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This page was generated on 2024-06-14 14:38 -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 palomino3

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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GRaNIE_1.8.0.tar.gz
StartedAt: 2024-06-13 04:38:07 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 04:50:30 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 743.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GRaNIE.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GRaNIE_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 whether package 'GRaNIE' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
See 'F:/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck/00install.out' for details.
* 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 ... 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           8.83   0.42    9.72
addConnections_TF_peak         5.33   3.60   10.70
addSNPData                     6.64   1.01   10.81
plotDiagnosticPlots_peakGene   6.11   0.85    7.39
calculateCommunitiesEnrichment 4.43   0.39    5.52
* 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: 2 WARNINGs, 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck/00check.log'
for details.


Installation output

GRaNIE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL GRaNIE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'GRaNIE' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
** 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 5.33 3.6010.70
addConnections_peak_gene2.420.173.06
addData000
addSNPData 6.64 1.0110.81
addTFBS000
add_TF_gene_correlation1.970.203.33
add_featureVariation0.000.020.01
build_eGRN_graph1.590.112.17
calculateCommunitiesEnrichment4.430.395.52
calculateCommunitiesStats2.010.152.66
calculateGeneralEnrichment2.770.273.45
calculateTFEnrichment2.180.252.95
changeOutputDirectory3.050.223.74
deleteIntermediateData2.170.263.06
filterConnectionsForPlotting2.140.192.73
filterData2.960.163.60
filterGRNAndConnectGenes1.900.252.74
generateStatsSummary8.830.429.72
getCounts2.410.273.22
getGRNConnections1.840.282.67
getGRNSummary3.060.343.89
getParameters3.080.273.97
getTopNodes2.100.172.70
initializeGRN0.030.000.03
loadExampleObject1.970.192.52
nGenes2.840.173.47
nPeaks1.860.142.42
nTFs1.830.112.39
overlapPeaksAndTFBS1.840.142.47
performAllNetworkAnalyses000
plotCommunitiesEnrichment3.560.704.86
plotCommunitiesStats3.170.193.78
plotCorrelations3.220.344.06
plotDiagnosticPlots_TFPeaks3.860.394.69
plotDiagnosticPlots_peakGene6.110.857.39
plotGeneralEnrichment2.380.152.90
plotGeneralGraphStats3.080.193.66
plotPCA_all4.080.334.81
plotTFEnrichment2.470.233.09
plot_stats_connectionSummary2.870.723.42
visualizeGRN4.120.674.69