| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:32 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the GRaNIE package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 838/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GRaNIE 1.3.12 (landing page) Christian Arnold
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: GRaNIE |
| Version: 1.3.12 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GRaNIE_1.3.12.tar.gz |
| StartedAt: 2022-12-29 00:19:10 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 00:24:30 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 320.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GRaNIE.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GRaNIE_1.3.12.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GRaNIE.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GRaNIE/DESCRIPTION' ... OK
* this is package 'GRaNIE' version '1.3.12'
* 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-3.17-bioc-rtools43/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 R 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'GenomicDistributions'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotCorrelations: no visible binding for global variable 'sortby'
plotCorrelations: no visible binding for global variable 'TF_peak.r'
plotCorrelations: no visible global function definition for 'desc'
plotCorrelations: no visible binding for global variable
'TF_peak.r_abs'
plotCorrelations: no visible binding for global variable 'TF.exp.norm'
plotCorrelations: no visible binding for global variable
'peak.acc.norm'
plotCorrelations: no visible binding for global variable 'cor_all'
plotCorrelations: no visible binding for global variable
'cor_nonZeroAll'
plotCorrelations: no visible binding for global variable 'cor_nonZero'
plot_peaks: no visible global function definition for 'plotChromBins'
Undefined global functions or variables:
TF.exp.norm TF_peak.r TF_peak.r_abs cor_all cor_nonZero
cor_nonZeroAll desc peak.acc.norm plotChromBins sortby
* 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 12.19 0.37 12.72
addConnections_TF_peak 7.01 1.64 11.78
getCounts 7.37 0.57 8.25
getGRNConnections 6.31 0.51 7.12
plotCommunitiesEnrichment 5.86 0.40 6.40
visualizeGRN 5.74 0.36 6.27
plot_stats_connectionSummary 5.70 0.39 6.48
plotTFEnrichment 5.38 0.32 5.86
plotDiagnosticPlots_peakGene 4.83 0.39 5.36
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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, 1 NOTE
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GRaNIE.Rcheck/00check.log'
for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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 ** 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)
GRaNIE.Rcheck/GRaNIE-Ex.timings
| name | user | system | elapsed | |
| AR_classification_wrapper | 0 | 0 | 0 | |
| addConnections_TF_peak | 7.01 | 1.64 | 11.78 | |
| addConnections_peak_gene | 3.35 | 0.37 | 3.98 | |
| addData | 0 | 0 | 0 | |
| addTFBS | 0 | 0 | 0 | |
| add_TF_gene_correlation | 3.64 | 0.41 | 4.20 | |
| add_featureVariation | 0 | 0 | 0 | |
| build_eGRN_graph | 3.87 | 0.54 | 4.57 | |
| calculateCommunitiesEnrichment | 3.80 | 0.52 | 4.48 | |
| calculateCommunitiesStats | 3.76 | 0.39 | 4.31 | |
| calculateGeneralEnrichment | 3.55 | 0.21 | 3.91 | |
| calculateTFEnrichment | 3.86 | 0.47 | 4.46 | |
| changeOutputDirectory | 3.22 | 0.50 | 3.88 | |
| deleteIntermediateData | 3.25 | 0.25 | 3.64 | |
| filterData | 3.90 | 0.35 | 4.41 | |
| filterGRNAndConnectGenes | 4.13 | 0.28 | 4.56 | |
| generateStatsSummary | 12.19 | 0.37 | 12.72 | |
| getCounts | 7.37 | 0.57 | 8.25 | |
| getGRNConnections | 6.31 | 0.51 | 7.12 | |
| getParameters | 3.29 | 0.20 | 3.64 | |
| getTopNodes | 3.56 | 0.29 | 3.99 | |
| initializeGRN | 0.01 | 0.00 | 0.01 | |
| loadExampleObject | 3.97 | 0.28 | 4.41 | |
| nGenes | 3.08 | 0.34 | 3.58 | |
| nPeaks | 3.72 | 0.41 | 4.28 | |
| nTFs | 4.11 | 0.34 | 4.59 | |
| overlapPeaksAndTFBS | 3.44 | 0.30 | 3.88 | |
| performAllNetworkAnalyses | 0 | 0 | 0 | |
| plotCommunitiesEnrichment | 5.86 | 0.40 | 6.40 | |
| plotCommunitiesStats | 3.81 | 0.38 | 4.33 | |
| plotDiagnosticPlots_TFPeaks | 4.20 | 0.30 | 4.64 | |
| plotDiagnosticPlots_peakGene | 4.83 | 0.39 | 5.36 | |
| plotGeneralEnrichment | 3.69 | 0.37 | 4.20 | |
| plotGeneralGraphStats | 4.20 | 0.44 | 4.79 | |
| plotPCA_all | 3.98 | 0.30 | 4.48 | |
| plotTFEnrichment | 5.38 | 0.32 | 5.86 | |
| plot_stats_connectionSummary | 5.70 | 0.39 | 6.48 | |
| visualizeGRN | 5.74 | 0.36 | 6.27 | |