Back to Multiple platform build/check report for BioC 3.16:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:04:57 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (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

CHECK results for AnnotationHub on nebbiolo2


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.

raw results

Package 59/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHub 3.6.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/AnnotationHub
git_branch: RELEASE_3_16
git_last_commit: 3315a73
git_last_commit_date: 2022-11-01 11:08:05 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    ERROR    OK  

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.


Installation output

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)

Tests output

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

Example timings

AnnotationHub.Rcheck/AnnotationHub-Ex.timings

nameusersystemelapsed
AnnotationHub-class34.540 2.15237.930
AnnotationHub-package000
Hub-utils0.0010.0000.000
convertHub000
getAnnotationHubOption0.0010.0000.000
utils0.0010.0000.000