Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:39 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 906/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.8.0 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 1.8.0 |
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: 2024-06-23 23:53:30 -0400 (Sun, 23 Jun 2024) |
EndedAt: 2024-06-24 00:03:51 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 620.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GRaNIE.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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 9.272 0.136 11.932 plotCommunitiesStats 6.326 0.100 6.886 plotDiagnosticPlots_peakGene 5.600 0.120 6.171 addSNPData 5.157 0.224 7.553 getGRNSummary 4.967 0.196 6.335 visualizeGRN 4.511 0.056 5.087 plotDiagnosticPlots_TFPeaks 4.231 0.056 5.227 plotCommunitiesEnrichment 4.121 0.122 5.339 filterData 4.006 0.064 5.688 * 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.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
GRaNIE.Rcheck/GRaNIE-Ex.timings
name | user | system | elapsed | |
AR_classification_wrapper | 0.001 | 0.000 | 0.000 | |
addConnections_TF_peak | 2.924 | 0.172 | 4.075 | |
addConnections_peak_gene | 2.812 | 0.104 | 3.376 | |
addData | 0 | 0 | 0 | |
addSNPData | 5.157 | 0.224 | 7.553 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 1.607 | 0.032 | 2.066 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 1.687 | 0.036 | 2.176 | |
calculateCommunitiesEnrichment | 3.480 | 0.112 | 4.027 | |
calculateCommunitiesStats | 1.590 | 0.032 | 2.055 | |
calculateGeneralEnrichment | 1.873 | 0.052 | 2.379 | |
calculateTFEnrichment | 2.061 | 0.072 | 2.563 | |
changeOutputDirectory | 1.605 | 0.036 | 2.105 | |
deleteIntermediateData | 2.701 | 0.057 | 3.189 | |
filterConnectionsForPlotting | 1.680 | 0.022 | 2.134 | |
filterData | 4.006 | 0.064 | 5.688 | |
filterGRNAndConnectGenes | 1.900 | 0.020 | 2.362 | |
generateStatsSummary | 9.272 | 0.136 | 11.932 | |
getCounts | 3.187 | 0.124 | 4.899 | |
getGRNConnections | 2.119 | 0.036 | 2.622 | |
getGRNSummary | 4.967 | 0.196 | 6.335 | |
getParameters | 2.804 | 0.051 | 4.047 | |
getTopNodes | 2.267 | 0.048 | 3.212 | |
initializeGRN | 0.037 | 0.004 | 0.041 | |
loadExampleObject | 2.834 | 0.088 | 3.534 | |
nGenes | 2.730 | 0.088 | 3.957 | |
nPeaks | 3.711 | 0.160 | 4.334 | |
nTFs | 2.758 | 0.043 | 4.322 | |
overlapPeaksAndTFBS | 2.119 | 0.064 | 2.656 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 4.121 | 0.122 | 5.339 | |
plotCommunitiesStats | 6.326 | 0.100 | 6.886 | |
plotCorrelations | 2.489 | 0.063 | 3.116 | |
plotDiagnosticPlots_TFPeaks | 4.231 | 0.056 | 5.227 | |
plotDiagnosticPlots_peakGene | 5.600 | 0.120 | 6.171 | |
plotGeneralEnrichment | 2.047 | 0.040 | 2.525 | |
plotGeneralGraphStats | 2.733 | 0.040 | 3.213 | |
plotPCA_all | 3.676 | 0.164 | 4.270 | |
plotTFEnrichment | 2.253 | 0.031 | 2.735 | |
plot_stats_connectionSummary | 2.304 | 0.045 | 2.807 | |
visualizeGRN | 4.511 | 0.056 | 5.087 | |