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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SISPA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SISPA_1.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SISPA.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 ‘SISPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SISPA’ version ‘1.29.0’
* 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 ... 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 ... 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 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
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
cptSamples 1.814  4.025   3.108
SISPA      1.639  3.503   2.454
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/SISPA.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SISPA
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SISPA)