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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SISPA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SISPA_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/SISPA.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 ‘/Users/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 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 ... 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/SISPA.Rcheck/00check.log’
for details.