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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings clusterExperiment_2.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/clusterExperiment.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘clusterExperiment/DESCRIPTION’ ... OK
* this is package ‘clusterExperiment’ version ‘2.22.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘clusterExperiment’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   3.6Mb
    libs   2.4Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .C(ape::node_depth, ...)
  .C(ape::node_depth_edgelength, ...)
  .C(ape::node_height, ...)
  .C(ape::node_height_clado, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Output for data("rsecFluidigm", package = "clusterExperiment"):
  Search path was changed
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘clusterExperiment-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mainClustering
> ### Title: Cluster distance matrix from subsampling
> ### Aliases: mainClustering mainClustering,character-method
> ###   mainClustering,ClusterFunction-method
> ###   getPostProcessingArgs,ClusterFunction-method getPostProcessingArgs
> 
> ### ** Examples
> 
> data(simData)
> cl1<-mainClustering(inputMatrix=simData, inputType="X", 
+     clusterFunction="pam",clusterArgs=list(k=3))
> #supply a dissimilarity, use algorithm type "01"
> diss<-as.matrix(dist(t(simData),method="manhattan"))
> cl2<-mainClustering(diss, inputType="diss", clusterFunction="hierarchical01",
+     clusterArgs=list(alpha=.1))
> cl3<-mainClustering(inputMatrix=diss, inputType="diss", clusterFunction="pam",
+     clusterArgs=list(k=3))
> 
> # run hierarchical method for finding blocks, with method of evaluating
> # coherence of block set to evalClusterMethod="average", and the hierarchical
> # clustering using single linkage:
> # (clustering function requires type 'diss'),
> clustSubHier <- mainClustering(diss, inputType="diss",
+     clusterFunction="hierarchical01", minSize=5,
+     clusterArgs=list(alpha=0.1,evalClusterMethod="average", method="single"))
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat_a-c.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 818670 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat_a-c.R’ failed.
Last 13 lines of output:
      '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
  
  Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
  Also defined by 'RNeXML'
* 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: 2 ERRORs, 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.