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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:copa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings copa_1.75.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/copa.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘copa/DESCRIPTION’ ... OK
* this is package ‘copa’ version ‘1.75.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 for sufficient/correct file permissions ... OK
* checking whether package ‘copa’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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.
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
copa: warning in matrix(1:dim(mat)[1], nc = dim(mat)[1], nr =
  dim(mat)[1]): partial argument match of 'nr' to 'nrow'
copa: warning in matrix(1:dim(mat)[1], nc = dim(mat)[1], nr =
  dim(mat)[1]): partial argument match of 'nc' to 'ncol'
pSum: warning in matrix(out, nc = length(a), nr = length(a)): partial
  argument match of 'nr' to 'nrow'
pSum: warning in matrix(out, nc = length(a), nr = length(a)): partial
  argument match of 'nc' to 'ncol'
plotCopa: warning in matrix(1:2, nc = 1): partial argument match of
  'nc' to 'ncol'
copa: no visible binding for global variable ‘quantile’
do.copaFilter: no visible binding for global variable ‘median’
do.copaFilter: no visible binding for global variable ‘mad’
do.copaFilter: no visible global function definition for ‘quantile’
pSum: no visible binding for global variable ‘mat’
plotCopa: no visible global function definition for ‘par’
plotCopa: no visible global function definition for ‘layout’
plotCopa: no visible global function definition for ‘barplot’
copaFilter,ExpressionSet: no visible global function definition for
  ‘exprs’
Undefined global functions or variables:
  barplot exprs layout mad mat median par quantile
Consider adding
  importFrom("graphics", "barplot", "layout", "par")
  importFrom("stats", "mad", "median", "quantile")
to your NAMESPACE file.
* 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 ... NOTE
Objects in \usage without \alias in Rd file 'copaFilter.Rd':
  ‘\S4method{copaFilter}{matrix}’ ‘\S4method{copaFilter}{data.frame}’
  ‘\S4method{copaFilter}{ExpressionSet}’

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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/copa.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL copa
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘copa’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c copa.c -o copa.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o copa.so copa.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-copa/00new/copa/libs
** R
** inst
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (copa)