Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-01 12:03 -0400 (Wed, 01 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" | 4843 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4575 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 912/2337 | 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 12.7.1 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 | OK | ERROR | ||||||||||
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: 2025-10-01 00:22:56 -0400 (Wed, 01 Oct 2025) |
EndedAt: 2025-10-01 00:33:32 -0400 (Wed, 01 Oct 2025) |
EllapsedTime: 635.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRaNIE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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 8.841 0.209 9.996 plotDiagnosticPlots_peakGene 7.090 0.373 8.753 addSNPData 6.284 0.475 8.324 calculateCommunitiesEnrichment 5.281 0.543 7.256 calculateGeneralEnrichment 4.948 0.489 6.439 plotGeneralGraphStats 4.835 0.098 5.344 visualizeGRN 4.392 0.080 5.262 getCounts 4.007 0.260 5.498 addConnections_TF_peak 3.530 0.304 6.606 * 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 | 3.530 | 0.304 | 6.606 | |
addConnections_peak_gene | 2.732 | 0.094 | 3.287 | |
addData | 0 | 0 | 0 | |
addSNPData | 6.284 | 0.475 | 8.324 | |
addTFBS | 0.001 | 0.000 | 0.000 | |
add_TF_gene_correlation | 3.029 | 0.119 | 4.851 | |
add_featureVariation | 0.000 | 0.001 | 0.000 | |
build_eGRN_graph | 2.663 | 0.079 | 3.353 | |
calculateCommunitiesEnrichment | 5.281 | 0.543 | 7.256 | |
calculateCommunitiesStats | 2.720 | 0.148 | 3.550 | |
calculateGeneralEnrichment | 4.948 | 0.489 | 6.439 | |
calculateTFEnrichment | 3.530 | 0.121 | 4.220 | |
changeOutputDirectory | 1.979 | 0.094 | 2.503 | |
deleteIntermediateData | 2.929 | 0.088 | 3.623 | |
filterConnectionsForPlotting | 1.992 | 0.065 | 2.512 | |
filterData | 3.638 | 0.134 | 4.456 | |
filterGRNAndConnectGenes | 3.407 | 0.268 | 4.142 | |
generateStatsSummary | 8.841 | 0.209 | 9.996 | |
getCounts | 4.007 | 0.260 | 5.498 | |
getGRNConnections | 2.070 | 0.057 | 2.771 | |
getGRNSummary | 2.970 | 0.106 | 3.762 | |
getParameters | 2.809 | 0.074 | 3.669 | |
getTopNodes | 3.186 | 0.066 | 3.762 | |
initializeGRN | 0.031 | 0.003 | 0.036 | |
loadExampleObject | 2.509 | 0.041 | 3.646 | |
nGenes | 1.779 | 0.030 | 2.219 | |
nPeaks | 1.686 | 0.040 | 2.181 | |
nTFs | 1.596 | 0.019 | 2.026 | |
overlapPeaksAndTFBS | 1.680 | 0.023 | 2.134 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 3.372 | 0.097 | 3.950 | |
plotCommunitiesStats | 4.086 | 0.078 | 4.584 | |
plotCorrelations | 2.067 | 0.028 | 2.526 | |
plotDiagnosticPlots_TFPeaks | 3.343 | 0.013 | 3.764 | |
plotDiagnosticPlots_peakGene | 7.090 | 0.373 | 8.753 | |
plotGeneralEnrichment | 3.719 | 0.130 | 4.335 | |
plotGeneralGraphStats | 4.835 | 0.098 | 5.344 | |
plotPCA_all | 3.909 | 0.056 | 4.378 | |
plotTFEnrichment | 2.611 | 0.020 | 3.054 | |
plot_stats_connectionSummary | 2.216 | 0.025 | 2.691 | |
visualizeGRN | 4.392 | 0.080 | 5.262 | |