Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:45 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the MetaNeighbor package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1090/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MetaNeighbor 1.12.0 (landing page) Stephan Fischer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: MetaNeighbor |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MetaNeighbor.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MetaNeighbor_1.12.0.tar.gz |
StartedAt: 2021-10-14 10:31:12 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:33:04 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 111.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MetaNeighbor.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MetaNeighbor.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MetaNeighbor_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MetaNeighbor.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MetaNeighbor/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetaNeighbor’ version ‘1.12.0’ * 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 ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: data 7.1Mb * 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 R 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 ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... WARNING LazyData DB of 7.1 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * 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 18.044 0.548 18.592 neighborVoting 11.748 0.136 11.884 plotBPlot 11.628 0.144 11.772 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/MetaNeighbor.Rcheck/00check.log’ for details.
MetaNeighbor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MetaNeighbor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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 0.401 0.040 0.423
MetaNeighbor.Rcheck/MetaNeighbor-Ex.timings
name | user | system | elapsed | |
MetaNeighbor | 18.044 | 0.548 | 18.592 | |
MetaNeighborUS | 2.726 | 0.156 | 2.883 | |
neighborVoting | 11.748 | 0.136 | 11.884 | |
plotBPlot | 11.628 | 0.144 | 11.772 | |
plotHeatmap | 2.495 | 0.032 | 2.527 | |
plotHeatmapPretrained | 2.024 | 0.052 | 2.076 | |
plotUpset | 1.676 | 0.068 | 1.743 | |
topHits | 1.859 | 0.088 | 1.947 | |
topHitsByStudy | 2.471 | 0.112 | 2.583 | |
trainModel | 0.524 | 0.048 | 0.573 | |
variableGenes | 0.967 | 0.047 | 1.015 | |