Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:40 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 239/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
broadSeq 1.1.0 (landing page) Rishi Das Roy
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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: 1.1.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:broadSeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings broadSeq_1.1.0.tar.gz |
StartedAt: 2024-12-22 20:25:42 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 20:31:49 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 366.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: broadSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:broadSeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings broadSeq_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/broadSeq.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘broadSeq/DESCRIPTION’ ... OK * this is package ‘broadSeq’ version ‘1.1.0’ * 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 loading without being on the library search path ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: genes_plot.Rd: SummarizedExperiment, ggboxplot normalizeEdgerCPM.Rd: SummarizedExperiment, normLibSizes, cpm plotHeatmapCluster.Rd: SummarizedExperiment, pheatmap plot_MDS.Rd: SummarizedExperiment, ggscatter prcompTidy.Rd: SummarizedExperiment, ggscatter sampleAssay_plot.Rd: SummarizedExperiment, ggboxplot transformDESeq2.Rd: SummarizedExperiment, varianceStabilizingTransformation, normTransform, rlog use_DELocal.Rd: SummarizedExperiment, DELocal use_EBSeq.Rd: SummarizedExperiment, GetDEResults use_NOIseq.Rd: noiseqbio, SummarizedExperiment use_SAMseq.Rd: SummarizedExperiment use_deseq2.Rd: SummarizedExperiment, results, DESeqResults use_edgeR.Rd: SummarizedExperiment, glmLRT, exactTest, topTags use_limma.Rd: SummarizedExperiment use_multDE.Rd: SummarizedExperiment Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 sampleAssay_plot 8.655 0.082 8.738 use_multDE 8.016 0.096 8.111 plot_MDS 5.541 0.035 5.576 transformDESeq2 5.173 0.004 5.181 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/broadSeq.Rcheck/00check.log’ for details.
broadSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL broadSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 | 2.935 | 0.182 | 3.118 | |
normalizeEdgerCPM | 1.381 | 0.016 | 1.396 | |
plotHeatmapCluster | 0.417 | 0.012 | 0.430 | |
plot_MDS | 5.541 | 0.035 | 5.576 | |
prcompTidy | 1.705 | 0.008 | 1.712 | |
round_df | 0.005 | 0.001 | 0.006 | |
sampleAssay_plot | 8.655 | 0.082 | 8.738 | |
transformDESeq2 | 5.173 | 0.004 | 5.181 | |
use_DELocal | 2.494 | 0.021 | 2.517 | |
use_EBSeq | 0.612 | 0.016 | 0.629 | |
use_NOIseq | 0.455 | 0.005 | 0.461 | |
use_deseq2 | 3.885 | 0.031 | 3.917 | |
use_edgeR | 0.369 | 0.001 | 0.371 | |
use_limma | 0.164 | 0.002 | 0.165 | |
use_multDE | 8.016 | 0.096 | 8.111 | |