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### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clstutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings clstutils_1.40.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/clstutils.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clstutils/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clstutils' version '1.40.1'
* 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 'clstutils' 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 ... NOTE
'library' or 'require' call to 'rjson' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'ape' 'rjson'
  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 ... NOTE
Foreign function call to a different package:
  .Call("seq_root2tip", ..., PACKAGE = "ape")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
edgeMap: no visible global function definition for 'fromJSON'
prettyTree: no visible binding for global variable '.PlotPhyloEnv'
refpkgContents: no visible global function definition for 'fromJSON'
Undefined global functions or variables:
  .PlotPhyloEnv fromJSON
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  tests/unit/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable
packages' in the 'Writing R Extensions' manual.
* checking include directives in Makefiles ... 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
classifyPlacements 3.37   0.09    5.68
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runalltests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runalltests.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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/clstutils.Rcheck/00check.log'
for details.