Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MetaNeighbor |
Version: 1.26.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MetaNeighbor.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MetaNeighbor_1.26.0.tar.gz |
StartedAt: 2024-11-20 09:38:51 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 09:52:12 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 801.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MetaNeighbor.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:MetaNeighbor.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MetaNeighbor_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MetaNeighbor.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MetaNeighbor 218.844 0.638 218.997 neighborVoting 210.844 0.220 210.662 plotBPlot 209.667 0.115 209.341 MetaNeighborUS 20.844 0.052 20.850 topHits 20.807 0.088 20.848 plotHeatmapPretrained 20.787 0.060 20.802 plotHeatmap 20.154 0.040 20.150 topHitsByStudy 20.158 0.020 20.129 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/MetaNeighbor.Rcheck/00check.log’ for details.
MetaNeighbor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MetaNeighbor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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 0.617 0.055 0.573
MetaNeighbor.Rcheck/MetaNeighbor-Ex.timings
name | user | system | elapsed | |
MetaNeighbor | 218.844 | 0.638 | 218.997 | |
MetaNeighborUS | 20.844 | 0.052 | 20.850 | |
neighborVoting | 210.844 | 0.220 | 210.662 | |
plotBPlot | 209.667 | 0.115 | 209.341 | |
plotHeatmap | 20.154 | 0.040 | 20.150 | |
plotHeatmapPretrained | 20.787 | 0.060 | 20.802 | |
plotUpset | 1.652 | 0.024 | 1.558 | |
topHits | 20.807 | 0.088 | 20.848 | |
topHitsByStudy | 20.158 | 0.020 | 20.129 | |
trainModel | 0.616 | 0.007 | 0.542 | |
variableGenes | 0.487 | 0.000 | 0.406 | |