##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Banksy.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Banksy_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Banksy.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Banksy/DESCRIPTION’ ... OK
* this is package ‘Banksy’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘Banksy’ 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 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) computeBanksy.Rd:81: Lost braces in \itemize; meant \describe ?
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Banksy.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Banksy
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘Banksy’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (Banksy)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(Banksy)
> 
> test_check("Banksy")
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing harmonic m = 0
Using 15 neighbors
Done
Computing harmonic m = 1
Using 15 neighbors
Centering
Done
Using seed=1000
Using seed=1000
Using seed=1000
Using seed=1000
clust_M1_lam0.2_k50_res1 --> cluster
Iteration 1
Change: 25
Iteration 2
Change: 19
Iteration 3
Change: 13
Iteration 4
Change: 10
Iteration 5
Change: 1
Iteration 6
Change: 0
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing harmonic m = 0
Using 15 neighbors
Done
Computing harmonic m = 1
Using 15 neighbors
Centering
Done
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing harmonic m = 0
Using 15 neighbors
Done
Computing harmonic m = 1
Using 15 neighbors
Centering
Done
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=30
Subsampling to 15 neighbors
Using seed=1000
Done
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=30
Subsampling to 15 neighbors
Using seed=1000
Done
Computing harmonic m = 0
Using 15 neighbors
Done
Computing harmonic m = 1
Using 15 neighbors
Centering
Done
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=309
Computing neighbors...
Spatial mode is kNN_unif
Parameters: k_geom = 15
Done
Computing neighbors...
Spatial mode is kNN_unif
Parameters: k_geom = 15
Done
Computing harmonic m = 0
Using 15 neighbors
Done
Computing harmonic m = 1
Using 15 neighbors
Centering
Done
Computing neighbors...
Spatial mode is kNN_unif
Parameters: k_geom = 309
Computing neighbors...
Spatial mode is kNN_rn
Parameters: k_geom=15, n=2
Done
Computing neighbors...
Spatial mode is kNN_rn
Parameters: k_geom=15, n=2
Done
Computing harmonic m = 0
Using 15 neighbors
Done
Computing harmonic m = 1
Using 15 neighbors
Centering
Done
Computing neighbors...
Spatial mode is kNN_rn
Parameters: k_geom=309, n=2
Computing neighbors...
Spatial mode is kNN_r
Parameters: k_geom=15
Done
Computing neighbors...
Spatial mode is kNN_r
Parameters: k_geom=15
Done
Computing harmonic m = 0
Using 15 neighbors
Done
Computing harmonic m = 1
Using 15 neighbors
Centering
Done
Computing neighbors...
Spatial mode is kNN_r
Parameters: k_geom=309
Computing neighbors...
Spatial mode is kNN_rank
Parameters: k_geom=15
Done
Computing neighbors...
Spatial mode is kNN_rank
Parameters: k_geom=15
Done
Computing harmonic m = 0
Using 15 neighbors
Done
Computing harmonic m = 1
Using 15 neighbors
Centering
Done
Computing neighbors...
Spatial mode is kNN_rank
Parameters: k_geom=309
Computing neighbors...
Spatial mode is rNN gaussian
Parameters: sigma=1.5, k_spatial=100
Done
Computing neighbors...
Spatial mode is rNN gaussian
Parameters: sigma=1.5, k_spatial=100
Done
Computing harmonic m = 0
Using 9 neighbors
Done
Computing harmonic m = 1
Using 9 neighbors
Centering
Done
Computing neighbors...
Spatial mode is rNN gaussian
Parameters: sigma=1.5, k_spatial=309
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing harmonic m = 0
Using 15 neighbors
Done
Computing harmonic m = 1
Using 15 neighbors
Centering
Done
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing harmonic m = 0
Using 15 neighbors
Done
Computing harmonic m = 1
Using 15 neighbors
Centering
Done
Scaling counts
Group: 1
Group: 2
Group: 3
Group: 4
Scaling harmonic m = 0
Group: 1
Group: 2
Group: 3
Group: 4
Scaling harmonic m = 1
Group: 1
Group: 2
Group: 3
Group: 4
Scaling counts
Group: 1
Group: 2
Group: 3
Group: 4
Scaling harmonic m = 0
Group: 1
Group: 2
Group: 3
Group: 4
Scaling harmonic m = 1
Group: 1
Group: 2
Group: 3
Group: 4
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing neighbors...
Spatial mode is kNN_median
Parameters: k_geom=15
Done
Computing harmonic m = 0
Using 15 neighbors
Done
Computing harmonic m = 1
Using 15 neighbors
Centering
Done
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 70 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 70 ]
> 
> proc.time()
   user  system elapsed 
 20.776   0.789  20.703