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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 1220/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaNeighbor 1.24.0  (landing page)
Stephan Fischer
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/MetaNeighbor
git_branch: RELEASE_3_19
git_last_commit: ddb782c
git_last_commit_date: 2024-04-30 11:03:00 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for MetaNeighbor on nebbiolo1

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.

raw results


Summary

Package: MetaNeighbor
Version: 1.24.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MetaNeighbor.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MetaNeighbor_1.24.0.tar.gz
StartedAt: 2024-06-20 00:52:53 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 00:54:55 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 122.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MetaNeighbor.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MetaNeighbor.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MetaNeighbor_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MetaNeighbor.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MetaNeighbor/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaNeighbor’ version ‘1.24.0’
* 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   18.215  0.488  18.704
plotBPlot      11.503  0.277  11.780
neighborVoting 10.748  0.228  10.976
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/MetaNeighbor.Rcheck/00check.log’
for details.


Installation output

MetaNeighbor.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MetaNeighbor
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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)

Tests output

MetaNeighbor.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
  0.417   0.050   0.454 

Example timings

MetaNeighbor.Rcheck/MetaNeighbor-Ex.timings

nameusersystemelapsed
MetaNeighbor18.215 0.48818.704
MetaNeighborUS2.8290.1602.990
neighborVoting10.748 0.22810.976
plotBPlot11.503 0.27711.780
plotHeatmap1.7260.0281.754
plotHeatmapPretrained2.4380.0282.466
plotUpset1.1480.0281.176
topHits1.7390.0201.759
topHitsByStudy1.9040.0241.928
trainModel1.0860.0631.149
variableGenes0.2470.0160.263