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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 906/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.8.0  (landing page)
Christian Arnold
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/GRaNIE
git_branch: RELEASE_3_19
git_last_commit: 47f7e04
git_last_commit_date: 2024-04-30 11:42:38 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


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: 1.8.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GRaNIE_1.8.0.tar.gz
StartedAt: 2024-06-12 23:43:56 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 23:54:12 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 615.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GRaNIE.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GRaNIE_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... WARNING
Missing or unexported object: 'AnnotationHub::getAnnotationHub'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getAnnotationHub: no visible global function definition for 'is'
.performIHW: no visible binding for global variable 'adj_pvalue'
.retrieveAnnotationData: no visible global function definition for 'is'
Undefined global functions or variables:
  adj_pvalue is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                             ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                   ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                           ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                                        ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                                                                                            ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                                                                                                        ^
* 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         11.281  0.284  12.058
plotCommunitiesStats          6.720  0.280   7.547
addSNPData                    6.129  0.609   8.877
getGRNSummary                 5.373  0.356   6.950
plotDiagnosticPlots_peakGene  5.542  0.084   6.032
plotDiagnosticPlots_TFPeaks   4.593  0.124   5.560
plotCommunitiesEnrichment     4.393  0.176   6.424
nPeaks                        4.196  0.100   5.482
filterData                    3.968  0.147   5.274
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.


Installation output

GRaNIE.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GRaNIE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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_wrapper000
addConnections_TF_peak3.1820.0924.336
addConnections_peak_gene2.9420.1883.575
addData0.0000.0000.001
addSNPData6.1290.6098.877
addTFBS000
add_TF_gene_correlation1.8080.0792.328
add_featureVariation000
build_eGRN_graph1.8810.0842.376
calculateCommunitiesEnrichment3.8860.3004.607
calculateCommunitiesStats1.7180.0602.175
calculateGeneralEnrichment2.1500.1082.654
calculateTFEnrichment2.3340.0882.877
changeOutputDirectory1.7060.0682.234
deleteIntermediateData3.2710.2163.954
filterConnectionsForPlotting1.9280.0882.440
filterData3.9680.1475.274
filterGRNAndConnectGenes2.2470.0562.728
generateStatsSummary11.281 0.28412.058
getCounts2.8580.1083.438
getGRNConnections2.3740.1043.076
getGRNSummary5.3730.3566.950
getParameters2.6330.0763.247
getTopNodes2.6100.0553.165
initializeGRN0.0210.0010.021
loadExampleObject3.0470.1033.757
nGenes2.3040.1042.814
nPeaks4.1960.1005.482
nTFs2.3880.0642.940
overlapPeaksAndTFBS2.4160.0923.211
performAllNetworkAnalyses0.0010.0000.000
plotCommunitiesEnrichment4.3930.1766.424
plotCommunitiesStats6.7200.2807.547
plotCorrelations2.2290.0842.873
plotDiagnosticPlots_TFPeaks4.5930.1245.560
plotDiagnosticPlots_peakGene5.5420.0846.032
plotGeneralEnrichment1.9430.0442.452
plotGeneralGraphStats2.4790.0482.950
plotPCA_all3.8280.0994.395
plotTFEnrichment2.3960.0642.883
plot_stats_connectionSummary2.2120.0482.656
visualizeGRN3.0430.0483.627