Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:04:57 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 59/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AnnotationHub 3.6.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
Package: AnnotationHub |
Version: 3.6.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings AnnotationHub_3.6.0.tar.gz |
StartedAt: 2023-04-10 18:58:21 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 19:03:44 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 323.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: AnnotationHub.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings AnnotationHub_3.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/AnnotationHub.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘AnnotationHub/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AnnotationHub’ version ‘3.6.0’ * 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 loading without being on the library search path ... 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 ... 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 AnnotationHub-class 34.54 2.152 37.93 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: test_AnnotationHub-class.R test_accessors_setters test_db_utils.R test_db_connections Error in BiocGenerics:::testPackage("AnnotationHub") : unit tests failed for package AnnotationHub In addition: Warning message: download failed hub path: 'bogus/url' cache resource: 'AHInvalid : 5012' reason: all(rtype == "web" | file.exists(fpath)) is not TRUE Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘AnnotationHub-HOWTO.Rmd’... OK ‘AnnotationHub.Rmd’ using ‘UTF-8’... OK ‘TroubleshootingTheCache.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING See ‘/home/biocbuild/bbs-3.16-bioc/meat/AnnotationHub.Rcheck/00check.log’ for details.
AnnotationHub.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL AnnotationHub ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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.fail
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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(): 2022-10-31 Timing stopped at: 0.119 0.032 0.153 Error in checkIdentical(dates[length(dates)], hubDate(ah)) : FALSE Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use snapshotDate(): 2023-04-06 snapshotDate(): 2022-10-31 snapshotDate(): 2022-10-31 snapshotDate(): 2022-10-31 snapshotDate(): 2022-10-31 snapshotDate(): 2022-10-31 snapshotDate(): 2022-10-31 Timing stopped at: 2.69 0.356 3.608 Error in checkIdentical(ids2, AnnotationHub:::.db_uid(hub)) : FALSE In addition: Warning message: call dbDisconnect() when finished working with a connection snapshotDate(): 2022-10-31 snapshotDate(): 2022-10-31 snapshotDate(): 2022-10-31 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 -- Mon Apr 10 19:01:43 2023 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 2 1 Test Suite : AnnotationHub RUnit Tests - 20 test functions, 0 errors, 2 failures FAILURE in test_accessors_setters: Error in checkIdentical(dates[length(dates)], hubDate(ah)) : FALSE FAILURE in test_db_connections: Error in checkIdentical(ids2, AnnotationHub:::.db_uid(hub)) : FALSE Test files with failing tests test_AnnotationHub-class.R test_accessors_setters test_db_utils.R test_db_connections Error in BiocGenerics:::testPackage("AnnotationHub") : unit tests failed for package AnnotationHub In addition: Warning message: download failed hub path: 'bogus/url' cache resource: 'AHInvalid : 5012' reason: all(rtype == "web" | file.exists(fpath)) is not TRUE Execution halted
AnnotationHub.Rcheck/AnnotationHub-Ex.timings
name | user | system | elapsed | |
AnnotationHub-class | 34.540 | 2.152 | 37.930 | |
AnnotationHub-package | 0 | 0 | 0 | |
Hub-utils | 0.001 | 0.000 | 0.000 | |
convertHub | 0 | 0 | 0 | |
getAnnotationHubOption | 0.001 | 0.000 | 0.000 | |
utils | 0.001 | 0.000 | 0.000 | |