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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:oposSOM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings oposSOM_2.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/oposSOM.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘oposSOM/DESCRIPTION’ ... OK
* this is package ‘oposSOM’ version ‘2.17.0’
* 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 ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
  installed size is 19.1Mb
  sub-directories of 1Mb or more:
    data  17.0Mb
    libs   1.6Mb
* 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘tools:::makeLazyLoadDB’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
plot:
  function(x, ...)
plot.psf.pathway.keggrest:
  function(kegg.pathway, signal.values, signal.values.lim, main,
           highlight.genes, color.palette)

plot:
  function(x, ...)
plot.psf.titlepage:
  function(env, psf.object, signal.values, bar.colors)

sort:
  function(x, decreasing, ...)
sort.label:
  function(x)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  plot.psf.pathway.keggrest plot.psf.titlepage sort.label
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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’
Undefined global functions or variables:
  add_edges 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
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.portraits’ ‘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.detectEnsemblDataset’ ‘pipeline.detectSpotsModules’
  ‘pipeline.detectSpotsSamples’ ‘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’ ‘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 ... 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 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)
[2023-02-24 15:38:38][INFO] Started:
[2023-02-24 15:38:38][INFO] Name: Example
[2023-02-24 15:38:38][WARN] No rownames found. Set them to 1,2,3,4...
[2023-02-24 15:38:38][WARN] No colnames found. Set them to 1,2,3,4...
[2023-02-24 15:38:38][INFO] Writing: Example - Results/Data Overview/Data Distribution.pdf
[2023-02-24 15:38:39][INFO] Loading gene annotation data.
[2023-02-24 15:38:42][INFO] Autodetecting annotation parameters
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [jan2020.archive.ensembl.org:443] Operation timed out after 10000 milliseconds with 361103 bytes received
Calls: opossom.run ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Vignette.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/oposSOM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL oposSOM
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘oposSOM’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c DeltaMatrix.cpp -o DeltaMatrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c DistanceCalculator.cpp -o DistanceCalculator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c NeighborhoodMatrix.cpp -o NeighborhoodMatrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o oposSOM.so DeltaMatrix.o DistanceCalculator.o NeighborhoodMatrix.o RcppExports.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-oposSOM/00new/oposSOM/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (oposSOM)