Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:37 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 |
To the developers/maintainers of the MetaNeighbor package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1136/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MetaNeighbor 1.19.0 (landing page) Stephan Fischer
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: MetaNeighbor |
Version: 1.19.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MetaNeighbor.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MetaNeighbor_1.19.0.tar.gz |
StartedAt: 2022-12-29 01:12:26 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 01:13:56 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 89.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MetaNeighbor.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MetaNeighbor.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MetaNeighbor_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MetaNeighbor.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'MetaNeighbor/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MetaNeighbor' version '1.19.0' * 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 whether package 'MetaNeighbor' 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 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 ... 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 13.82 0.50 14.32 neighborVoting 9.14 0.14 9.29 plotBPlot 8.64 0.18 8.81 * 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 NOTE See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MetaNeighbor.Rcheck/00check.log' for details.
MetaNeighbor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL MetaNeighbor ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 0.45 0.06 0.50
MetaNeighbor.Rcheck/MetaNeighbor-Ex.timings
name | user | system | elapsed | |
MetaNeighbor | 13.82 | 0.50 | 14.32 | |
MetaNeighborUS | 2.08 | 0.18 | 2.26 | |
neighborVoting | 9.14 | 0.14 | 9.29 | |
plotBPlot | 8.64 | 0.18 | 8.81 | |
plotHeatmap | 1.48 | 0.07 | 1.57 | |
plotHeatmapPretrained | 1.74 | 0.08 | 1.81 | |
plotUpset | 0.98 | 0.08 | 1.08 | |
topHits | 1.46 | 0.16 | 1.63 | |
topHitsByStudy | 1.54 | 0.11 | 1.64 | |
trainModel | 0.43 | 0.06 | 0.50 | |
variableGenes | 0.71 | 0.04 | 0.74 | |