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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:looking4clusters.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings looking4clusters_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/looking4clusters.Rcheck’
* using R Under development (unstable) (2026-03-26 r89717)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-09 23:02:27 UTC
* using option ‘--no-vignettes’
* checking for file ‘looking4clusters/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘looking4clusters’ version ‘1.1.0’
* 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 ‘looking4clusters’ 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 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 ... 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 ‘looking4clusters-Tests.R’
 ERROR
Running the tests in ‘tests/looking4clusters-Tests.R’ failed.
Last 13 lines of output:
  
  The following object is masked from 'package:BiocGenerics':
  
      intersect
  
  The following objects are masked from 'package:base':
  
      intersect, t
  
  Error: package or namespace load failed for 'Seurat' in dyn.load(file, DLLpath = DLLpath, ...):
   unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
    dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
    Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
    Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
  Execution halted
* 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 ERROR
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/looking4clusters.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL looking4clusters
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘looking4clusters’ ...
** this is package ‘looking4clusters’ version ‘1.1.0’
** 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 (looking4clusters)

R Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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(looking4clusters)
> 
> object <- looking4clusters(iris[,1:4],running_all=FALSE)
> object <- addcluster(object,iris[,5],"species",myGroups=TRUE)
> PCAcomponents <- prcomp(data.matrix(iris[,1:4]),scale=FALSE)
> pca<-PCAcomponents$x[,1:2]
> object <- addreduction(object,pca,"pca")
> l4chtml(object,includeData=TRUE,directory="l4c_saved")
The graph has been generated in the "/Users/biocbuild/bbs-3.23-bioc/meat/looking4clusters.Rcheck/tests/l4c_saved" path.
> 
> # get clusters (auto)
> obj <- looking4clusters(iris[,1:4], groups=iris[,5])
Running kmeans...
Running pam and hclust...
Running pca...
Running tsne...
Running mds...
Running nmf...
Running umap...
> print(object)
An object of class looking4clusters
4 variables across 150 samples
1 clusters added: species
1 dimensional reductions added: pca
> 
> # single-cell RNAseq
> library(scRNAseq)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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

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

    rowMedians

Loading required package: GenomicRanges
Loading required package: stats4
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: Seqinfo
> sce <- ReprocessedAllenData("tophat_counts")
> counts <- assay(sce, "tophat_counts")
> 
> obj <- looking4clusters(t(counts), groups=colData(sce)[,'dissection_s'],
+     components=TRUE)
Too large matrix, could cause performance problems with some methods,
they will be omitted
Running kmeans...
Running pam and hclust...
Running pca...
Running tsne...
Running mds...
Running umap...
> l4chtml(obj, includeData=TRUE)
> 
> # SingleCellExperiment
> libsizes <- colSums(counts)
> size.factors <- libsizes/mean(libsizes)
> logcounts(sce) <- log2(t(t(counts)/size.factors) + 1)
The application cannot be opened for an unexpected reason, error=Error Domain=RBSRequestErrorDomain Code=5 "Launch failed." UserInfo={NSLocalizedFailureReason=Launch failed., NSUnderlyingError=0x7c6c39da0 {Error Domain=OSLaunchdErrorDomain Code=125 "Domain does not support specified action" UserInfo={NSLocalizedFailureReason=Domain does not support specified action}}}
> 
> pca_data <- prcomp(t(logcounts(sce)), rank=50)
> 
> reducedDims(sce) <- list(PCA=pca_data$x)
> 
> obj <- looking4clusters(sce, groups="dissection_s")
> l4chtml(object,directory="l4c_saved")
The graph has been generated in the "/Users/biocbuild/bbs-3.23-bioc/meat/looking4clusters.Rcheck/tests/l4c_saved" path.
> 
> # seurat
> library(Seurat)
Loading required package: SeuratObject
Loading required package: sp

Attaching package: 'sp'

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

    %over%


Attaching package: 'SeuratObject'

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

    Assays

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

    intersect

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

    intersect

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

    intersect

The following object is masked from 'package:S4Vectors':

    intersect

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

    intersect

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

    intersect, t

Error: package or namespace load failed for 'Seurat' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
Execution halted