##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SpatialFeatureExperiment_1.1.5.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.1.5’
* package encoding: UTF-8
* 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 ‘SpatialFeatureExperiment’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::disableValidity’ ‘spdep:::minmax.listw’
  See the note in ?`:::` about the use of this operator.
* 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 ... 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                      user system elapsed
dimGeometries                                        5.266  0.667   6.529
findVisiumGraph                                      5.067  0.701   6.314
cbind-SpatialFeatureExperiment-method                4.949  0.712   6.209
removeEmptySpace                                     5.086  0.470   5.847
SpatialFeatureExperiment-subset                      4.879  0.417   5.709
spatialGraphs                                        4.653  0.496   5.699
findSpatialNeighbors-SpatialFeatureExperiment-method 4.477  0.548   5.566
* 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 ...
  ‘SFE.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SpatialFeatureExperiment
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘SpatialFeatureExperiment’ ...
** using staged installation
** R
** data
** 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 (SpatialFeatureExperiment)

R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(SpatialFeatureExperiment)
> 
> test_check("SpatialFeatureExperiment")
Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE
Loading required package: SummarizedExperiment
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, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

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

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Testing dist_type none style W 
Testing dist_type idw style W 
Testing dist_type exp style W 
Testing dist_type dpd style W 
Testing dist_type idw style raw 
Testing dist_type idw style W 
Testing dist_type idw style B 
Testing dist_type idw style C 
Testing dist_type idw style U 
Testing dist_type idw style minmax 
Testing dist_type idw style S 
Testing dist_type none style W 
Testing dist_type idw style W 
Testing dist_type exp style W 
Testing dist_type dpd style W 
Testing dist_type idw style raw 
Testing dist_type idw style W 
Testing dist_type idw style B 
Testing dist_type idw style C 
Testing dist_type idw style U 
Testing dist_type idw style minmax 
Testing dist_type idw style S 
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'dgCMatrix'
updateObjectFromSlots(object = 'dgCMatrix' class = 'dgCMatrix')
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object = 'list')
updateObject(object="ANY") default for object of class 'character'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'character'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'numeric'
[updateObject] Validating the updated object ... OK
updateObject(object = 'list')
[updateObject] Validating the updated object ... OK
heuristic updateObjectFromSlots, method 1
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] CompressedGRangesList object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of GRanges object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of IRanges object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Internal representation of GRanges object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of IRanges object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Internal representation of PartitioningByEnd object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 441 ]
> 
> proc.time()
   user  system elapsed 
 67.900   4.528  74.107