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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterStab.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings clusterStab_1.66.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/clusterStab.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 'clusterStab/DESCRIPTION' ... OK
* this is package 'clusterStab' version '1.66.0'
* 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 whether package 'clusterStab' 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 'Biobase' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Biobase' '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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'clusterStab/R/zzz.R':
  .First.lib calls:
    require(Biobase)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim): partial
  argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim): partial
  argument match of 'nc' to 'ncol'
do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nc' to 'ncol'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim): partial
  argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim): partial
  argument match of 'nc' to 'ncol'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nc' to 'ncol'
show,ClusterComp: warning in matrix(paste(round(object@percent, 0),
  "%", sep = ""), nr = 1): partial argument match of 'nr' to 'nrow'
.First.lib: no visible global function definition for 'addVigs2WinMenu'
do.benhur: no visible global function definition for 'hclust'
do.benhur: no visible global function definition for 'cutree'
do.benhur: no visible global function definition for 'new'
do.clusterComp: no visible global function definition for 'hclust'
do.clusterComp: no visible global function definition for 'cutree'
do.clusterComp: no visible global function definition for 'new'
makeDist: no visible global function definition for 'as.dist'
makeDist: no visible global function definition for 'cor'
makeDist: no visible global function definition for 'dist'
benhur,ExpressionSet: no visible global function definition for 'exprs'
clusterComp,ExpressionSet: no visible global function definition for
  'exprs'
ecdf,BenHur: no visible global function definition for 'par'
ecdf,BenHur: no visible global function definition for 'legend'
hist,BenHur: no visible global function definition for 'par'
Undefined global functions or variables:
  addVigs2WinMenu as.dist cor cutree dist exprs hclust legend new par
Consider adding
  importFrom("graphics", "legend", "par")
  importFrom("methods", "new")
  importFrom("stats", "as.dist", "cor", "cutree", "dist", "hclust")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/clusterStab.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/clusterStab_1.66.0.tar.gz && rm -rf clusterStab.buildbin-libdir && mkdir clusterStab.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterStab.buildbin-libdir clusterStab_1.66.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL clusterStab_1.66.0.zip && rm clusterStab_1.66.0.tar.gz clusterStab_1.66.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 10121  100 10121    0     0   116k      0 --:--:-- --:--:-- --:--:--  117k

install for i386

* installing *source* package 'clusterStab' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'clusterStab'
    finding HTML links ... done
    BenHur-class                            html  
    ClusterComp-class                       html  
    benhur                                  html  
    clusterComp                             html  
** 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

install for x64

* installing *source* package 'clusterStab' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterStab' as clusterStab_1.66.0.zip
* DONE (clusterStab)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'clusterStab' successfully unpacked and MD5 sums checked