sangerseqR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL sangerseqR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘sangerseqR’ ... ** 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 (sangerseqR)
sangerseqR.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. > BiocGenerics:::testPackage("sangerseqR") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'pwalign' The following objects are masked from 'package:Biostrings': PairwiseAlignments, PairwiseAlignmentsSingleSubject, aligned, alignedPattern, alignedSubject, compareStrings, deletion, errorSubstitutionMatrices, indel, insertion, mismatchSummary, mismatchTable, nedit, nindel, nucleotideSubstitutionMatrix, pairwiseAlignment, pid, qualitySubstitutionMatrices, stringDist, unaligned, writePairwiseAlignments RUNIT TEST PROTOCOL -- Fri Nov 29 06:04:02 2024 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : sangerseqR RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 3.031 0.167 3.189
sangerseqR.Rcheck/sangerseqR-Ex.timings
name | user | system | elapsed | |
PolyPeakParser | 0 | 0 | 0 | |
abif-class | 0.159 | 0.006 | 0.166 | |
chromatogram | 8.629 | 0.065 | 8.695 | |
makeBaseCalls | 8.370 | 0.070 | 8.441 | |
read.abif | 0.104 | 0.002 | 0.106 | |
read.scf | 0.109 | 0.000 | 0.109 | |
readsangerseq | 0.169 | 0.002 | 0.171 | |
sangerseq-class | 0.170 | 0.001 | 0.171 | |
sangerseqAccessors | 0.066 | 0.001 | 0.068 | |
scf-class | 0.102 | 0.000 | 0.102 | |
setAllelePhase | 9.340 | 0.120 | 9.459 | |