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 1210/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MetaNeighbor 1.26.0 (landing page) Stephan Fischer
| 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 MetaNeighbor package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetaNeighbor.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: MetaNeighbor |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetaNeighbor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetaNeighbor_1.26.0.tar.gz |
StartedAt: 2024-12-20 05:45:31 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:48:43 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 191.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MetaNeighbor.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetaNeighbor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetaNeighbor_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MetaNeighbor.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 ‘MetaNeighbor/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetaNeighbor’ version ‘1.26.0’ * 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 ‘MetaNeighbor’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE MetaNeighbor : <anonymous>: no visible binding for global variable ‘cell_type’ ggPlotHeatmap: no visible binding for global variable ‘target_ct’ ggPlotHeatmap: no visible binding for global variable ‘ref_ct’ ggPlotHeatmap: no visible binding for global variable ‘auroc’ is_reciprocal_top_hit: no visible binding for global variable ‘auroc’ is_reciprocal_top_hit: no visible binding for global variable ‘ref_cell_type’ is_reciprocal_top_hit: no visible binding for global variable ‘target_cell_type’ is_reciprocal_top_hit: no visible binding for global variable ‘reciprocal_cell_type’ is_reciprocal_top_hit: no visible binding for global variable ‘is_reciprocal’ plotDotPlot: no visible binding for global variable ‘cluster’ plotDotPlot: no visible binding for global variable ‘gene’ plotDotPlot: no visible binding for global variable ‘cell_type’ plotDotPlot: no visible binding for global variable ‘average_expression’ plotDotPlot: no visible binding for global variable ‘percent_expressing’ plotMetaClusters: no visible global function definition for ‘order_sym_matrix’ topHitsByStudy: no visible binding for global variable ‘ref_cell_type’ topHitsByStudy: no visible binding for global variable ‘target_cell_type’ topHitsByStudy: no visible binding for global variable ‘ref_study’ topHitsByStudy: no visible binding for global variable ‘target_study’ topHitsByStudy: no visible binding for global variable ‘.’ topHitsByStudy: no visible binding for global variable ‘pair_id’ topHitsByStudy: no visible binding for global variable ‘is_reciprocal’ topHitsByStudy: no visible global function definition for ‘desc’ topHitsByStudy: no visible binding for global variable ‘Match_type’ variableGenes: no visible binding for global variable ‘gene’ variableGenes: no visible binding for global variable ‘is_hvg’ variableGenes: no visible binding for global variable ‘var_quant’ variableGenes: no visible binding for global variable ‘recurrence’ variableGenes: no visible global function definition for ‘desc’ variableGenes: no visible binding for global variable ‘score’ variable_genes_single_exp: no visible binding for global variable ‘bin_med’ variable_genes_single_exp: no visible binding for global variable ‘variance’ variable_genes_single_exp: no visible binding for global variable ‘var_quant’ Undefined global functions or variables: . Match_type auroc average_expression bin_med cell_type cluster desc gene is_hvg is_reciprocal order_sym_matrix pair_id percent_expressing reciprocal_cell_type recurrence ref_cell_type ref_ct ref_study score target_cell_type target_ct target_study var_quant variance * checking Rd files ... NOTE checkRd: (-1) extractMetaClusters.Rd:25: Lost braces; missing escapes or markup? 25 | if 1<->2 and 1<->3 are reciprocal top hits, {1, 2, 3} is a meta-cluster, | ^ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MetaNeighbor 33.129 1.209 34.885 neighborVoting 19.708 0.410 20.489 plotBPlot 19.436 0.395 20.133 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MetaNeighbor.Rcheck/00check.log’ for details.
MetaNeighbor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MetaNeighbor ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MetaNeighbor’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (MetaNeighbor)
MetaNeighbor.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(MetaNeighbor) > > test_check("MetaNeighbor") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] > > proc.time() user system elapsed 0.969 0.169 1.118
MetaNeighbor.Rcheck/MetaNeighbor-Ex.timings
name | user | system | elapsed | |
MetaNeighbor | 33.129 | 1.209 | 34.885 | |
MetaNeighborUS | 4.299 | 0.342 | 4.700 | |
neighborVoting | 19.708 | 0.410 | 20.489 | |
plotBPlot | 19.436 | 0.395 | 20.133 | |
plotHeatmap | 3.243 | 0.115 | 3.473 | |
plotHeatmapPretrained | 3.685 | 0.101 | 3.988 | |
plotUpset | 3.152 | 0.079 | 3.281 | |
topHits | 3.114 | 0.097 | 3.262 | |
topHitsByStudy | 3.312 | 0.099 | 3.445 | |
trainModel | 1.319 | 0.065 | 1.402 | |
variableGenes | 0.489 | 0.011 | 0.502 | |