Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:52 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tokay2


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1102/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaNeighbor 1.14.0  (landing page)
Stephan Fischer
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MetaNeighbor
git_branch: RELEASE_3_14
git_last_commit: 9ed0bce
git_last_commit_date: 2021-10-26 12:40:37 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MetaNeighbor
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaNeighbor.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MetaNeighbor_1.14.0.tar.gz
StartedAt: 2022-04-12 22:32:57 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 22:36:31 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 214.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MetaNeighbor.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaNeighbor.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MetaNeighbor_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MetaNeighbor.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MetaNeighbor/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetaNeighbor' version '1.14.0'
* 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 ... NOTE
  installed size is  7.5Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ยง1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
MetaNeighbor   22.55   0.81   23.36
neighborVoting 15.25   0.51   15.77
plotBPlot      14.66   0.39   15.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
MetaNeighbor   17.97   0.68   18.64
plotBPlot      12.78   0.43   13.21
neighborVoting 12.42   0.39   12.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MetaNeighbor.Rcheck/00check.log'
for details.



Installation output

MetaNeighbor.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MetaNeighbor_1.14.0.tar.gz && rm -rf MetaNeighbor.buildbin-libdir && mkdir MetaNeighbor.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MetaNeighbor.buildbin-libdir MetaNeighbor_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MetaNeighbor_1.14.0.zip && rm MetaNeighbor_1.14.0.tar.gz MetaNeighbor_1.14.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 2634k    1 44467    0     0   278k      0  0:00:09 --:--:--  0:00:09  278k
 60 2634k   60 1601k    0     0  1385k      0  0:00:01  0:00:01 --:--:-- 1385k
100 2634k  100 2634k    0     0  1641k      0  0:00:01  0:00:01 --:--:-- 1641k

install for i386

* 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
  converting help for package 'MetaNeighbor'
    finding HTML links ... done
    GOhuman                                 html  
    GOmouse                                 html  
    MetaNeighbor                            html  
    MetaNeighborUS                          html  
    extendClusterSet                        html  
    extractMetaClusters                     html  
    getCellType                             html  
    getStudyId                              html  
    ggPlotHeatmap                           html  
    makeClusterGraph                        html  
    makeClusterName                         html  
    mergeSCE                                html  
    mn_data                                 html  
    neighborVoting                          html  
    orderCellTypes                          html  
    plotBPlot                               html  
    plotClusterGraph                        html  
    plotDotPlot                             html  
    plotHeatmap                             html  
    plotHeatmapPretrained                   html  
    plotMetaClusters                        html  
    plotUpset                               html  
    scoreMetaClusters                       html  
    splitClusters                           html  
    splitTestClusters                       html  
    splitTrainClusters                      html  
    standardizeLabel                        html  
    subsetClusterGraph                      html  
    topHits                                 html  
    topHitsByStudy                          html  
    trainModel                              html  
    variableGenes                           html  
** 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

install for x64

* installing *source* package 'MetaNeighbor' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MetaNeighbor' as MetaNeighbor_1.14.0.zip
* DONE (MetaNeighbor)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MetaNeighbor' successfully unpacked and MD5 sums checked

Tests output

MetaNeighbor.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   0.87    0.06    0.92 

MetaNeighbor.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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 
   0.68    0.10    0.78 

Example timings

MetaNeighbor.Rcheck/examples_i386/MetaNeighbor-Ex.timings

nameusersystemelapsed
MetaNeighbor22.55 0.8123.36
MetaNeighborUS3.490.604.07
neighborVoting15.25 0.5115.77
plotBPlot14.66 0.3915.04
plotHeatmap2.800.172.97
plotHeatmapPretrained2.440.132.56
plotUpset1.370.091.47
topHits2.990.253.23
topHitsByStudy2.640.052.69
trainModel0.840.080.92
variableGenes1.080.011.10

MetaNeighbor.Rcheck/examples_x64/MetaNeighbor-Ex.timings

nameusersystemelapsed
MetaNeighbor17.97 0.6818.64
MetaNeighborUS3.060.183.25
neighborVoting12.42 0.3912.81
plotBPlot12.78 0.4313.21
plotHeatmap2.720.152.87
plotHeatmapPretrained2.280.172.45
plotUpset1.690.081.77
topHits1.920.142.06
topHitsByStudy2.060.112.17
trainModel1.170.031.21
variableGenes0.500.040.53