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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SparseSignatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SparseSignatures_2.4.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SparseSignatures.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SparseSignatures/DESCRIPTION' ... OK
* this is package 'SparseSignatures' version '2.4.0'
* package encoding: UTF-8
* 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 whether package 'SparseSignatures' 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
import.trinucleotides.counts: no visible global function definition for
  '.'
patients.plot: no visible binding for global variable 'Context'
patients.plot: no visible binding for global variable 'alt'
patients.plot: no visible binding for global variable 'patient'
patients.plot: no visible binding for global variable 'value'
signatures.plot: no visible binding for global variable 'Context'
signatures.plot: no visible binding for global variable 'alt'
signatures.plot: no visible binding for global variable 'value'
Undefined global functions or variables:
  . Context alt patient value
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
lambdaRangeBetaEvaluation    84.00   0.09   84.09
lambdaRangeAlphaEvaluation   77.07   0.20   77.34
nmfLassoBootstrap            12.27   0.39   12.65
nmfLassoCV                   11.84   0.01   11.86
nmfLasso                      5.25   0.07    5.32
import.trinucleotides.counts  2.77   1.58   83.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
lambdaRangeBetaEvaluation  89.10   0.03   89.13
lambdaRangeAlphaEvaluation 83.34   0.02   83.36
nmfLassoBootstrap          11.59   0.02   11.61
nmfLassoCV                 11.19   0.01   11.20
nmfLasso                    5.34   0.00    5.34
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/SparseSignatures.Rcheck/00check.log'
for details.