Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:05:14 -0400 (Wed, 22 Sep 2021).

CHECK results for epigraHMM on tokay2

To the developers/maintainers of the epigraHMM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epigraHMM.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 583/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigraHMM 1.0.3  (landing page)
Pedro Baldoni
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/epigraHMM
git_branch: RELEASE_3_13
git_last_commit: 04cb67e
git_last_commit_date: 2021-08-26 02:32:01 -0400 (Thu, 26 Aug 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: epigraHMM
Version: 1.0.3
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epigraHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings epigraHMM_1.0.3.tar.gz
StartedAt: 2021-09-21 22:26:56 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 22:37:43 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 647.9 seconds
RetCode: 0
Status:   OK  
CheckDir: epigraHMM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epigraHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings epigraHMM_1.0.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/epigraHMM.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 'epigraHMM/DESCRIPTION' ... OK
* this is package 'epigraHMM' version '1.0.3'
* package encoding: UTF-8
* 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 'epigraHMM' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
* 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 ... OK
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* 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 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/epigraHMM/libs/i386/epigraHMM.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 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/epigraHMM/libs/x64/epigraHMM.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
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
epigraHMMDataSetFromBam 13.59   1.20   22.53
plotPatterns             9.59   0.94   13.22
segmentGenome            9.00   1.03   13.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
epigraHMMDataSetFromBam 13.10   0.34   18.86
plotPatterns            11.06   0.17   11.34
segmentGenome            8.49   1.20   12.88
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/epigraHMM.Rcheck/00check.log'
for details.



Installation output

epigraHMM.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/epigraHMM_1.0.3.tar.gz && rm -rf epigraHMM.buildbin-libdir && mkdir epigraHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=epigraHMM.buildbin-libdir epigraHMM_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL epigraHMM_1.0.3.zip && rm epigraHMM_1.0.3.tar.gz epigraHMM_1.0.3.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
100 58082  100 58082    0     0   316k      0 --:--:-- --:--:-- --:--:--  318k

install for i386

* installing *source* package 'epigraHMM' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c aggregate.cpp -o aggregate.o
aggregate.cpp: In function 'arma::mat aggregate(arma::vec, arma::vec)':
aggregate.cpp:26:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         while( index >= vec.size() ){
                ~~~~~~^~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c computeBIC.cpp -o computeBIC.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c computeQFunction.cpp -o computeQFunction.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c computeViterbiSequence.cpp -o computeViterbiSequence.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c consensusRejectionControlled.cpp -o consensusRejectionControlled.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c differentialRejectionControlled.cpp -o differentialRejectionControlled.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c expStep.cpp -o expStep.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getMarginalProbability.cpp -o getMarginalProbability.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c innerMaxStepProb.cpp -o innerMaxStepProb.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c maxStepProb.cpp -o maxStepProb.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rbinomVectorized.cpp -o rbinomVectorized.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c reweight.cpp -o reweight.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c simulateMarkovChain.cpp -o simulateMarkovChain.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o epigraHMM.dll tmp.def RcppExports.o aggregate.o computeBIC.o computeQFunction.o computeViterbiSequence.o consensusRejectionControlled.o differentialRejectionControlled.o expStep.o getMarginalProbability.o innerMaxStepProb.o maxStepProb.o rbinomVectorized.o reweight.o simulateMarkovChain.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/epigraHMM.buildbin-libdir/00LOCK-epigraHMM/00new/epigraHMM/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'epigraHMM'
    finding HTML links ... done
    addOffsets                              html  
    callPeaks                               html  
    cleanCounts                             html  
    controlEM                               html  
    epigraHMM                               html  
    epigraHMMDataSetFromBam                 html  
    epigraHMMDataSetFromMatrix              html  
    initializer                             html  
    normalizeCounts                         html  
    plotCounts                              html  
    plotPatterns                            html  
    segmentGenome                           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 'epigraHMM' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c aggregate.cpp -o aggregate.o
aggregate.cpp: In function 'arma::mat aggregate(arma::vec, arma::vec)':
aggregate.cpp:26:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         while( index >= vec.size() ){
                ~~~~~~^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c computeBIC.cpp -o computeBIC.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c computeQFunction.cpp -o computeQFunction.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c computeViterbiSequence.cpp -o computeViterbiSequence.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c consensusRejectionControlled.cpp -o consensusRejectionControlled.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c differentialRejectionControlled.cpp -o differentialRejectionControlled.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c expStep.cpp -o expStep.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getMarginalProbability.cpp -o getMarginalProbability.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c innerMaxStepProb.cpp -o innerMaxStepProb.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c maxStepProb.cpp -o maxStepProb.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rbinomVectorized.cpp -o rbinomVectorized.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c reweight.cpp -o reweight.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c simulateMarkovChain.cpp -o simulateMarkovChain.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o epigraHMM.dll tmp.def RcppExports.o aggregate.o computeBIC.o computeQFunction.o computeViterbiSequence.o consensusRejectionControlled.o differentialRejectionControlled.o expStep.o getMarginalProbability.o innerMaxStepProb.o maxStepProb.o rbinomVectorized.o reweight.o simulateMarkovChain.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/epigraHMM.buildbin-libdir/epigraHMM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'epigraHMM' as epigraHMM_1.0.3.zip
* DONE (epigraHMM)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'epigraHMM' successfully unpacked and MD5 sums checked

Tests output

epigraHMM.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(epigraHMM)
> 
> test_check("epigraHMM")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 64 ]
> 
> proc.time()
   user  system elapsed 
  69.89    4.75   80.84 

epigraHMM.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(epigraHMM)
> 
> test_check("epigraHMM")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 64 ]
> 
> proc.time()
   user  system elapsed 
  78.90    2.34   89.06 

Example timings

epigraHMM.Rcheck/examples_i386/epigraHMM-Ex.timings

nameusersystemelapsed
addOffsets1.080.021.09
callPeaks1.720.111.80
cleanCounts1.680.141.78
controlEM000
epigraHMM1.490.051.47
epigraHMMDataSetFromBam13.59 1.2022.53
epigraHMMDataSetFromMatrix0.160.010.18
initializer1.260.114.81
normalizeCounts0.460.020.45
plotCounts0.360.030.39
plotPatterns 9.59 0.9413.22
segmentGenome 9.00 1.0313.53

epigraHMM.Rcheck/examples_x64/epigraHMM-Ex.timings

nameusersystemelapsed
addOffsets0.330.040.38
callPeaks2.290.052.75
cleanCounts1.310.081.47
controlEM000
epigraHMM1.300.151.34
epigraHMMDataSetFromBam13.10 0.3418.86
epigraHMMDataSetFromMatrix0.140.000.14
initializer0.900.081.03
normalizeCounts0.470.000.46
plotCounts0.390.030.42
plotPatterns11.06 0.1711.34
segmentGenome 8.49 1.2012.88