CHECK results for alternativeSplicingEvents.hg38 on nebbiolo2
To the developers/maintainers of the alternativeSplicingEvents.hg38 package:
- 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
Command output
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### Running command:
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### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:alternativeSplicingEvents.hg38.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings alternativeSplicingEvents.hg38_1.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.24-data-annotation/meat/alternativeSplicingEvents.hg38.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-20 10:06:45 UTC
* checking for file ‘alternativeSplicingEvents.hg38/DESCRIPTION’ ... OK
* this is package ‘alternativeSplicingEvents.hg38’ version ‘1.1.0’
* 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 ‘alternativeSplicingEvents.hg38’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... ERROR
Running examples in ‘alternativeSplicingEvents.hg38-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alternativeSplicingEvents.hg38_V2.rda
> ### Title: Alternative splicing event annotation for Human (hg38)
> ### Aliases: alternativeSplicingEvents.hg38_V2.rda
> ### Keywords: datasets
>
> ### ** Examples
>
> library(AnnotationHub)
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: BiocFileCache
Loading required package: dbplyr
> hub <- AnnotationHub()
>
> ## Load the alternative splicing events for Human (hg38)
> events <- query(hub, "alternativeSplicingEvents.hg38_V2")[[1]]
downloading 1 resources
retrieving 1 resource
Warning: download failed
web resource path: ‘https://annotationhub.bioconductor.org/fetch/70403’
local file path: ‘/home/biocbuild/.cache/R/AnnotationHub/2e964f5a7ed245_70403’
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [mghp.osn.xsede.org]:
SSL connection timeout
Warning: bfcadd() failed; resource removed
rid: BFC238
fpath: ‘https://annotationhub.bioconductor.org/fetch/70403’
reason: download failed
Warning: download failed
hub path: ‘https://annotationhub.bioconductor.org/fetch/70403’
cache resource: ‘AH63657 : 70403’
reason: bfcadd() failed; see warnings()
Error loading resource.
attempting to re-download
downloading 1 resources
retrieving 1 resource
Warning: download failed
web resource path: ‘https://annotationhub.bioconductor.org/fetch/70403’
local file path: ‘/home/biocbuild/.cache/R/AnnotationHub/2e964f2a4e6043_70403’
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [mghp.osn.xsede.org]:
SSL connection timeout
Warning: bfcadd() failed; resource removed
rid: BFC239
fpath: ‘https://annotationhub.bioconductor.org/fetch/70403’
reason: download failed
Warning: download failed
hub path: ‘https://annotationhub.bioconductor.org/fetch/70403’
cache resource: ‘AH63657 : 70403’
reason: bfcadd() failed; see warnings()
Error: failed to load resource
name: AH63657
title: Alternative Splicing Annotation for Homo sapiens (Human)
reason: 1 resources failed to download
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.24-data-annotation/meat/alternativeSplicingEvents.hg38.Rcheck/00check.log’
for details.
Installation output
alternativeSplicingEvents.hg38.Rcheck/00install.out
Tests output
Example timings
alternativeSplicingEvents.hg38.Rcheck/alternativeSplicingEvents.hg38-Ex.timings