##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:VisiumIO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings VisiumIO_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/VisiumIO.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VisiumIO/DESCRIPTION’ ... OK
* this is package ‘VisiumIO’ version ‘1.2.0’
* 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 ‘VisiumIO’ 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 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
.file_or_filelist: no visible global function definition for ‘TENxH5’
.file_or_filelist: no visible global function definition for
  ‘TENxFileList’
.find_file_or_dir: no visible global function definition for ‘TENxH5’
.find_file_or_dir: no visible global function definition for
  ‘TENxFileList’
TENxSpatialList: no visible global function definition for
  ‘TENxFileList’
TENxVisium: no visible global function definition for ‘TENxH5’
TENxVisium: no visible global function definition for ‘TENxFileList’
TENxVisiumHD: no visible global function definition for ‘TENxH5’
TENxVisiumHD: no visible global function definition for ‘TENxFileList’
Undefined global functions or variables:
  TENxFileList TENxH5
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/VisiumIO.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL VisiumIO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘VisiumIO’ ...
** using staged installation
** R
** 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 (VisiumIO)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> if (requireNamespace("tinytest", quietly = TRUE))
+     tinytest::test_package("VisiumIO")
Loading required package: TENxIO
Loading required package: SingleCellExperiment
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, 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


test_TENxSpatialList-class.R..    0 tests    
test_TENxSpatialList-class.R..    0 tests    
test_TENxSpatialList-class.R..    1 tests OK 
test_TENxSpatialList-class.R..    2 tests OK 
test_TENxSpatialList-class.R..    3 tests OK 
test_TENxSpatialList-class.R..    4 tests OK 
test_TENxSpatialList-class.R..    5 tests OK 
test_TENxSpatialList-class.R..    6 tests OK 
test_TENxSpatialList-class.R..    6 tests OK 
test_TENxSpatialList-class.R..    7 tests OK 
test_TENxSpatialList-class.R..    7 tests OK 
test_TENxSpatialList-class.R..    8 tests OK 
test_TENxSpatialList-class.R..    8 tests OK 
test_TENxSpatialList-class.R..    9 tests OK 
test_TENxSpatialList-class.R..   10 tests OK 
test_TENxSpatialList-class.R..   10 tests OK 
test_TENxSpatialList-class.R..   10 tests OK 
test_TENxSpatialList-class.R..   11 tests OK 
test_TENxSpatialList-class.R..   12 tests OK 
test_TENxSpatialList-class.R..   13 tests OK 
test_TENxSpatialList-class.R..   14 tests OK 
test_TENxSpatialList-class.R..   15 tests OK 0.3s

test_TENxSpaticalCSV.R........    0 tests    
test_TENxSpaticalCSV.R........    1 tests OK 
test_TENxSpaticalCSV.R........    1 tests OK 
test_TENxSpaticalCSV.R........    1 tests OK 
test_TENxSpaticalCSV.R........    2 tests OK 
test_TENxSpaticalCSV.R........    3 tests OK 
test_TENxSpaticalCSV.R........    4 tests OK 
test_TENxSpaticalCSV.R........    5 tests OK 
test_TENxSpaticalCSV.R........    6 tests OK 
test_TENxSpaticalCSV.R........    6 tests OK 
test_TENxSpaticalCSV.R........    6 tests OK 
test_TENxSpaticalCSV.R........    6 tests OK 
test_TENxSpaticalCSV.R........    7 tests OK 1.0s

test_TENxVisium-class.R.......    0 tests    
test_TENxVisium-class.R.......    0 tests    
test_TENxVisium-class.R.......    1 tests OK 
test_TENxVisium-class.R.......    2 tests OK 
test_TENxVisium-class.R.......    3 tests OK 
test_TENxVisium-class.R.......    3 tests OK 
test_TENxVisium-class.R.......    4 tests OK 
test_TENxVisium-class.R.......    5 tests OK 
test_TENxVisium-class.R.......    5 tests OK 
test_TENxVisium-class.R.......    6 tests OK 
test_TENxVisium-class.R.......    7 tests OK 
test_TENxVisium-class.R.......    8 tests OK 
test_TENxVisium-class.R.......    8 tests OK 
test_TENxVisium-class.R.......    9 tests OK 
test_TENxVisium-class.R.......   10 tests OK 
test_TENxVisium-class.R.......   11 tests OK 
test_TENxVisium-class.R.......   12 tests OK 
test_TENxVisium-class.R.......   13 tests OK 3.2s

test_TENxVisiumList-class.R...    0 tests    
test_TENxVisiumList-class.R...    0 tests    
test_TENxVisiumList-class.R...    1 tests OK 
test_TENxVisiumList-class.R...    2 tests OK 
test_TENxVisiumList-class.R...    3 tests OK 
test_TENxVisiumList-class.R...    4 tests OK 
test_TENxVisiumList-class.R...    4 tests OK 
test_TENxVisiumList-class.R...    5 tests OK 2.9s
All ok, 40 results (7.5s)
> 
> proc.time()
   user  system elapsed 
 17.257   0.674  17.872