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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SigFuge.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SigFuge_1.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SigFuge.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SigFuge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SigFuge’ version ‘1.46.0’
* 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 ‘SigFuge’ 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 code 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 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
SFfigure: no visible binding for global variable ‘base’
SFfigure: no visible binding for global variable ‘s’
SFfigure: no visible binding for global variable ‘e’
SFfigure: no visible global function definition for ‘rgb’
SFfigure: no visible global function definition for ‘hcl’
SFfigure: no visible binding for global variable ‘cluster’
SFfigure: no visible binding for global variable ‘median’
SFfigure: no visible binding for global variable ‘x’
SFfigure: no visible binding for global variable ‘y1’
SFfigure: no visible binding for global variable ‘label’
SFfigure: no visible binding for global variable ‘value’
SFfigure: no visible binding for global variable ‘Clusters’
SFfigure: no visible binding for global variable ‘y2’
SFfigure: no visible global function definition for ‘pdf’
SFfigure: no visible global function definition for ‘dev.off’
SFlabels: no visible global function definition for ‘kmeans’
SFnormalize : <anonymous>: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  Clusters base cluster dev.off e hcl kmeans label median pdf rgb s
  value x y1 y2
Consider adding
  importFrom("grDevices", "dev.off", "hcl", "pdf", "rgb")
  importFrom("stats", "kmeans", "median")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SFpval.Rd: sigclust, sigclust-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
SFfigure 11.687  0.271  11.958
SFpval    8.718  0.142   8.860
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/SigFuge.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL SigFuge
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘SigFuge’ ...
** this is package ‘SigFuge’ version ‘1.46.0’
** using staged installation
** R
** data
** 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 (SigFuge)