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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GRaNIE_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GRaNIE.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: 2026-05-29 04:45:50 UTC
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 37 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘GRaNIE’ 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 whether startup messages can be suppressed ... 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 ... NOTE
.performIHW: no visible binding for global variable 'adj_pvalue'
Undefined global functions or variables:
  adj_pvalue
* 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 ... ERROR
Running examples in ‘GRaNIE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addSNPData
> ### Title: Add SNP data to a 'GRN' object and associate SNPs to peaks.
> ### Aliases: addSNPData
> 
> ### ** Examples
> 
> # See the Workflow vignette on the GRaNIE website for examples
> GRN = loadExampleObject()
Downloading GRaNIE example object from https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds
Finished successfully. You may explore the example object. Start by typing the object name to the console to see a summaty. Happy GRaNIE'ing!
> GRN = addSNPData(GRN, SNP_IDs = c("rs7570219", "rs6445264", "rs12067275"), forceRerun = FALSE)
INFO [2026-05-29 00:51:15]  Not retrieving SNPS in LD, use only user-provided SNPs
INFO [2026-05-29 00:51:15]  Quering biomaRt for 3 rsid annotation, this may take a while, particularly if the number of provided IDs is large
WARN [2026-05-29 00:51:17] Attempt 1 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:51:18] Attempt 2 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:51:19] Attempt 3 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:51:21] Attempt 4 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:51:22] Attempt 5 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:51:23] Attempt 6 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:51:24] Attempt 7 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:51:52] Attempt 8 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in .getAttributes(mart, verbose = verbose): biomaRt error: looks like we're connecting to incompatible version of BioMart.

WARN [2026-05-29 00:51:56] Attempt 9 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:51:57] Attempt 10 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:51:59] Attempt 11 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:00] Attempt 12 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:03] Attempt 13 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:06] Attempt 14 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:07] Attempt 15 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:09] Attempt 16 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:10] Attempt 17 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:11] Attempt 18 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:12] Attempt 19 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:13] Attempt 20 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:15] Attempt 21 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:16] Attempt 22 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:17] Attempt 23 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:19] Attempt 24 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:20] Attempt 25 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:21] Attempt 26 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:22] Attempt 27 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:23] Attempt 28 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:24] Attempt 29 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:25] Attempt 30 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:26] Attempt 31 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:28] Attempt 32 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:29] Attempt 33 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:30] Attempt 34 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:31] Attempt 35 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:32] Attempt 36 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:33] Attempt 37 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:35] Attempt 38 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:36] Attempt 39 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:38] Attempt 40 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

WARN [2026-05-29 00:52:39] Attempt 41 out of 40 failed. Another automatic attempt will be performed using a different mirror. The error message was: Error in checkDataset(dataset = dataset, mart = mart): The given dataset: hsapiens_snp, is not valid.  Correct dataset names can be obtained with the listDatasets() function.

ERROR [2026-05-29 00:52:39] A temporary error occured with biomaRt::getBM or biomaRt::useEnsembl despite trying 40 times via different mirrors. This is often caused by an unresponsive Ensembl site. Try again at a later time. Note that this error is not caused by GRaNIE but external services.

########################################################################################
# An error occurred. See details above. If you think this is a bug, please contact us. #
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Error in .checkAndLogWarningsAndErrors(NULL, error_Biomart, isWarning = FALSE) : 
  A temporary error occured with biomaRt::getBM or biomaRt::useEnsembl despite trying 40 times via different mirrors. This is often caused by an unresponsive Ensembl site. Try again at a later time. Note that this error is not caused by GRaNIE but external services.

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# An error occurred. See details above. If you think this is a bug, please contact us. #
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Calls: addSNPData ... .biomart_getEnsembl -> .checkAndLogWarningsAndErrors
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
addConnections_TF_peak 3.251  0.369   6.292
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GRaNIE
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘GRaNIE’ ...
** this is package ‘GRaNIE’ version ‘1.16.0’
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (GRaNIE)