Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 245/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
broadSeq 1.0.0 (landing page) Rishi Das Roy
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the broadSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/broadSeq.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: broadSeq |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:broadSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings broadSeq_1.0.0.tar.gz |
StartedAt: 2024-12-20 00:34:46 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:43:49 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 542.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: broadSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:broadSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings broadSeq_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/broadSeq.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘broadSeq/DESCRIPTION’ ... OK * this is package ‘broadSeq’ version ‘1.0.0’ * 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 ‘broadSeq’ 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘BiocStyle’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE genes_plot: warning in facet(facet.by, scale = "free"): partial argument match of 'scale' to 'scales' volcanoPlot: warning in ggscatter(x = lFCName, y = "padj", color = "Significant", palette = palette, title = "Volcano plot", label = labelName, repel = TRUE, label.rectangle = TRUE, show.legend = FALSE, label.select = selectedLabel): partial argument match of 'show.legend' to 'show.legend.text' assay_plot: no visible global function definition for ‘ggarrange’ assay_plot: no visible global function definition for ‘text_grob’ biplotAnyPC: no visible binding for global variable ‘PC’ biplotAnyPC: no visible binding for global variable ‘var_pct’ biplotAnyPC: no visible global function definition for ‘pull’ biplotAnyPC: no visible binding for global variable ‘gene’ biplotAnyPC: no visible global function definition for ‘aes’ biplotAnyPC: no visible global function definition for ‘arrow’ biplotAnyPC: no visible global function definition for ‘unit’ combinedEnrichment: no visible global function definition for ‘keytypes’ extract_topGeneLoadings: no visible global function definition for ‘desc’ extract_topGeneLoadings: no visible global function definition for ‘all_of’ genes_plot: no visible global function definition for ‘rowData’ normalizeEdgerCPM: no visible global function definition for ‘is’ plotAnyPC: no visible binding for global variable ‘PC’ plotAnyPC: no visible binding for global variable ‘var_pct’ plotHeatmapCluster: no visible global function definition for ‘is’ plotHeatmapCluster: no visible global function definition for ‘colData’ plotHeatmapCluster: no visible global function definition for ‘rowData’ plotHeatmapCluster: no visible global function definition for ‘all_of’ plot_MDS: no visible global function definition for ‘is’ plot_MDS: no visible global function definition for ‘dist’ plot_MDS: no visible global function definition for ‘cmdscale’ plot_MDS: no visible global function definition for ‘colData’ prcompTidy: no visible global function definition for ‘is’ prcompTidy: no visible global function definition for ‘prcomp’ prcompTidy: no visible binding for global variable ‘stdev’ prcompTidy: no visible binding for global variable ‘var’ prcompTidy: no visible binding for global variable ‘var_pct’ prcompTidy: no visible binding for global variable ‘PC’ prcompTidy: no visible binding for global variable ‘.’ prcompTidy: no visible binding for global variable ‘gene’ transformDESeq2: no visible global function definition for ‘is’ transformDESeq2: no visible global function definition for ‘assays<-’ transformDESeq2: no visible global function definition for ‘assay’ use_DELocal: no visible global function definition for ‘desc’ use_DELocal: no visible binding for global variable ‘relative.logFC’ use_EBSeq: no visible global function definition for ‘desc’ use_EBSeq: no visible binding for global variable ‘PPDE’ use_NOIseq: no visible global function definition for ‘desc’ use_NOIseq: no visible binding for global variable ‘prob’ use_SAMseq: no visible binding for global variable ‘q-value(%)’ use_deseq2: no visible binding for global variable ‘padj’ use_edgeR: no visible binding for global variable ‘logFC’ use_edgeR: no visible binding for global variable ‘FDR’ use_edgeR: no visible global function definition for ‘:=’ use_limma: no visible global function definition for ‘par’ use_limma: no visible binding for global variable ‘logFC’ use_limma: no visible binding for global variable ‘B’ use_limma: no visible global function definition for ‘:=’ volcanoPlot: no visible global function definition for ‘labs’ volcanoPlot: no visible global function definition for ‘geom_abline’ Undefined global functions or variables: . := B FDR PC PPDE aes all_of arrow assay assays<- cmdscale colData desc dist gene geom_abline ggarrange is keytypes labs logFC padj par prcomp prob pull q-value(%) relative.logFC rowData stdev text_grob unit var var_pct Consider adding importFrom("graphics", "par") importFrom("methods", "is") importFrom("stats", "cmdscale", "dist", "prcomp", "var") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 use_multDE 13.585 0.231 15.951 sampleAssay_plot 10.265 0.452 13.341 plot_MDS 7.632 0.155 9.102 transformDESeq2 6.332 0.061 7.182 use_deseq2 6.162 0.097 7.126 use_DELocal 5.268 0.058 5.947 * 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 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/broadSeq.Rcheck/00check.log’ for details.
broadSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL broadSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘broadSeq’ ... ** using staged installation ** R ** inst ** 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 (broadSeq)
broadSeq.Rcheck/broadSeq-Ex.timings
name | user | system | elapsed | |
genes_plot | 3.928 | 0.200 | 4.948 | |
normalizeEdgerCPM | 1.302 | 0.043 | 1.506 | |
plotHeatmapCluster | 0.559 | 0.021 | 0.611 | |
plot_MDS | 7.632 | 0.155 | 9.102 | |
prcompTidy | 1.258 | 0.040 | 2.339 | |
round_df | 0.008 | 0.005 | 0.022 | |
sampleAssay_plot | 10.265 | 0.452 | 13.341 | |
transformDESeq2 | 6.332 | 0.061 | 7.182 | |
use_DELocal | 5.268 | 0.058 | 5.947 | |
use_EBSeq | 1.044 | 0.040 | 1.270 | |
use_NOIseq | 0.723 | 0.016 | 0.825 | |
use_deseq2 | 6.162 | 0.097 | 7.126 | |
use_edgeR | 0.497 | 0.004 | 0.524 | |
use_limma | 0.238 | 0.004 | 0.309 | |
use_multDE | 13.585 | 0.231 | 15.951 | |