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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:oposSOM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings oposSOM_2.25.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/oposSOM.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oposSOM/DESCRIPTION’ ... OK
* this is package ‘oposSOM’ version ‘2.25.0’
* 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 ‘oposSOM’ can be installed ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/oposSOM.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 19.2Mb
  sub-directories of 1Mb or more:
    data  17.2Mb
    libs   1.4Mb
* 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 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
Warning: program compiled against libxml 212 using older 211
Unexported object imported by a ':::' call: ‘tools:::makeLazyLoadDB’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
psf.overview.heatmaps: warning in heatmap(x =
  log1p(log1p(mean.psf.matrix)), cex.main = 2, col =
  color.palette(1000), scale = "r", mar = c(10, 20), ColSideColors =
  group.colors, cexDend = 0.6): partial argument match of 'mar' to
  'margins'
psf.overview.heatmaps: warning in heatmap(x =
  log1p(log1p(mean.psf.matrix)), cex.main = 2, col =
  color.palette(1000), scale = "r", mar = c(10, 20), ColSideColors =
  group.colors, Colv = NA, cexDend = 0.6): partial argument match of
  'mar' to 'margins'
Smooth.Matrix: no visible binding for global variable ‘v’
modules.relations: no visible global function definition for
  ‘graph.empty’
modules.relations: no visible global function definition for
  ‘add_edges’
pipeline.PSFcalculation: no visible binding for global variable
  ‘kegg.collection’
pipeline.checkInputParameters: no visible binding for global variable
  ‘preferences’
pipeline.diffExpressionStatistics : <anonymous>: no visible global
  function definition for ‘t.test’
pipeline.differenceAnalyses : <anonymous>: no visible global function
  definition for ‘t.test’
pipeline.groupAnalysis : <anonymous>: no visible global function
  definition for ‘t.test’
pipeline.htmlPsfAnalysis: no visible binding for global variable
  ‘kegg.collection’
pipeline.prepareAnnotation: no visible binding for global variable
  ‘opossom.genesets’
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for ‘get.edgelist’
pipeline.topologyProfiles: no visible binding for global variable
  ‘group.labels’
plot.psf.pathway.keggrest: no visible global function definition for
  ‘rasterImage’
psf.report.sheets: no visible binding for global variable ‘kegg.data’
spot.borders: no visible binding for global variable ‘env’
Undefined global functions or variables:
  add_edges env get.edgelist graph.empty group.labels kegg.collection
  kegg.data opossom.genesets preferences rasterImage t.test v
Consider adding
  importFrom("graphics", "rasterImage")
  importFrom("stats", "t.test")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
Undocumented code objects:
  ‘GeneSet.Fisher’ ‘GeneSet.maxmean’ ‘Get.Running.Average’
  ‘Quantile.Normalization’ ‘Sample.GSZ’ ‘Smooth.Matrix’
  ‘_oposSOM_calculateDelta’ ‘_oposSOM_calculateEuclideanDistances’
  ‘_oposSOM_calculateNeighborhoodMatrix’
  ‘_oposSOM_matrixToCodebookMatrix’ ‘biomart.available’
  ‘calculateDelta’ ‘calculateEuclideanDistances’
  ‘calculateNeighborhoodMatrix’ ‘circle’ ‘col.pix’
  ‘color.palette.discrete’ ‘color.palette.heatmaps’
  ‘color.palette.interlace’ ‘color.palette.portraits’
  ‘color.palette.portraits.cbs’ ‘get.beta.statistic’ ‘get.neighbors’
  ‘heatmap’ ‘heatmap.A4’ ‘matrixToCodebookMatrix’ ‘modules.CSV.sheets’
  ‘modules.chromosomes’ ‘modules.profiles’ ‘modules.relations’
  ‘modules.report.sheets’ ‘newProgressBar’ ‘pathway.expression.mapping’
  ‘pipeline.PSFcalculation’ ‘pipeline.PSFoutput’
  ‘pipeline.affymetrixQualityCheck’ ‘pipeline.cancerHallmarks’
  ‘pipeline.checkInputParameters’
  ‘pipeline.chromosomeExpressionReports’
  ‘pipeline.detectCorrelationModules’ ‘pipeline.detectDMapModules’
  ‘pipeline.detectEnsemblDataset’
  ‘pipeline.detectGroupOverexpressionModules’
  ‘pipeline.detectKMeansModules’ ‘pipeline.detectOverexpressionModules’
  ‘pipeline.detectSpotsModules’ ‘pipeline.detectUnderexpressionModules’
  ‘pipeline.diffExpressionStatistics’ ‘pipeline.differenceAnalyses’
  ‘pipeline.entropyProfiles’ ‘pipeline.geneLists’
  ‘pipeline.generateSOM’ ‘pipeline.genesetOverviews’
  ‘pipeline.genesetProfilesAndMaps’ ‘pipeline.genesetStatisticModules’
  ‘pipeline.genesetStatisticSamples’ ‘pipeline.groupAnalysis’
  ‘pipeline.groupAssignment’ ‘pipeline.groupSpecificGenesets’
  ‘pipeline.htmlDifferencesSummary’ ‘pipeline.htmlGenesetAnalysis’
  ‘pipeline.htmlGroupSummary’ ‘pipeline.htmlModuleSummary’
  ‘pipeline.htmlPsfAnalysis’ ‘pipeline.htmlSampleSummary’
  ‘pipeline.htmlSummary’ ‘pipeline.moduleCorrelationMap’
  ‘pipeline.patAssignment’ ‘pipeline.prepareAnnotation’
  ‘pipeline.prepareIndata’ ‘pipeline.qualityCheck’
  ‘pipeline.sampleExpressionPortraits’
  ‘pipeline.sampleSimilarityAnalysisCor’
  ‘pipeline.sampleSimilarityAnalysisED’
  ‘pipeline.sampleSimilarityAnalysisICA’
  ‘pipeline.sampleSimilarityAnalysisSOM’ ‘pipeline.summarySheetsGroups’
  ‘pipeline.summarySheetsModules’ ‘pipeline.summarySheetsPATs’
  ‘pipeline.summarySheetsSamples’ ‘pipeline.supportingMaps’
  ‘pipeline.topologyProfiles’ ‘plot.psf.pathway.keggrest’
  ‘plot.psf.titlepage’ ‘psf.flow’ ‘psf.overview.heatmaps’
  ‘psf.report.sheets’ ‘radarchart’ ‘som.linear.init’
  ‘som.linear.init.subdata’ ‘som.training’ ‘som.training.phase’
  ‘sort.label’ ‘spot.borders’ ‘util.call’ ‘util.cat’ ‘util.fatal’
  ‘util.info’ ‘util.load’ ‘util.log’ ‘util.progress’
  ‘util.progress.terminate’ ‘util.save’ ‘util.warn’ ‘workspace.check’
Undocumented data sets:
  ‘hsa03320.RData’ ‘hsa04010.RData’ ‘hsa04012.RData’ ‘hsa04014.RData’
  ‘hsa04015.RData’ ‘hsa04020.RData’ ‘hsa04022.RData’ ‘hsa04024.RData’
  ‘hsa04062.RData’ ‘hsa04064.RData’ ‘hsa04066.RData’ ‘hsa04068.RData’
  ‘hsa04070.RData’ ‘hsa04071.RData’ ‘hsa04072.RData’ ‘hsa04115.RData’
  ‘hsa04150.RData’ ‘hsa04151.RData’ ‘hsa04152.RData’ ‘hsa04261.RData’
  ‘hsa04310.RData’ ‘hsa04330.RData’ ‘hsa04340.RData’ ‘hsa04350.RData’
  ‘hsa04370.RData’ ‘hsa04371.RData’ ‘hsa04390.RData’ ‘hsa04392.RData’
  ‘hsa04550.RData’ ‘hsa04620.RData’ ‘hsa04621.RData’ ‘hsa04622.RData’
  ‘hsa04625.RData’ ‘hsa04630.RData’ ‘hsa04657.RData’ ‘hsa04660.RData’
  ‘hsa04662.RData’ ‘hsa04664.RData’ ‘hsa04668.RData’ ‘hsa04722.RData’
  ‘hsa04723.RData’ ‘hsa04910.RData’ ‘hsa04912.RData’ ‘hsa04915.RData’
  ‘hsa04917.RData’ ‘hsa04919.RData’ ‘hsa04920.RData’ ‘hsa04921.RData’
  ‘hsa04922.RData’ ‘hsa04926.RData’ ‘hsa04933.RData’ ‘hsa05120.RData’
  ‘kegg.collection.RData’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* 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 ‘oposSOM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: oposSOM-package
> ### Title: Comprehensive analysis of transciptome data
> ### Aliases: oposSOM-package oposSOM
> ### Keywords: package
> 
> ### ** Examples
> 
> # Example with artificial data
> env <- opossom.new(list(dataset.name="Example",
+                         dim.1stLvlSom=20))
> 
> env$indata <- matrix(rnorm(10000), 1000, 10)
> 
> env$group.labels <- "auto"
> 
> opossom.run(env)
[2025-01-28 13:36:47][INFO] oposSOM is ready to fly! Starting analysis.
[2025-01-28 13:36:47][INFO] Name: Example
[2025-01-28 13:36:47][WARN] No rownames found. Set them to 1,2,3,4...
[2025-01-28 13:36:47][WARN] No colnames found. Set them to 1,2,3,4...
[2025-01-28 13:36:47][INFO] Writing: Data Overview/Data Distribution.pdf
[2025-01-28 13:36:47][INFO] Loading gene annotation data.
[2025-01-28 13:36:49][INFO] Autodetecting annotation parameters
[2025-01-28 13:37:09][WARN] Could not find valid annotation parameters.
[2025-01-28 13:37:09][WARN] Disabling geneset & PSF analyses.
[2025-01-28 13:37:09][INFO] Processing SOM. This may take several time until next notification.

 *** caught segfault ***
address 0x32303200656d61, cause 'memory not mapped'

Traceback:
 1: calculateDelta(weightMatrix, indata[it, ], any.na, deltaMatrix)
 2: som.training.phase(indata, weightMatrix, metricSamples, epochs = 2 *     prolongationFactor, initLearnRate = 0.05, inverseLearnRate = nrow(indata) *     2 * prolongationFactor/100, initRadius = somSize, pb)
 3: som.training(env$indata, env$som.result, prolongationFactor = env$preferences$training.extension,     verbose = TRUE)
 4: pipeline.generateSOM(env)
 5: opossom.run(env)
An irrecoverable exception occurred. R is aborting now ...
* 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, 6 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/oposSOM.Rcheck/00check.log’
for details.