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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CGHregions.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings CGHregions_1.66.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/CGHregions.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CGHregions/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHregions' 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 'CGHregions' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  GPL (http://www.gnu.org/copyleft/gpl.html)
Standardizable: FALSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... NOTE
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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.countlevels' '.deterreg' '.dist1' '.dist2mid' '.dm' '.findbp'
  '.findchr' '.gradients' '.jump' '.ntd' '.rightgrad' '.td' '.tdind'
  '.wh' '.whichsign2'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.rightgrad : <anonymous>: no visible global function definition for
  'dist'
CGHregions: no visible global function definition for 'sampleNames'
CGHregions: no visible global function definition for 'read.table'
CGHregions: no visible global function definition for 'new'
Undefined global functions or variables:
  dist new read.table sampleNames
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
  importFrom("utils", "read.table")
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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'CGHregions.Rd':
  '[CGHbase:class.cghCall]{cghCall}'
  '[CGHbase:class.cghRegions]{cghRegions}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/CGHregions.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL CGHregions
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'CGHregions' ...
** this is package 'CGHregions' version '1.66.0'
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (CGHregions)