##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SISPA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SISPA_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SISPA.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SISPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SISPA’ version ‘1.32.0’
* 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 ‘SISPA’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'SISPA' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.18-bioc/meat/SISPA.Rcheck/00install.out’ for details.
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Version 0.99.1: Original
  Cannot process chunk/lines:
    Version 0.99.2: 
                  Bugfix:
                        - Example ERROR fixed, generates ERROR message when no change points are identified.
  Cannot process chunk/lines:
    Version 0.99.3: 
                  Bugfix:
                        - Example ERROR fixed, generates ERROR message when no change points are identified.
  Cannot process chunk/lines:
    Version 0.99.4: 
                  Bugfix:
                        - Example ERROR fixed, generates ERROR message when no change points are identified.
  Cannot process chunk/lines:
    Version 1.1.0
    	      First Release version
  Cannot process chunk/lines:
    Version 1.1.1:
                  New Features:
    		                - For more than 3 genes, standard zscore is computed instead of GSVA enrichment scores
    		                - For sample size less than 3, zscore can not be computed, program generates an error
    		                - SISPA can now run on a single data type or any combination of two numeric data types
    		                - changepoint R method options as input parameters
    		                - implemented ggplot to create barplot in the freqplot function
    		                - Updated vignettes as pdf file to perform 1D and 2D SISPA analysis
    			         	    - SISPA.R numeric ERROR fixed
  Cannot process chunk/lines:
    Version 1.1.2:
                  New Features:
    			       - cptSamples.R changepoint ERROR fixed
  Cannot process chunk/lines:
    Bhakti Dwivedi and Jeanne Kowalski
  Cannot process chunk/lines:
    The Winship Cancer Institute, Emory University
  Cannot process chunk/lines:
    https://bbisr.winship.emory.edu/
* 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 ... NOTE
cptSamples : cptsPlot: no visible global function definition for
  ‘abline’
cptSamples : cptsPlot: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline text
Consider adding
  importFrom("graphics", "abline", "text")
to your NAMESPACE file.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SISPA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: freqplot
> ### Title: A plotting function for SISPA sample identifiers
> ### Aliases: freqplot
> 
> ### ** Examples
> 
> samples <- c("s1","s2","s3","s4","s5","s6","s7","s8","s9","s10")
> zscores <- c(3.83,2.70,2.67,2.31,1.70,1.25,-0.42,-1.01,-2.43,-3.37)
> changepoints <- c(1,1,1,2,2,3,3,NA,NA,NA)
> sample_groups <- c(1,1,1,0,0,0,0,0,0,0)
> my.data = data.frame(samples,zscores,changepoints,sample_groups)
> freqplot(my.data)
Error: The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(count_data) or as.data.table(count_data). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is superseded and is no longer actively developed.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SISPA.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/SISPA.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL SISPA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘SISPA’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
Warning: Package 'SISPA' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'SISPA' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (SISPA)