| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| 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 903/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GRaNIE 1.13.0 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the GRaNIE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRaNIE.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. |
| Package: GRaNIE |
| Version: 1.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRaNIE_1.13.0.tar.gz |
| StartedAt: 2025-08-08 19:42:38 -0400 (Fri, 08 Aug 2025) |
| EndedAt: 2025-08-08 19:45:08 -0400 (Fri, 08 Aug 2025) |
| EllapsedTime: 149.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GRaNIE.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRaNIE_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.13.0’
* 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 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 [2025-08-08 19:44:40] Not retrieving SNPS in LD, use only user-provided SNPs
INFO [2025-08-08 19:44:40] Quering biomaRt for 3 rsid annotation, this may take a while, particularly if the number of provided IDs is large
WARN [2025-08-08 19:44:41] 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 [2025-08-08 19:44:42] 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 [2025-08-08 19:44:42] 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 [2025-08-08 19:44:43] 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 [2025-08-08 19:44:43] 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 [2025-08-08 19:44:44] 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 [2025-08-08 19:44:44] 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 [2025-08-08 19:44:45] Attempt 8 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 [2025-08-08 19:44:45] 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 [2025-08-08 19:44:46] 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 [2025-08-08 19:44:46] 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 [2025-08-08 19:44:47] 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 [2025-08-08 19:44:47] 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 [2025-08-08 19:44:48] 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 [2025-08-08 19:44:49] 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 [2025-08-08 19:44:49] 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 [2025-08-08 19:44:50] 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 [2025-08-08 19:44:50] 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 [2025-08-08 19:44:51] 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 [2025-08-08 19:44:51] 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 [2025-08-08 19:44:52] 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 [2025-08-08 19:44:53] 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 [2025-08-08 19:44:53] 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 [2025-08-08 19:44:54] 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 [2025-08-08 19:44:55] 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 [2025-08-08 19:44:56] 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 [2025-08-08 19:44:56] 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 [2025-08-08 19:44:57] 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 [2025-08-08 19:44:57] 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 [2025-08-08 19:44:58] 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 [2025-08-08 19:44:59] 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 [2025-08-08 19:44:59] 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 [2025-08-08 19:45:00] 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 [2025-08-08 19:45:00] 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 [2025-08-08 19:45:01] 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 [2025-08-08 19:45:01] 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 [2025-08-08 19:45:02] 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 [2025-08-08 19:45:02] 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 [2025-08-08 19:45:03] 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 [2025-08-08 19:45:03] 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 [2025-08-08 19:45:04] 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 [2025-08-08 19:45:04] 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. #
########################################################################################
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.
########################################################################################
# An error occurred. See details above. If you think this is a bug, please contact us. #
########################################################################################
Calls: addSNPData ... .biomart_getEnsembl -> .checkAndLogWarningsAndErrors
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘GRaNIE’ ... ** this is package ‘GRaNIE’ version ‘1.13.0’ ** 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)
GRaNIE.Rcheck/GRaNIE-Ex.timings
| name | user | system | elapsed | |
| AR_classification_wrapper | 0 | 0 | 0 | |
| addConnections_TF_peak | 2.163 | 0.224 | 4.977 | |
| addConnections_peak_gene | 1.168 | 0.019 | 1.589 | |
| addData | 0 | 0 | 0 | |