Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-09-25 12:05:50 -0400 (Sat, 25 Sep 2021).

CHECK results for STAN on riesling1

To the developers/maintainers of the STAN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/STAN.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1842/2034HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.21.0  (landing page)
Rafael Campos-Martin
Snapshot Date: 2021-09-24 14:50:08 -0400 (Fri, 24 Sep 2021)
git_url: https://git.bioconductor.org/packages/STAN
git_branch: master
git_last_commit: e5232b3
git_last_commit_date: 2021-05-19 12:06:26 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: STAN
Version: 2.21.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:STAN.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings STAN_2.21.0.tar.gz
StartedAt: 2021-09-25 03:37:15 -0400 (Sat, 25 Sep 2021)
EndedAt: 2021-09-25 03:43:10 -0400 (Sat, 25 Sep 2021)
EllapsedTime: 354.8 seconds
RetCode: 0
Status:   OK  
CheckDir: STAN.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:STAN.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings STAN_2.21.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/STAN.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'STAN/DESCRIPTION' ... OK
* this is package 'STAN' version '2.21.0'
* 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 ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.14-bioc/R/library/STAN/libs/i386/STAN.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/STAN/libs/x64/STAN.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'D:/biocbuild/bbs-3.14-bioc/meat/STAN.Rcheck/00check.log'
for details.



Installation output

STAN.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/STAN_2.21.0.tar.gz && rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=STAN.buildbin-libdir STAN_2.21.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL STAN_2.21.0.zip && rm STAN_2.21.0.tar.gz STAN_2.21.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 67  291k   67  197k    0     0  1034k      0 --:--:-- --:--:-- --:--:-- 1034k
100  291k  100  291k    0     0  1286k      0 --:--:-- --:--:-- --:--:-- 1286k

install for i386

* installing *source* package 'STAN' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Bernoulli.cpp -o Bernoulli.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EmissionFactory.cpp -o EmissionFactory.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EmissionFunction.cpp -o EmissionFunction.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c HMM.cpp -o HMM.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c InitialProbability.cpp -o InitialProbability.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c JointlyIndependent.cpp -o JointlyIndependent.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MemoryAllocation.cpp -o MemoryAllocation.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Multinomial.cpp -o Multinomial.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MultivariateGaussian.cpp -o MultivariateGaussian.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c NegativeBinomial.cpp -o NegativeBinomial.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Poisson.cpp -o Poisson.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PoissonLogNormal.cpp -o PoissonLogNormal.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RAccessUtils.cpp -o RAccessUtils.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/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]
         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]
         return sexpemissionParam;
                ^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TransitionMatrix.cpp -o TransitionMatrix.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matUtils.cpp -o matUtils.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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 -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lRlapack -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/STAN.buildbin-libdir/00LOCK-STAN/00new/STAN/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'STAN'
    finding HTML links ... done
    DimNames                                html  
    DirScore                                html  
    Emission                                html  
    EmissionParams                          html  
    HMM-class                               html  
    HMM                                     html  
    HMMEmission-class                       html  
    HMMEmission                             html  
    InitProb                                html  
    LogLik                                  html  
    STAN-package                            html  
    StateNames                              html  
    Transitions                             html  
    bdHMM-class                             html  
    bdHMM                                   html  
    binarizeData                            html  
    c2optimize                              html  
    call_dpoilog                            html  
    data2Gviz                               html  
    example                                 html  
    fitBdClust                              html  
    fitHMM                                  html  
    flags                                   html  
    getAvgSignal                            html  
    getLogLik                               html  
    getPosterior                            html  
    getSizeFactors                          html  
    getViterbi                              html  
    initBdClust                             html  
    initBdHMM                               html  
    initHMM                                 html  
    observations                            html  
    pilot.hg19                              html  
    runningMean                             html  
    sub-HMM-ANY-ANY-ANY-method              html  
    sub-bdHMM-ANY-ANY-ANY-method            html  
    trainRegions                            html  
    ucscGenes                               html  
    viterbi2GRanges                         html  
    viterbi2Gviz                            html  
    yeastTF_SGDGenes                        html  
    yeastTF_databychrom_ex                  html  
** 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

install for x64

* installing *source* package 'STAN' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Bernoulli.cpp -o Bernoulli.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EmissionFactory.cpp -o EmissionFactory.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EmissionFunction.cpp -o EmissionFunction.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c HMM.cpp -o HMM.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c InitialProbability.cpp -o InitialProbability.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c JointlyIndependent.cpp -o JointlyIndependent.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MemoryAllocation.cpp -o MemoryAllocation.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Multinomial.cpp -o Multinomial.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MultivariateGaussian.cpp -o MultivariateGaussian.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c NegativeBinomial.cpp -o NegativeBinomial.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Poisson.cpp -o Poisson.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PoissonLogNormal.cpp -o PoissonLogNormal.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RAccessUtils.cpp -o RAccessUtils.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/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]
         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]
         return sexpemissionParam;
                ^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TransitionMatrix.cpp -o TransitionMatrix.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D_RDLL_ -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matUtils.cpp -o matUtils.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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 -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/STAN.buildbin-libdir/STAN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'STAN' as STAN_2.21.0.zip
* DONE (STAN)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'STAN' successfully unpacked and MD5 sums checked

Tests output


Example timings

STAN.Rcheck/examples_i386/STAN-Ex.timings

nameusersystemelapsed
DimNames0.010.000.01
DirScore0.130.000.16
Emission000
EmissionParams000
HMM-class0.010.000.01
HMM000
HMMEmission-class000
HMMEmission000
InitProb000
LogLik0.020.000.04
StateNames0.010.000.01
Transitions000
bdHMM-class000
bdHMM0.020.000.02
binarizeData0.050.000.04
call_dpoilog000
fitBdClust0.060.000.10
fitHMM0.010.000.04
getAvgSignal0.630.010.65
getLogLik0.030.000.06
getPosterior0.020.000.03
getSizeFactors0.090.000.09
getViterbi0.030.000.05
initBdHMM000
initHMM0.020.000.02
runningMean0.010.020.03
viterbi2GRanges0.830.000.86

STAN.Rcheck/examples_x64/STAN-Ex.timings

nameusersystemelapsed
DimNames000
DirScore0.110.000.25
Emission000
EmissionParams000
HMM-class000
HMM0.020.000.02
HMMEmission-class000
HMMEmission000
InitProb000
LogLik0.010.000.06
StateNames000
Transitions000
bdHMM-class0.020.000.02
bdHMM000
binarizeData0.030.020.04
call_dpoilog000
fitBdClust0.040.000.07
fitHMM0.020.010.04
getAvgSignal0.380.020.41
getLogLik0.030.000.05
getPosterior0.000.020.03
getSizeFactors0.030.010.04
getViterbi0.030.020.07
initBdHMM0.010.000.01
initHMM000
runningMean0.020.030.05
viterbi2GRanges0.660.030.70