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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:conclus.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings conclus_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/conclus.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'conclus/DESCRIPTION' ... OK
* this is package 'conclus' version '1.0.0'
* 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 whether package 'conclus' 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'conclus-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: exportResults,scRNAseq-method
> ### Title: exportResults
> ### Aliases: exportResults,scRNAseq-method exportResults
> 
> ### ** Examples
> 
> ## Object scr containing the results of previous steps
> load(system.file("extdata/scrFull.Rdat", package="conclus"))
> 
> ## Saving all results
> exportResults(scr, saveAll=TRUE)
Saving all results.
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/tmp/RtmpTrdVjW/Results/1_MatrixInfo/LightExperience_expression_matrix.tsv': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: exportResults ... .saveNormalizedMatrix -> .exportNormInfo -> write.table -> file
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'conclus-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: exportResults,scRNAseq-method
> ### Title: exportResults
> ### Aliases: exportResults,scRNAseq-method exportResults
> 
> ### ** Examples
> 
> ## Object scr containing the results of previous steps
> load(system.file("extdata/scrFull.Rdat", package="conclus"))
> 
> ## Saving all results
> exportResults(scr, saveAll=TRUE)
Saving all results.
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/tmp/RtmpTrdVjW/Results/1_MatrixInfo/LightExperience_expression_matrix.tsv': Permission denied
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: exportResults ... .saveNormalizedMatrix -> .exportNormInfo -> write.table -> file
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.R'
 OK
* 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
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/conclus.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/conclus_1.0.0.tar.gz && rm -rf conclus.buildbin-libdir && mkdir conclus.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=conclus.buildbin-libdir conclus_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL conclus_1.0.0.zip && rm conclus_1.0.0.tar.gz conclus_1.0.0.zip
###
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100 1445k  100 1445k    0     0  2387k      0 --:--:-- --:--:-- --:--:-- 2392k

install for i386

* installing *source* package 'conclus' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'conclus'
    finding HTML links ... done
    Dbscan-class                            html  
    Tsne-class                              html  
    addClustering-scRNAseq                  html  
    calculateClustersSimilarity-scRNAseq    html  
    clusterCellsInternal-scRNAseq           html  
    conclusCacheClear                       html  
    constructors                            html  
    exportResults-scRNAseq                  html  
    generateTSNECoordinates-scRNAseq        html  
    getters                                 html  
    loadDataOrMatrix                        html  
    normaliseCountMatrix-scRNAseq           html  
    plotCellHeatmap                         html  
    plotCellSimilarity-scRNAseq             html  
    plotClusteredTSNE-scRNAseq              html  
    plotClustersSimilarity                  html  
    plotGeneExpression-scRNAseq             html  
    rankGenes-scRNAseq                      html  
    retrieveFromGEO                         html  
    retrieveGenesInfo-scRNAseq              html  
    retrieveTableClustersCells-scRNAseq     html  
    retrieveTopClustersMarkers-scRNAseq     html  
    runCONCLUS                              html  
    runDBSCAN-scRNAseq                      html  
    scRNAseq-class                          html  
    setters                                 html  
    testClustering-scRNAseq                 html  
** 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

install for x64

* installing *source* package 'conclus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'conclus' as conclus_1.0.0.zip
* DONE (conclus)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'conclus' successfully unpacked and MD5 sums checked