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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bgx.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings bgx_1.72.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/bgx.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 ... 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 whether package 'bgx' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* 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 ... OK
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/bgx/libs/x64/bgx.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 73.66  17.14   91.01
* 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: 6 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/bgx.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL bgx
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'bgx' ...
** using staged installation
Untarring Boost header files...
tar: Ignoring unknown extended header keyword 'SCHILY.fflags'
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I ../boostIncl -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -DUSING_R -ffast-math -O3   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bgx.cc -o bgx.o
In file included from bgx.cc:32:
rand.hh: In member function 'RealType Rand<GenType, RealType>::Normal()':
rand.hh:399:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  399 |       if(u0<.5) return y; return -y;
      |       ^~
rand.hh:399:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  399 |       if(u0<.5) return y; return -y;
      |                           ^~~~~~
rand.hh:406:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  406 |       if(u0<.5) return y; return -y;
      |       ^~
rand.hh:406:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  406 |       if(u0<.5) return y; return -y;
      |                           ^~~~~~
rand.hh:413:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  413 |       if(u0<.5) return y; return -y;
      |       ^~
rand.hh:413:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  413 |       if(u0<.5) return y; return -y;
      |                           ^~~~~~
rand.hh:420:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  420 |     if(u0<.5) return y; return -y;
      |     ^~
rand.hh:420:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  420 |     if(u0<.5) return y; return -y;
      |                         ^~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I ../boostIncl -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -DUSING_R -ffast-math -O3   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bgx_frontend.cc -o bgx_frontend.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I ../boostIncl -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -DUSING_R -ffast-math -O3  -std=c99   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c qnorm.c -o qnorm.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I ../boostIncl -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -DUSING_R -ffast-math -O3   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rundir.cc -o rundir.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I ../boostIncl -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -DUSING_R -ffast-math -O3   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sokal.cc -o sokal.o
g++ -std=gnu++17 -shared -s -static-libgcc -o bgx.dll tmp.def bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-bgx/00new/bgx/libs/x64
** 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 (bgx)