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This page was generated on 2024-06-28 17:40 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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: 2024-06-26 14:00 -0400 (Wed, 26 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
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


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: 2024-06-26 23:49:56 -0400 (Wed, 26 Jun 2024)
EndedAt: 2024-06-27 00:00:21 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 625.4 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
###
##############################################################################
##############################################################################


* 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           10.834  0.455  12.097
getGRNSummary                   5.841  0.471   6.969
calculateCommunitiesEnrichment  5.556  0.511   8.110
addSNPData                      5.280  0.676   8.095
plotDiagnosticPlots_peakGene    5.012  0.611   6.111
deleteIntermediateData          4.411  0.496   5.642
plotCommunitiesStats            4.458  0.311   5.201
plotTFEnrichment                3.630  0.212   5.396
filterData                      3.636  0.199   5.343
calculateCommunitiesStats       3.038  0.160   5.322
* 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_wrapper0.0000.0010.000
addConnections_TF_peak3.2790.1204.491
addConnections_peak_gene2.6850.2643.395
addData000
addSNPData5.2800.6768.095
addTFBS000
add_TF_gene_correlation2.8220.1313.758
add_featureVariation000
build_eGRN_graph2.0440.0882.612
calculateCommunitiesEnrichment5.5560.5118.110
calculateCommunitiesStats3.0380.1605.322
calculateGeneralEnrichment3.1590.2804.132
calculateTFEnrichment2.7120.1963.670
changeOutputDirectory3.0040.1844.968
deleteIntermediateData4.4110.4965.642
filterConnectionsForPlotting2.1160.1202.759
filterData3.6360.1995.343
filterGRNAndConnectGenes2.7730.1754.682
generateStatsSummary10.834 0.45512.097
getCounts2.5390.1363.116
getGRNConnections2.1760.0842.744
getGRNSummary5.8410.4716.969
getParameters3.0170.1564.038
getTopNodes2.1510.1432.751
initializeGRN0.0160.0080.024
loadExampleObject1.7770.1132.324
nGenes1.8750.1162.435
nPeaks2.7680.2153.431
nTFs1.5850.0402.055
overlapPeaksAndTFBS1.6300.0562.124
performAllNetworkAnalyses0.0010.0000.001
plotCommunitiesEnrichment3.4200.1954.066
plotCommunitiesStats4.4580.3115.201
plotCorrelations2.7700.2363.668
plotDiagnosticPlots_TFPeaks3.8200.2754.638
plotDiagnosticPlots_peakGene5.0120.6116.111
plotGeneralEnrichment1.9110.1082.463
plotGeneralGraphStats2.5900.1763.280
plotPCA_all3.6280.5324.695
plotTFEnrichment3.6300.2125.396
plot_stats_connectionSummary2.2060.1282.810
visualizeGRN2.5150.1563.103