Christian Arnold
| Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/GRaNIE |
| git_branch: devel |
| git_last_commit: b40c0c8 |
| git_last_commit_date: 2023-12-12 08:44:51 -0400 (Tue, 12 Dec 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-27 11:38:01 -0400 (Wed, 27 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4698 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4436 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4461 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4376 |
| 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 892/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GRaNIE 1.7.2 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. |
| Package: GRaNIE |
| Version: 1.7.2 |
| 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_1.7.2.tar.gz |
| StartedAt: 2024-03-27 02:34:10 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 02:44:53 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 642.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GRaNIE.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.7.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 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 '1.7.2'
* 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 ... 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 ... 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
addConnections_TF_peak 6.89 2.51 47.15
generateStatsSummary 8.77 0.31 9.50
addSNPData 7.21 0.51 28.52
plotDiagnosticPlots_peakGene 6.13 0.19 6.81
calculateCommunitiesEnrichment 4.75 0.19 5.48
plotPCA_all 4.39 0.20 5.06
* 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 WARNING, 2 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck/00check.log'
for details.
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)
GRaNIE.Rcheck/GRaNIE-Ex.timings
| name | user | system | elapsed | |
| AR_classification_wrapper | 0 | 0 | 0 | |
| addConnections_TF_peak | 6.89 | 2.51 | 47.15 | |
| addConnections_peak_gene | 3.59 | 0.05 | 4.56 | |
| addData | 0 | 0 | 0 | |
| addSNPData | 7.21 | 0.51 | 28.52 | |
| addTFBS | 0 | 0 | 0 | |
| add_TF_gene_correlation | 2.36 | 0.19 | 3.01 | |
| add_featureVariation | 0 | 0 | 0 | |
| build_eGRN_graph | 2.25 | 0.16 | 3.13 | |
| calculateCommunitiesEnrichment | 4.75 | 0.19 | 5.48 | |
| calculateCommunitiesStats | 2.48 | 0.17 | 3.10 | |
| calculateGeneralEnrichment | 2.90 | 0.22 | 3.84 | |
| calculateTFEnrichment | 3.07 | 0.14 | 3.77 | |
| changeOutputDirectory | 3.68 | 0.18 | 4.54 | |
| deleteIntermediateData | 2.25 | 0.08 | 2.77 | |
| filterConnectionsForPlotting | 2.46 | 0.21 | 3.42 | |
| filterData | 2.60 | 0.15 | 3.20 | |
| filterGRNAndConnectGenes | 2.29 | 0.16 | 2.89 | |
| generateStatsSummary | 8.77 | 0.31 | 9.50 | |
| getCounts | 1.91 | 0.16 | 2.52 | |
| getGRNConnections | 2.07 | 0.06 | 2.61 | |
| getGRNSummary | 4.19 | 0.17 | 4.78 | |
| getParameters | 2.24 | 0.24 | 2.89 | |
| getTopNodes | 2.22 | 0.10 | 2.78 | |
| initializeGRN | 0.03 | 0.00 | 0.03 | |
| loadExampleObject | 1.86 | 0.15 | 2.41 | |
| nGenes | 3.36 | 0.12 | 3.92 | |
| nPeaks | 2.00 | 0.11 | 2.51 | |
| nTFs | 1.80 | 0.06 | 2.27 | |
| overlapPeaksAndTFBS | 2.00 | 0.10 | 2.51 | |
| performAllNetworkAnalyses | 0 | 0 | 0 | |
| plotCommunitiesEnrichment | 4.11 | 0.31 | 4.93 | |
| plotCommunitiesStats | 3.72 | 0.12 | 4.31 | |
| plotCorrelations | 3.89 | 0.14 | 4.42 | |
| plotDiagnosticPlots_TFPeaks | 3.59 | 0.13 | 4.24 | |
| plotDiagnosticPlots_peakGene | 6.13 | 0.19 | 6.81 | |
| plotGeneralEnrichment | 2.54 | 0.12 | 3.33 | |
| plotGeneralGraphStats | 3.52 | 0.10 | 4.06 | |
| plotPCA_all | 4.39 | 0.20 | 5.06 | |
| plotTFEnrichment | 3.25 | 0.16 | 3.86 | |
| plot_stats_connectionSummary | 3.05 | 0.63 | 3.67 | |
| visualizeGRN | 4.34 | 0.45 | 4.83 | |