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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bgx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bgx_1.72.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/bgx.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘bgx/DESCRIPTION’ ... OK
* this is package ‘bgx’ version ‘1.72.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bgx’ can be installed ... WARNING
Found the following significant warnings:
  clang: warning: argument unused during compilation: '-mcpu=pentium2' [-Wunused-command-line-argument]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/bgx.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 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
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’
  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
bgx: no visible global function definition for ‘geneNames’
bgx: no visible global function definition for ‘sampleNames’
bgx: no visible global function definition for ‘new’
bgx: no visible global function definition for ‘annotation’
bgx: no visible global function definition for ‘description’
bgx: no visible global function definition for
  ‘assayDataElementReplace’
loessNorm: no visible global function definition for ‘loess’
loessNorm: no visible global function definition for ‘predict’
plotDEDensity: no visible global function definition for ‘density’
plotDEDensity: no visible global function definition for ‘abline’
plotDEHistogram: no visible global function definition for ‘hist’
plotDEHistogram: no visible global function definition for ‘glm’
plotDEHistogram: no visible binding for global variable ‘poisson’
plotDEHistogram: no visible global function definition for ‘lines’
plotDEHistogram: no visible global function definition for ‘points’
plotDiffRank: no visible global function definition for ‘quantile’
plotDiffRank: no visible global function definition for ‘sd’
plotDiffRank: no visible global function definition for ‘segments’
plotDiffRank: no visible global function definition for ‘abline’
plotExpressionDensity: no visible global function definition for
  ‘density’
plotExpressionDensity: no visible global function definition for
  ‘lines’
plotExpressionDensity: no visible global function definition for
  ‘legend’
readSingle.bgx: no visible global function definition for ‘read.delim’
saveAffinityPlot.bgx: no visible global function definition for ‘pdf’
saveAffinityPlot.bgx: no visible global function definition for ‘par’
saveAffinityPlot.bgx: no visible global function definition for
  ‘dev.off’
setupVars.bgx : calcProbeAffCategories: no visible global function
  definition for ‘cdfName’
setupVars.bgx : calcProbeAffCategories: no visible global function
  definition for ‘median’
setupVars.bgx: no visible global function definition for ‘pData’
setupVars.bgx: no visible global function definition for ‘indexProbes’
standalone.bgx: no visible global function definition for ‘write.table’
standalone.bgx: no visible global function definition for ‘geneNames’
standalone.bgx: no visible global function definition for ‘sampleNames’
Undefined global functions or variables:
  abline annotation assayDataElementReplace cdfName density description
  dev.off geneNames glm hist indexProbes legend lines loess median new
  pData par pdf points poisson predict quantile read.delim sampleNames
  sd segments write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "hist", "legend", "lines", "par",
             "points", "segments")
  importFrom("methods", "new")
  importFrom("stats", "density", "glm", "loess", "median", "poisson",
             "predict", "quantile", "sd")
  importFrom("utils", "read.delim", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: analysis.bgx.Rd:48-49: Dropping empty section \examples
checkRd: (-1) bgx.Rd:9: Escaped LaTeX specials: \_ \_
checkRd: (-1) bgx.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bgx.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bgx.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bgx.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bgx.Rd:45: Lost braces in \itemize; meant \describe ?
prepare_Rd: mcmc.bgx.Rd:48-49: Dropping empty section \examples
prepare_Rd: readOutput.bgx.Rd:23-24: Dropping empty section \examples
prepare_Rd: saveAffinityPlot.bgx.Rd:18-19: Dropping empty section \details
prepare_Rd: saveAffinityPlot.bgx.Rd:20-21: Dropping empty section \value
prepare_Rd: saveAffinityPlot.bgx.Rd:26-27: Dropping empty section \examples
prepare_Rd: setupVars.bgx.Rd:21-22: Dropping empty section \details
prepare_Rd: setupVars.bgx.Rd:43-44: Dropping empty section \examples
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
bgx 16.115  0.285  16.537
* 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: 1 WARNING, 7 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/bgx.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bgx
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘bgx’ ...
** using staged installation
checking for gcc... clang -arch x86_64
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... x86_64-apple-darwin21.6.0
checking host system type... x86_64-apple-darwin21.6.0
checking for gcc architecture flag... 
checking for x86 cpuid 0 output... 16:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 50657:16400800:7ffefbff:bfebfbff
checking whether C compiler accepts -march=pentium2... no
checking whether C compiler accepts -mcpu=pentium2... yes
checking for gcc architecture flag... -mcpu=pentium2
checking for clang -arch x86_64 option to accept ISO C99... none needed
checking for main in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
bgx.cc:44:13: warning: 'FLUSH' macro redefined [-Wmacro-redefined]
    #define FLUSH {R_FlushConsole(); R_ProcessEvents();}
            ^
./rand.hh:42:13: note: previous definition is here
    #define FLUSH R_FlushConsole();
            ^
In file included from bgx.cc:36:
./bgx_updates.hh:47:8: warning: private field 'categories' is not used [-Wunused-private-field]
  int* categories;
       ^
./bgx_updates.hh:310:8: warning: private field 'categories' is not used [-Wunused-private-field]
  int *categories;
       ^
./bgx_updates.hh:311:7: warning: private field 'numberCategories' is not used [-Wunused-private-field]
  int numberCategories;
      ^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -falign-functions=64 -Wall -g -O2 -mcpu=pentium2  -ffast-math -O3 -c qnorm.c -o qnorm.o
clang: warning: argument unused during compilation: '-mcpu=pentium2' [-Wunused-command-line-argument]
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -r ../boostIncl
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-bgx/00new/bgx/libs
** 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
** 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 (bgx)