Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -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 810/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomeInfoDb 1.43.2 (landing page) Hervé Pagès
| 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 GenomeInfoDb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomeInfoDb.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: GenomeInfoDb |
Version: 1.43.2 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomeInfoDb_1.43.2.tar.gz |
StartedAt: 2024-12-24 07:01:04 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 07:32:21 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 1876.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomeInfoDb.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomeInfoDb_1.43.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomeInfoDb.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK * this is package ‘GenomeInfoDb’ version ‘1.43.2’ * 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 ‘GenomeInfoDb’ can be installed ... OK * checking installed package size ... INFO installed size is 5.3Mb sub-directories of 1Mb or more: extdata 3.7Mb * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘utils:::.roman2numeric’ See the note in ?`:::` about the use of this operator. * 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 loadTaxonomyDb 10.812 0.180 11.016 GenomeDescription-class 9.924 0.295 10.251 seqinfo 5.380 0.205 5.690 seqlevelsStyle 4.302 0.100 26.382 getChromInfoFromEnsembl 1.496 1.064 108.794 getChromInfoFromNCBI 0.382 0.028 22.791 NCBI-utils 0.241 0.048 18.733 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.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 ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomeInfoDb.Rcheck/00check.log’ for details.
GenomeInfoDb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GenomeInfoDb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘GenomeInfoDb’ ... ** 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 (GenomeInfoDb)
GenomeInfoDb.Rcheck/tests/run_unitTests.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package") Loading required package: GenomeInfoDb Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges [1] TRUE > GenomeInfoDb:::.test() RUNIT TEST PROTOCOL -- Tue Dec 24 07:32:16 2024 *********************************************** Number of test functions: 21 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomeInfoDb RUnit Tests - 21 test functions, 0 errors, 0 failures Number of test functions: 21 Number of errors: 0 Number of failures: 0 There were 50 or more warnings (use warnings() to see the first 50) > > proc.time() user system elapsed 501.619 7.491 1584.429
GenomeInfoDb.Rcheck/GenomeInfoDb-Ex.timings
name | user | system | elapsed | |
GenomeDescription-class | 9.924 | 0.295 | 10.251 | |
NCBI-utils | 0.241 | 0.048 | 18.733 | |
Seqinfo-class | 0.313 | 0.020 | 0.334 | |
getChromInfoFromEnsembl | 1.496 | 1.064 | 108.794 | |
getChromInfoFromNCBI | 0.382 | 0.028 | 22.791 | |
getChromInfoFromUCSC | 0.901 | 0.076 | 4.910 | |
loadTaxonomyDb | 10.812 | 0.180 | 11.016 | |
mapGenomeBuilds | 0.044 | 0.004 | 0.048 | |
rankSeqlevels | 0.129 | 0.004 | 0.151 | |
seqinfo | 5.380 | 0.205 | 5.690 | |
seqlevels-wrappers | 4.058 | 0.195 | 4.264 | |
seqlevelsStyle | 4.302 | 0.100 | 26.382 | |