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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:branchpointer.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings branchpointer_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/branchpointer.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: 2026-05-08 02:00:21 UTC
* checking for file ‘branchpointer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘branchpointer’ version ‘1.38.0’
* 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 ‘branchpointer’ 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 code 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 ... OK
* 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 R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘branchpointer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeBranchpointWindowForSNP
> ### Title: Makes a branchpointer formatted GRanges object from refsnp ids
> ### Aliases: makeBranchpointWindowForSNP
> 
> ### ** Examples
> 
> smallExons <- system.file("extdata","gencode.v26.annotation.small.gtf",package = "branchpointer")
> exons <- gtfToExons(smallExons)
> 
> mart.snp <- biomaRt::useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp", host="www.ensembl.org")
Error in .getAttributes(mart, verbose = verbose) : 
  biomaRt error: looks like we're connecting to incompatible version of BioMart.
Calls: <Anonymous> -> .useMart -> useDataset -> .getAttributes
Execution halted
* 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 ‘branchpointer.Rnw’ using knitr

Quitting from branchpointer.Rnw:219-227 [read_snp_mart]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `checkDataset()`:
! The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.
---
Backtrace:
    x
 1. \-biomaRt::useMart(...)
 2.   \-biomaRt:::.useMart(...)
 3.     \-biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
 4.       \-biomaRt:::checkDataset(dataset = dataset, mart = mart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'branchpointer.Rnw' failed with diagnostics:
The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.
--- failed re-building ‘branchpointer.Rnw’

SUMMARY: processing the following file failed:
  ‘branchpointer.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/branchpointer.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL branchpointer
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘branchpointer’ ...
** this is package ‘branchpointer’ version ‘1.38.0’
** 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 (branchpointer)