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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrixMethods.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrixMethods_1.69.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrixMethods.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrixMethods/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BufferedMatrixMethods’ version ‘1.69.0’
* 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 ‘BufferedMatrixMethods’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' calls in package code:
  ‘affy’ ‘affyio’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘BufferedMatrix’ ‘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 ... NOTE
Foreign function calls to a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
  .Call("read_probeintensities", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

BufferedMatrix.bg.correct.normalize.quantiles: no visible global
  function definition for ‘is’
BufferedMatrix.bg.correct.normalize.quantiles: no visible global
  function definition for ‘duplicate’
BufferedMatrix.bg.correct.normalize.quantiles : bg.dens: no visible
  global function definition for ‘density’
BufferedMatrix.justRMA: no visible global function definition for ‘new’
BufferedMatrix.justRMA: no visible global function definition for
  ‘pData’
BufferedMatrix.justRMA: no visible global function definition for
  ‘read.celfile.header’
BufferedMatrix.justRMA: no visible global function definition for
  ‘cleancdfname’
BufferedMatrix.justRMA: no visible global function definition for
  ‘pmindex’
BufferedMatrix.justRMA: no visible global function definition for
  ‘geneNames’
BufferedMatrix.justRMA: no visible global function definition for
  ‘set.buffer.dim’
BufferedMatrix.justRMA: no visible global function definition for
  ‘RowMode’
BufferedMatrix.justRMA: no visible global function definition for
  ‘notes<-’
BufferedMatrix.read.celfiles: no visible global function definition for
  ‘createBufferedMatrix’
BufferedMatrix.read.celfiles: no visible global function definition for
  ‘read.celfile’
BufferedMatrix.read.celfiles: no visible global function definition for
  ‘AddColumn’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘new’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘cleancdfname’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘getCdfInfo’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘createBufferedMatrix’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘AddColumn’
bg.correct.BufferedMatrix: no visible global function definition for
  ‘is’
bg.correct.BufferedMatrix: no visible global function definition for
  ‘duplicate’
bg.correct.BufferedMatrix : bg.dens: no visible global function
  definition for ‘density’
normalize.BufferedMatrix.quantiles: no visible global function
  definition for ‘is’
normalize.BufferedMatrix.quantiles: no visible global function
  definition for ‘duplicate’
Undefined global functions or variables:
  AddColumn RowMode cleancdfname createBufferedMatrix density duplicate
  geneNames getCdfInfo is new notes<- pData pmindex read.celfile
  read.celfile.header set.buffer.dim
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "density")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrixMethods.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BufferedMatrixMethods
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘BufferedMatrixMethods’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BufferedMatrix/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init_package.c -o init_package.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BufferedMatrix/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c preprocess_bm.c -o preprocess_bm.o
preprocess_bm.c:344:7: warning: unused variable 'i' [-Wunused-variable]
  int i,j;
      ^
preprocess_bm.c:378:7: warning: unused variable 'current_mode' [-Wunused-variable]
  int current_mode;
      ^
preprocess_bm.c:593:7: warning: unused variable 'current_mode' [-Wunused-variable]
  int current_mode;
      ^
preprocess_bm.c:924:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
  int first_ind;
      ^
preprocess_bm.c:1151:7: warning: unused variable 'current_mode' [-Wunused-variable]
  int current_mode;
      ^
preprocess_bm.c:453:12: warning: unused function 'min' [-Wunused-function]
static int min(int x1,int x2){
           ^
6 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BufferedMatrixMethods.so init_package.o preprocess_bm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-BufferedMatrixMethods/00new/BufferedMatrixMethods/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (BufferedMatrixMethods)