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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:sigsquared.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings sigsquared_1.31.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/sigsquared.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘sigsquared/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sigsquared’ version ‘1.31.0’
* 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 ‘sigsquared’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 3
Standardizable: TRUE
Standardized license specification:
  GPL-3
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analysisPipeline,ExpressionSet-geneSignature: no visible binding for
  global variable ‘nCores’
analysisPipeline,ExpressionSet-geneSignature: no visible global
  function definition for ‘mcparallel’
analysisPipeline,ExpressionSet-geneSignature: no visible global
  function definition for ‘mccollect’
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  binding for global variable ‘mc’
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  binding for global variable ‘nCores’
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  global function definition for ‘mcparallel’
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  global function definition for ‘mccollect’
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for ‘new’
eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for
  global variable ‘mc’
eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for
  global variable ‘nCores’
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for ‘rnorm’
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for ‘mcparallel’
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for ‘mccollect’
genGeneDirect,matrix: no visible global function definition for ‘sd’
optCF,ExpressionSet-geneSignature: no visible global function
  definition for ‘new’
optCF,ExpressionSet-geneSignature: no visible global function
  definition for ‘rnorm’
optCF,ExpressionSet-geneSignature: no visible global function
  definition for ‘optim’
summarizeSolnSpace,solnSpace: no visible global function definition for
  ‘sd’
Undefined global functions or variables:
  mc mccollect mcparallel nCores new optim rnorm sd
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "optim", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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
analysisPipeline 13.643  0.372  14.014
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘sigsquared.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/sigsquared.Rcheck/00check.log’
for details.