| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:03 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 920/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GRaNIE 1.13.0 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GRaNIE_1.13.0.tar.gz |
| StartedAt: 2025-10-25 00:18:48 -0400 (Sat, 25 Oct 2025) |
| EndedAt: 2025-10-25 00:29:16 -0400 (Sat, 25 Oct 2025) |
| EllapsedTime: 627.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GRaNIE.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GRaNIE_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
generateStatsSummary 7.727 0.150 9.292
plotDiagnosticPlots_TFPeaks 6.323 0.340 7.221
plotDiagnosticPlots_peakGene 6.197 0.165 6.785
plotCommunitiesStats 5.273 0.125 6.322
getCounts 5.030 0.179 6.344
addSNPData 4.997 0.204 6.534
addConnections_TF_peak 4.738 0.276 8.270
plotGeneralGraphStats 4.706 0.090 5.447
* 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 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 | 4.738 | 0.276 | 8.270 | |
| addConnections_peak_gene | 2.582 | 0.095 | 3.106 | |
| addData | 0.000 | 0.000 | 0.001 | |
| addSNPData | 4.997 | 0.204 | 6.534 | |
| addTFBS | 0 | 0 | 0 | |
| add_TF_gene_correlation | 1.770 | 0.013 | 2.207 | |
| add_featureVariation | 0 | 0 | 0 | |
| build_eGRN_graph | 1.793 | 0.020 | 2.223 | |
| calculateCommunitiesEnrichment | 3.682 | 0.028 | 4.095 | |
| calculateCommunitiesStats | 1.826 | 0.017 | 2.236 | |
| calculateGeneralEnrichment | 3.248 | 0.084 | 3.737 | |
| calculateTFEnrichment | 1.950 | 0.018 | 2.365 | |
| changeOutputDirectory | 1.744 | 0.034 | 2.176 | |
| deleteIntermediateData | 1.779 | 0.034 | 2.216 | |
| filterConnectionsForPlotting | 1.704 | 0.038 | 2.134 | |
| filterData | 2.187 | 0.049 | 2.637 | |
| filterGRNAndConnectGenes | 2.679 | 0.170 | 3.254 | |
| generateStatsSummary | 7.727 | 0.150 | 9.292 | |
| getCounts | 5.030 | 0.179 | 6.344 | |
| getGRNConnections | 2.193 | 0.022 | 2.765 | |
| getGRNSummary | 3.634 | 0.071 | 4.590 | |
| getParameters | 2.759 | 0.032 | 3.202 | |
| getTopNodes | 4.082 | 0.022 | 4.832 | |
| initializeGRN | 0.034 | 0.000 | 0.034 | |
| loadExampleObject | 2.999 | 0.020 | 3.911 | |
| nGenes | 1.889 | 0.016 | 2.308 | |
| nPeaks | 3.226 | 0.020 | 4.048 | |
| nTFs | 2.403 | 0.028 | 2.871 | |
| overlapPeaksAndTFBS | 3.424 | 0.044 | 3.903 | |
| performAllNetworkAnalyses | 0 | 0 | 0 | |
| plotCommunitiesEnrichment | 4.358 | 0.078 | 4.857 | |
| plotCommunitiesStats | 5.273 | 0.125 | 6.322 | |
| plotCorrelations | 3.230 | 0.097 | 4.655 | |
| plotDiagnosticPlots_TFPeaks | 6.323 | 0.340 | 7.221 | |
| plotDiagnosticPlots_peakGene | 6.197 | 0.165 | 6.785 | |
| plotGeneralEnrichment | 2.081 | 0.008 | 2.496 | |
| plotGeneralGraphStats | 4.706 | 0.090 | 5.447 | |
| plotPCA_all | 3.833 | 0.208 | 4.473 | |
| plotTFEnrichment | 2.466 | 0.043 | 2.902 | |
| plot_stats_connectionSummary | 2.247 | 0.036 | 2.689 | |
| visualizeGRN | 3.859 | 0.083 | 4.375 | |