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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:bigPint.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings bigPint_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/bigPint.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 ‘bigPint/DESCRIPTION’ ... OK
* this is package ‘bigPint’ version ‘1.18.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘bigPint’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'bigPint' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.18-bioc/meat/bigPint.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 22.6Mb
  sub-directories of 1Mb or more:
    data              10.9Mb
    help               3.2Mb
    shiny-dashboards   5.1Mb
    shiny-examples     3.1Mb
* 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 startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... WARNING
  LazyData DB of 10.9 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘bigPint-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotClusters
> ### Title: Plot static parallel coordinate clusters
> ### Aliases: plotClusters
> 
> ### ** Examples
> 
> # The first set of five examples use data and dataMetrics
> # objects as input. The last set of five examples create the same plots now
> # using the SummarizedExperiment (i.e. dataSE) object input.
> 
> # Example 1: Perform hierarchical clustering of size four using the 
> # default agglomeration method "ward.D". Cluster only on the genes that have
> # FDR < 1e-7 (n = 113) and overlay these genes.
> 
> library(grid)
> library(matrixStats)
> library(ggplot2)
> data(soybean_ir_sub)
> soybean_ir_sub[,-1] <- log(soybean_ir_sub[-1]+1)
> data(soybean_ir_sub_metrics)
> colList = c("#00A600FF", rainbow(5)[c(1,4,5)])
> ret <- plotClusters(data=soybean_ir_sub,
+     dataMetrics = soybean_ir_sub_metrics, nC=4, colList = colList,
+     clusterAllData = FALSE, threshVal = 1e-7, saveFile = FALSE)
Error in xtfrm.data.frame(x) : cannot xtfrm data frames
Calls: plotClusters ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.data.frame
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
       /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetrics.R 
  
     test_dataMetricsLitreApp.R 
       /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsLitreApp.R 
  
     test_dataMetricsVolcano.R 
       /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsVolcano.R 
  
     test_dataMetricsVolcanoApp.R 
       /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsVolcanoApp.R 
  
  
  Error in BiocGenerics:::testPackage("bigPint") : 
    unit tests failed for package bigPint
  Execution halted
* 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, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/bigPint.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL bigPint
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘bigPint’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'bigPint' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'bigPint' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (bigPint)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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.

> BiocGenerics:::testPackage("bigPint")
Error in xtfrm.data.frame(x) : cannot xtfrm data frames
In addition: Warning message:
Package 'bigPint' is deprecated and will be removed from Bioconductor
  version 3.19 
Error in xtfrm.data.frame(x) : cannot xtfrm data frames
Error in xtfrm.data.frame(x) : cannot xtfrm data frames
Error in xtfrm.data.frame(x) : cannot xtfrm data frames


RUNIT TEST PROTOCOL -- Thu Nov  2 08:42:37 2023 
*********************************************** 
Number of test functions: 5 
Number of errors: 4 
Number of failures: 0 

 
1 Test Suite : 
bigPint RUnit Tests - 5 test functions, 4 errors, 0 failures
ERROR in /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetrics.R: Error while sourcing  /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetrics.R : Error in xtfrm.data.frame(x) : cannot xtfrm data frames
ERROR in /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsLitreApp.R: Error while sourcing  /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsLitreApp.R : Error in xtfrm.data.frame(x) : cannot xtfrm data frames
ERROR in /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsVolcano.R: Error while sourcing  /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsVolcano.R : Error in xtfrm.data.frame(x) : cannot xtfrm data frames
ERROR in /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsVolcanoApp.R: Error while sourcing  /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsVolcanoApp.R : Error in xtfrm.data.frame(x) : cannot xtfrm data frames

Test files with failing tests

   test_dataMetrics.R 
     /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetrics.R 

   test_dataMetricsLitreApp.R 
     /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsLitreApp.R 

   test_dataMetricsVolcano.R 
     /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsVolcano.R 

   test_dataMetricsVolcanoApp.R 
     /home/biocbuild/tmp/RtmpY8K3zA/RLIBS_5e05940d41fd3/bigPint/unitTests/test_dataMetricsVolcanoApp.R 


Error in BiocGenerics:::testPackage("bigPint") : 
  unit tests failed for package bigPint
Execution halted