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This page was generated on 2023-01-02 09:00:37 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R 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

CHECK results for MetaNeighbor on palomino5


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.

raw results

Package 1136/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaNeighbor 1.19.0  (landing page)
Stephan Fischer
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/MetaNeighbor
git_branch: master
git_last_commit: f3779bf
git_last_commit_date: 2022-11-01 11:16:53 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

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

Command output

##############################################################################
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###
### 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
###
##############################################################################
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* 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.



Installation output

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)

Tests output

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 

Example timings

MetaNeighbor.Rcheck/MetaNeighbor-Ex.timings

nameusersystemelapsed
MetaNeighbor13.82 0.5014.32
MetaNeighborUS2.080.182.26
neighborVoting9.140.149.29
plotBPlot8.640.188.81
plotHeatmap1.480.071.57
plotHeatmapPretrained1.740.081.81
plotUpset0.980.081.08
topHits1.460.161.63
topHitsByStudy1.540.111.64
trainModel0.430.060.50
variableGenes0.710.040.74