Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-02-06 11:06:25 -0500 (Mon, 06 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4483 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" | 4249 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4272 |
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 |
To the developers/maintainers of the AnnotationHub package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnnotationHub.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 58/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AnnotationHub 3.7.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: AnnotationHub |
Version: 3.7.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AnnotationHub_3.7.0.tar.gz |
StartedAt: 2023-02-05 22:19:09 -0500 (Sun, 05 Feb 2023) |
EndedAt: 2023-02-05 22:28:06 -0500 (Sun, 05 Feb 2023) |
EllapsedTime: 537.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: AnnotationHub.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AnnotationHub_3.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/AnnotationHub.Rcheck’ * using R Under development (unstable) (2023-01-10 r83596) * using platform: x86_64-apple-darwin17.0 (64-bit) * R was compiled by Apple clang version 12.0.0 (clang-1200.0.32.29) GNU Fortran (GCC) 8.2.0 * running under: macOS Mojave 10.14.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AnnotationHub/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AnnotationHub’ version ‘3.7.0’ * 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 ‘AnnotationHub’ 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 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 dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘CompoundDb’ ‘ensembldb’ Unexported objects imported by ':::' calls: ‘BiocFileCache:::.get_tbl_rid’ ‘S4Vectors:::selectSome’ 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 ... WARNING checkRd: (5) AnnotationHub-class.Rd:134-142: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:151-154: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:155-158: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:159-162: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:163-166: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:167-171: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:172-178: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:179-213: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:215-217: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:219-221: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:223-225: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:234-238: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:239-243: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:244-250: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:251-272: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:273-281: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:282-287: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:288-293: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:300-304: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:305-309: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:310-321: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:322-325: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:326-329: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:330-337: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:338-345: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:346-351: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:358-362: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:363-367: \item in \describe must have non-empty label * 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 AnnotationHub-class 71.685 1.869 110.712 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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 WARNINGs See ‘/Users/biocbuild/bbs-3.17-bioc/meat/AnnotationHub.Rcheck/00check.log’ for details.
AnnotationHub.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AnnotationHub ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’ * installing *source* package ‘AnnotationHub’ ... ** 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 (AnnotationHub)
AnnotationHub.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > BiocGenerics:::testPackage("AnnotationHub") 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 snapshotDate(): 2022-12-16 Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use snapshotDate(): 2022-12-16 snapshotDate(): 2022-12-16 snapshotDate(): 2022-12-16 snapshotDate(): 2022-12-16 snapshotDate(): 2022-12-16 snapshotDate(): 2022-12-16 snapshotDate(): 2022-12-16 snapshotDate(): 2022-12-16 snapshotDate(): 2022-12-16 snapshotDate(): 2022-12-16 Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname require("xxx_foo") RUNIT TEST PROTOCOL -- Sun Feb 5 22:27:53 2023 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : AnnotationHub RUnit Tests - 20 test functions, 0 errors, 0 failures Number of test functions: 20 Number of errors: 0 Number of failures: 0 Warning messages: 1: call dbDisconnect() when finished working with a connection 2: download failed hub path: 'bogus/url' cache resource: 'AHInvalid : 5012' reason: all(rtype == "web" | file.exists(fpath)) is not TRUE > > proc.time() user system elapsed 84.098 8.034 124.723
AnnotationHub.Rcheck/AnnotationHub-Ex.timings
name | user | system | elapsed | |
AnnotationHub-class | 71.685 | 1.869 | 110.712 | |
AnnotationHub-package | 0.000 | 0.000 | 0.001 | |
Hub-utils | 0.000 | 0.000 | 0.001 | |
convertHub | 0 | 0 | 0 | |
getAnnotationHubOption | 0.000 | 0.000 | 0.001 | |
utils | 0.002 | 0.000 | 0.003 | |