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CHECK report for methimpute on tokay1

This page was generated on 2018-04-12 13:30:38 -0400 (Thu, 12 Apr 2018).

Package 831/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methimpute 1.0.0
Aaron Taudt
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/methimpute
Branch: RELEASE_3_6
Last Commit: 0d0322b
Last Changed Date: 2017-10-30 12:42:01 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: methimpute
Version: 1.0.0
Command: rm -rf methimpute.buildbin-libdir methimpute.Rcheck && mkdir methimpute.buildbin-libdir methimpute.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methimpute.buildbin-libdir methimpute_1.0.0.tar.gz >methimpute.Rcheck\00install.out 2>&1 && cp methimpute.Rcheck\00install.out methimpute-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=methimpute.buildbin-libdir --install="check:methimpute-install.out" --force-multiarch --no-vignettes --timings methimpute_1.0.0.tar.gz
StartedAt: 2018-04-12 01:19:17 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:24:36 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 318.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: methimpute.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf methimpute.buildbin-libdir methimpute.Rcheck && mkdir methimpute.buildbin-libdir methimpute.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methimpute.buildbin-libdir methimpute_1.0.0.tar.gz >methimpute.Rcheck\00install.out 2>&1 && cp methimpute.Rcheck\00install.out methimpute-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=methimpute.buildbin-libdir --install="check:methimpute-install.out" --force-multiarch --no-vignettes --timings methimpute_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/methimpute.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methimpute/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methimpute' version '1.0.0'
* 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 'methimpute' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/arabidopsis_TEs.Rd:9: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/arabidopsis_TEs.Rd:7: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/arabidopsis_genes.Rd:9: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/arabidopsis_genes.Rd:7: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binCounts.Rd:10: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binCounts.Rd:15: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binMethylome.Rd:11: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binMethylome.Rd:20: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binPositions.Rd:10: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binPositions.Rd:15: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/importRene.Rd:20: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/inflateMethylome.Rd:10: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/inflateMethylome.Rd:12: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/methimputeBinomialHMM.Rd:11: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/methimputeData.Rd:7: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/plotting.Rd:37: missing file link 'GRanges'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/methimpute.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 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 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-3.6-bioc/meat/methimpute.buildbin-libdir/methimpute/libs/i386/methimpute.dll':
  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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotting        21.00   0.16   20.54
exportMethylome  6.22   0.08    5.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
plotting                  23.14   0.20   22.86
exportMethylome            6.20   0.09    5.76
extractCytosinesFromFASTA  5.08   0.16    5.24
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/methimpute.Rcheck/00check.log'
for details.



Installation output

methimpute.Rcheck/00install.out


install for i386

* installing *source* package 'methimpute' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c densities.cpp -o densities.o
densities.cpp: In member function 'virtual void BinomialTestContext::calc_densities(Rcpp::Matrix<14>::Row&)':
densities.cpp:614:138: warning: 'prob_context' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (verbosity >= 4) Rprintf("obs_test[t=%d] = %d, obs_total[t] = %d, prob_context = %g\n", t, obs_test[t], obs_total[t], prob_context);
                                                                                                                                          ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c fitHMM.cpp -o fitHMM.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c fitHMM_context.cpp -o fitHMM_context.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c hmm_context.cpp -o hmm_context.o
hmm_context.cpp: In destructor 'HMM_context::˜HMM_context()':
hmm_context.cpp:68:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<this->emissionDensities.size(); i++)
                 ^
hmm_context.cpp: In member function 'Rcpp::List HMM_context::baumWelch(double, double, double)':
hmm_context.cpp:378:22: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if (this->NSTATES == 2 | this->UPDATE_PROCEDURE == 1)
                      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c methimpute_init.c -o methimpute_init.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp: In destructor 'ScaleHMM::˜ScaleHMM()':
scalehmm.cpp:311:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<this->emissionDensities.size(); i++)
                 ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o methimpute.dll tmp.def RcppExports.o densities.o fitHMM.o fitHMM_context.o hmm_context.o methimpute_init.o scalehmm.o -fopenmp -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/methimpute.buildbin-libdir/methimpute/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'methimpute'
    finding HTML links ... done
    arabidopsis_TEs                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/arabidopsis_TEs.Rd:9: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/arabidopsis_TEs.Rd:7: missing file link 'GRanges'
    arabidopsis_chromosomes                 html  
    arabidopsis_genes                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/arabidopsis_genes.Rd:9: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/arabidopsis_genes.Rd:7: missing file link 'GRanges'
    arabidopsis_toydata                     html  
    binCounts                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binCounts.Rd:10: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binCounts.Rd:15: missing file link 'GRanges'
    binMethylome                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binMethylome.Rd:11: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binMethylome.Rd:20: missing file link 'GRanges'
    binPositions                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binPositions.Rd:10: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/binPositions.Rd:15: missing file link 'GRanges'
    binomialTestMethylation                 html  
    callMethylation                         html  
    callMethylationSeparate                 html  
    collapseBins                            html  
    distanceCorrelation                     html  
    estimateTransDist                       html  
    exportMethylome                         html  
    extractCytosinesFromFASTA               html  
    finding level-2 HTML links ... done

    getDistinctColors                       html  
    getPosteriors                           html  
    getStateColors                          html  
    import                                  html  
    importRene                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/importRene.Rd:20: missing file link 'GRanges'
    inflateMethylome                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/inflateMethylome.Rd:10: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/inflateMethylome.Rd:12: missing file link 'GRanges'
    loadFromFiles                           html  
    methimpute-objects                      html  
    methimpute-package                      html  
    methimputeBinomialHMM                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/methimputeBinomialHMM.Rd:11: missing file link 'GRanges'
    methimputeData                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/methimputeData.Rd:7: missing file link 'GRanges'
    parameterScan                           html  
    plotting                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpk3ZSnb/R.INSTALL2d784cfc1174/methimpute/man/plotting.Rd:37: missing file link 'GRanges'
    print.methimputeBinomialHMM             html  
    transCoord                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'methimpute' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c densities.cpp -o densities.o
densities.cpp: In member function 'virtual void BinomialTestContext::calc_densities(Rcpp::Matrix<14>::Row&)':
densities.cpp:614:138: warning: 'prob_context' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (verbosity >= 4) Rprintf("obs_test[t=%d] = %d, obs_total[t] = %d, prob_context = %g\n", t, obs_test[t], obs_total[t], prob_context);
                                                                                                                                          ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c fitHMM.cpp -o fitHMM.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c fitHMM_context.cpp -o fitHMM_context.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c hmm_context.cpp -o hmm_context.o
hmm_context.cpp: In destructor 'HMM_context::˜HMM_context()':
hmm_context.cpp:68:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<this->emissionDensities.size(); i++)
                 ^
hmm_context.cpp: In member function 'Rcpp::List HMM_context::baumWelch(double, double, double)':
hmm_context.cpp:378:22: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if (this->NSTATES == 2 | this->UPDATE_PROCEDURE == 1)
                      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c methimpute_init.c -o methimpute_init.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"  -fopenmp   -O2 -Wall  -mtune=generic -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp: In destructor 'ScaleHMM::˜ScaleHMM()':
scalehmm.cpp:311:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<this->emissionDensities.size(); i++)
                 ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o methimpute.dll tmp.def RcppExports.o densities.o fitHMM.o fitHMM_context.o hmm_context.o methimpute_init.o scalehmm.o -fopenmp -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/methimpute.buildbin-libdir/methimpute/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methimpute' as methimpute_1.0.0.zip
* DONE (methimpute)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

methimpute.Rcheck/examples_i386/methimpute-Ex.timings

nameusersystemelapsed
arabidopsis_TEs0.140.030.17
arabidopsis_chromosomes000
arabidopsis_genes0.060.000.06
arabidopsis_toydata0.340.050.39
binomialTestMethylation0.80.00.8
callMethylation3.230.092.84
callMethylationSeparate3.530.213.39
collapseBins2.540.032.56
distanceCorrelation2.320.092.42
estimateTransDist2.160.032.19
exportMethylome6.220.085.81
extractCytosinesFromFASTA4.340.054.40
getDistinctColors0.050.010.06
getStateColors0.030.000.03
import0.920.020.94
importRene0.020.000.01
inflateMethylome0.760.000.77
loadFromFiles0.470.030.50
plotting21.00 0.1620.54

methimpute.Rcheck/examples_x64/methimpute-Ex.timings

nameusersystemelapsed
arabidopsis_TEs0.190.020.21
arabidopsis_chromosomes000
arabidopsis_genes0.060.020.08
arabidopsis_toydata0.440.010.45
binomialTestMethylation0.410.050.46
callMethylation4.000.043.62
callMethylationSeparate4.300.114.13
collapseBins3.840.053.89
distanceCorrelation3.260.033.34
estimateTransDist3.150.053.19
exportMethylome6.200.095.76
extractCytosinesFromFASTA5.080.165.24
getDistinctColors0.050.010.07
getStateColors0.030.000.03
import0.830.040.86
importRene0.030.000.03
inflateMethylome0.960.010.99
loadFromFiles0.160.020.17
plotting23.14 0.2022.86