##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:STAN.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings STAN_2.26.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/STAN.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'STAN/DESCRIPTION' ... OK
* this is package 'STAN' version '2.26.2'
* 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 'STAN' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
initBdClust: warning in initBdHMM(obs, dStates = dStates, uStates =
  uStates, method = method, directedObs = directedObs, sizeFactor =
  sizeFactors, sharedCov = sharedCov, dirFlags = dirFlags): partial
  argument match of 'sizeFactor' to 'sizeFactors'
binarizeData : <anonymous>: no visible global function definition for
  'ppois'
clusterMat : <anonymous>: no visible global function definition for
  'ppois'
clusterMat: no visible global function definition for 'kmeans'
myQNBinom: no visible global function definition for 'dnbinom'
optimizeNB : <anonymous>: no visible global function definition for
  'optim'
optimizeNBInit: no visible global function definition for 'optim'
optimizePoiLog : <anonymous>: no visible global function definition for
  'optim'
optimizePoiLogInit: no visible global function definition for 'optim'
Undefined global functions or variables:
  dnbinom kmeans optim ppois
Consider adding
  importFrom("stats", "dnbinom", "kmeans", "optim", "ppois")
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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-3.16-bioc/R/library/STAN/libs/x64/STAN.dll':
  Found '_assert', possibly from 'assert' (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. 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/STAN.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL STAN
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'STAN' ...
** using staged installation
** libs
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Bernoulli.cpp -o Bernoulli.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EmissionFactory.cpp -o EmissionFactory.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EmissionFunction.cpp -o EmissionFunction.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c HMM.cpp -o HMM.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c InitialProbability.cpp -o InitialProbability.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c JointlyIndependent.cpp -o JointlyIndependent.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MemoryAllocation.cpp -o MemoryAllocation.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Multinomial.cpp -o Multinomial.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MultivariateGaussian.cpp -o MultivariateGaussian.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c NegativeBinomial.cpp -o NegativeBinomial.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Poisson.cpp -o Poisson.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PoissonLogNormal.cpp -o PoissonLogNormal.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RAccessUtils.cpp -o RAccessUtils.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RWrapper.cpp -o RWrapper.o
RWrapper.cpp: In function 'EmissionFunction** RGETEMISSION(SEXP, int, SEXP, int*, const char*, double***, int*, int, SEXP, int*, int*, int*)':
RWrapper.cpp:350:16: warning: 'HMMEmissionFunctions' may be used uninitialized in this function [-Wmaybe-uninitialized]
  350 |         return HMMEmissionFunctions;
      |                ^~~~~~~~~~~~~~~~~~~~
RWrapper.cpp: In function 'SEXPREC* prepareEmission(const char*, SEXP, SEXP, EmissionFunction**, int)':
RWrapper.cpp:1157:16: warning: 'sexpemissionParam' may be used uninitialized in this function [-Wmaybe-uninitialized]
 1157 |         return sexpemissionParam;
      |                ^~~~~~~~~~~~~~~~~
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TransitionMatrix.cpp -o TransitionMatrix.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matUtils.cpp -o matUtils.o
g++ -std=gnu++14 -shared -s -static-libgcc -o STAN.dll tmp.def Bernoulli.o EmissionFactory.o EmissionFunction.o HMM.o InitialProbability.o JointlyIndependent.o MemoryAllocation.o Multinomial.o MultivariateGaussian.o NegativeBinomial.o ParamContainerEmissions.o Poisson.o PoissonLogNormal.o RAccessUtils.o RWrapper.o TransitionMatrix.o matUtils.o -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-STAN/00new/STAN/libs/x64
** R
** data
** 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 (STAN)