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This page was generated on 2024-12-12 11:44 -0500 (Thu, 12 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4752
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4464
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4415
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4370
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4279
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 891/2273HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.11.0  (landing page)
Christian Arnold
Snapshot Date: 2024-12-11 13:40 -0500 (Wed, 11 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  ERROR    ERROR  skipped


CHECK results for GRaNIE on lconway

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: /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_1.11.0.tar.gz
StartedAt: 2024-12-11 21:54:32 -0500 (Wed, 11 Dec 2024)
EndedAt: 2024-12-11 22:03:57 -0500 (Wed, 11 Dec 2024)
EllapsedTime: 564.7 seconds
RetCode: 0
Status:   OK  
CheckDir: GRaNIE.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GRaNIE.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
generateStatsSummary   4.468  0.135   5.070
addConnections_TF_peak 3.208  0.595  11.392
addSNPData             3.055  0.210  13.611
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.


Installation output

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-x86_64/Resources/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_wrapper000
addConnections_TF_peak 3.208 0.59511.392
addConnections_peak_gene1.8110.0312.394
addData0.0010.0000.000
addSNPData 3.055 0.21013.611
addTFBS000
add_TF_gene_correlation1.9800.0542.520
add_featureVariation0.0010.0000.000
build_eGRN_graph1.1490.0291.699
calculateCommunitiesEnrichment1.8490.1072.420
calculateCommunitiesStats1.9120.0402.470
calculateGeneralEnrichment1.4160.0322.038
calculateTFEnrichment1.4360.0412.144
changeOutputDirectory1.1660.0301.731
deleteIntermediateData1.2040.0311.750
filterConnectionsForPlotting1.2930.0371.853
filterData2.3000.0412.846
filterGRNAndConnectGenes1.2350.0301.741
generateStatsSummary4.4680.1355.070
getCounts2.1180.0762.674
getGRNConnections1.2630.0281.773
getGRNSummary2.3200.0762.852
getParameters1.2530.0371.759
getTopNodes1.2410.0301.738
initializeGRN0.0120.0010.014
loadExampleObject1.2670.0441.740
nGenes1.1940.0361.652
nPeaks1.1610.0331.633
nTFs1.2060.0321.682
overlapPeaksAndTFBS1.9340.0472.417
performAllNetworkAnalyses000
plotCommunitiesEnrichment2.2590.0712.924
plotCommunitiesStats2.2040.0422.692
plotCorrelations2.2540.0612.762
plotDiagnosticPlots_TFPeaks2.2790.0802.831
plotDiagnosticPlots_peakGene4.1940.1154.772
plotGeneralEnrichment1.3840.0411.959
plotGeneralGraphStats1.9630.0442.589
plotPCA_all2.6160.0843.274
plotTFEnrichment1.7840.0692.365
plot_stats_connectionSummary1.6950.0552.211
visualizeGRN1.9040.0682.413