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### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SEtools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SEtools_1.9.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/SEtools.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SEtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SEtools' version '1.9.1'
* 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 'SEtools' 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
* 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
castSE : <anonymous>: warning in sparseMatrix(i = as.integer(rowNames),
  j = as.integer(colNames), x = x[[y]], dim =
  c(length(levels(rowNames)), length(levels(colNames))), dimnames =
  list(levels(rowNames), levels(colNames))): partial argument match of
  'dim' to 'dims'
* 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 ... WARNING
Undocumented arguments in documentation object 'SE-heatmap'
  'annorow_title_side'
Documented arguments not in \usage in documentation object 'SE-heatmap':
  'annorows_title_side'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
* 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, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/SEtools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SEtools
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'SEtools' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SEtools'
    finding HTML links ... done
    SE-heatmap                              html  
    aggSE                                   html  
    castSE                                  html  
    crossHm                                 html  
    data                                    html  
    flattenPB                               html  
    getBreaks                               html  
    log2FC                                  html  
    meltSE                                  html  
    mergeSEs                                html  
    qualitativeColors                       html  
    resetAllSEtoolsOptions                  html  
    scale2                                  html  
    se2xls                                  html  
    sortRows                                html  
    svacor                                  html  
    finding level-2 HTML links ... done

** 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 (SEtools)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MIGSA' is missing or broken
 done