Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-04 11:37:23 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
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 816/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomeInfoDb 1.38.6 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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. |
Package: GenomeInfoDb |
Version: 1.38.6 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomeInfoDb_1.38.6.tar.gz |
StartedAt: 2024-03-03 20:48:40 -0500 (Sun, 03 Mar 2024) |
EndedAt: 2024-03-03 21:00:39 -0500 (Sun, 03 Mar 2024) |
EllapsedTime: 718.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomeInfoDb.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomeInfoDb_1.38.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GenomeInfoDb.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK * this is package ‘GenomeInfoDb’ version ‘1.38.6’ * 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 ... NOTE installed size is 5.2Mb 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 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 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed loadTaxonomyDb 11.707 0.241 12.061 GenomeDescription-class 8.962 0.425 9.493 seqlevels-wrappers 5.599 0.344 6.026 seqinfo 4.786 0.377 5.353 seqlevelsStyle 4.105 0.431 7.642 getChromInfoFromUCSC 2.359 1.166 5.385 getChromInfoFromEnsembl 1.409 0.159 47.439 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/GenomeInfoDb.Rcheck/00check.log’ for details.
GenomeInfoDb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomeInfoDb ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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. > require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package") Loading required package: GenomeInfoDb Loading required package: BiocGenerics 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, setdiff, sort, table, tapply, union, 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 -- Sun Mar 3 21:00:29 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 420.002 31.122 524.033
GenomeInfoDb.Rcheck/GenomeInfoDb-Ex.timings
name | user | system | elapsed | |
GenomeDescription-class | 8.962 | 0.425 | 9.493 | |
NCBI-utils | 0.066 | 0.018 | 1.334 | |
Seqinfo-class | 0.268 | 0.030 | 0.301 | |
getChromInfoFromEnsembl | 1.409 | 0.159 | 47.439 | |
getChromInfoFromNCBI | 0.254 | 0.036 | 1.074 | |
getChromInfoFromUCSC | 2.359 | 1.166 | 5.385 | |
loadTaxonomyDb | 11.707 | 0.241 | 12.061 | |
mapGenomeBuilds | 0.055 | 0.017 | 0.075 | |
rankSeqlevels | 0.148 | 0.019 | 0.173 | |
seqinfo | 4.786 | 0.377 | 5.353 | |
seqlevels-wrappers | 5.599 | 0.344 | 6.026 | |
seqlevelsStyle | 4.105 | 0.431 | 7.642 | |