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This page was generated on 2024-12-23 11:40 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 891/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.11.0  (landing page)
Christian Arnold
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/GRaNIE
git_branch: devel
git_last_commit: 7fdc850
git_last_commit_date: 2024-10-29 11:11:39 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  


CHECK results for GRaNIE on nebbiolo1

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.

raw results


Summary

Package: GRaNIE
Version: 1.11.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GRaNIE_1.11.0.tar.gz
StartedAt: 2024-12-22 22:42:02 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-22 22:52:25 -0500 (Sun, 22 Dec 2024)
EllapsedTime: 623.9 seconds
RetCode: 0
Status:   OK  
CheckDir: GRaNIE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GRaNIE_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GRaNIE.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.11.0’
* 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           10.118  0.567  12.602
plotDiagnosticPlots_TFPeaks     6.319  0.502   8.312
calculateCommunitiesEnrichment  6.173  0.583   7.956
addSNPData                      5.573  0.643   8.278
plotTFEnrichment                5.450  0.521   6.850
filterGRNAndConnectGenes        4.504  0.590   5.992
getCounts                       4.700  0.380   6.026
getParameters                   4.374  0.579   5.760
plotGeneralGraphStats           4.111  0.499   5.111
getGRNSummary                   4.039  0.363   5.249
calculateTFEnrichment           3.674  0.216   5.688
addConnections_TF_peak          3.464  0.288   5.039
* 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-3.21-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.


Installation output

GRaNIE.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GRaNIE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘GRaNIE’ ...
** 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)

Tests output


Example timings

GRaNIE.Rcheck/GRaNIE-Ex.timings

nameusersystemelapsed
AR_classification_wrapper0.0000.0000.001
addConnections_TF_peak3.4640.2885.039
addConnections_peak_gene2.8670.3013.674
addData000
addSNPData5.5730.6438.278
addTFBS000
add_TF_gene_correlation1.8250.1312.460
add_featureVariation000
build_eGRN_graph2.5160.1354.031
calculateCommunitiesEnrichment6.1730.5837.956
calculateCommunitiesStats2.6170.2123.441
calculateGeneralEnrichment3.4950.3894.587
calculateTFEnrichment3.6740.2165.688
changeOutputDirectory2.2970.1352.936
deleteIntermediateData2.8550.2194.050
filterConnectionsForPlotting2.0860.1042.741
filterData3.5690.2744.990
filterGRNAndConnectGenes4.5040.5905.992
generateStatsSummary10.118 0.56712.602
getCounts4.7000.3806.026
getGRNConnections1.9930.0942.614
getGRNSummary4.0390.3635.249
getParameters4.3740.5795.760
getTopNodes2.1380.1312.755
initializeGRN0.0190.0010.019
loadExampleObject1.6740.0852.302
nGenes1.8090.1472.466
nPeaks1.8170.1492.508
nTFs1.7060.0712.267
overlapPeaksAndTFBS1.8040.1352.461
performAllNetworkAnalyses000
plotCommunitiesEnrichment3.0190.2143.675
plotCommunitiesStats2.8730.1683.508
plotCorrelations2.2480.1212.958
plotDiagnosticPlots_TFPeaks6.3190.5028.312
plotDiagnosticPlots_peakGene4.1340.2144.884
plotGeneralEnrichment2.0980.1442.719
plotGeneralGraphStats4.1110.4995.111
plotPCA_all2.6560.2243.435
plotTFEnrichment5.4500.5216.850
plot_stats_connectionSummary2.2870.0842.873
visualizeGRN2.6520.2383.410