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This page was generated on 2024-03-18 11:36:10 -0400 (Mon, 18 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" 4685
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-06 r86056 ucrt) -- "Unsuffered Consequences" 4423
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-04 r86048) -- "Unsuffered Consequences" 4450
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" 4361
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 73/2257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationHub 3.11.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-03-17 14:00:14 -0400 (Sun, 17 Mar 2024)
git_url: https://git.bioconductor.org/packages/AnnotationHub
git_branch: devel
git_last_commit: cb9fc2f
git_last_commit_date: 2024-02-01 08:31:54 -0400 (Thu, 01 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for AnnotationHub on nebbiolo1


To the developers/maintainers of the AnnotationHub package:
- 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 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.

raw results


Summary

Package: AnnotationHub
Version: 3.11.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings AnnotationHub_3.11.1.tar.gz
StartedAt: 2024-03-17 20:08:15 -0400 (Sun, 17 Mar 2024)
EndedAt: 2024-03-17 20:15:14 -0400 (Sun, 17 Mar 2024)
EllapsedTime: 418.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: AnnotationHub.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings AnnotationHub_3.11.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/AnnotationHub.Rcheck’
* using R Under development (unstable) (2024-03-06 r86056)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘AnnotationHub/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHub’ version ‘3.11.1’
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
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:135-143: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:152-155: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:156-159: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:160-163: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:164-167: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:168-172: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:173-179: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:180-214: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:216-218: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:220-222: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:224-226: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:235-239: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:240-244: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:245-251: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:252-273: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:274-282: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:283-288: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:295-299: \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:305-316: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:317-320: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:321-324: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:325-332: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:333-340: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:341-346: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:353-357: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:358-362: \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 35.383  3.268  40.125
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘AnnotationHub-HOWTO.Rmd’ using rmarkdown

Quitting from lines 239-241 [takifugu-txdb] (AnnotationHub-HOWTO.Rmd)
Error: processing vignette 'AnnotationHub-HOWTO.Rmd' failed with diagnostics:
Could not load package txdbmaker. Is it installed?

  Note that Starting with BioC 3.19, calling makeTxDbFromGRanges() requires the txdbmaker
  package. Please install it with:

    BiocManager::install("txdbmaker")
--- failed re-building ‘AnnotationHub-HOWTO.Rmd’

--- re-building ‘AnnotationHub.Rmd’ using rmarkdown
--- finished re-building ‘AnnotationHub.Rmd’

--- re-building ‘TroubleshootingTheHubs.Rmd’ using rmarkdown
--- finished re-building ‘TroubleshootingTheHubs.Rmd’

SUMMARY: processing the following file failed:
  ‘AnnotationHub-HOWTO.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/AnnotationHub.Rcheck/00check.log’
for details.


Installation output

AnnotationHub.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL AnnotationHub
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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


R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
require("xxx_foo")


RUNIT TEST PROTOCOL -- Sun Mar 17 20:11:49 2024 
*********************************************** 
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 
There were 14 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 39.496   6.893  62.386 

Example timings

AnnotationHub.Rcheck/AnnotationHub-Ex.timings

nameusersystemelapsed
AnnotationHub-class35.383 3.26840.125
AnnotationHub-package0.0000.0000.001
Hub-utils0.0010.0000.000
convertHub000
getAnnotationHubOption000
utils0.0010.0000.002