Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-20 11:07:13 -0500 (Thu, 20 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4162
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4057
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3999
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4116
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

INSTALL results for epigraHMM on riesling1


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 589/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigraHMM 1.3.2  (landing page)
Pedro Baldoni
Snapshot Date: 2022-01-19 13:55:26 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/epigraHMM
git_branch: master
git_last_commit: a2e5af4
git_last_commit_date: 2022-01-13 17:00:11 -0500 (Thu, 13 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SummarizedExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: epigraHMM
Version: 1.3.2
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL epigraHMM
StartedAt: 2022-01-19 16:02:18 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 16:05:24 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 185.8 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL epigraHMM
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'epigraHMM' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c computeBIC.cpp -o computeBIC.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c computeQFunction.cpp -o computeQFunction.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c computeViterbiSequence.cpp -o computeViterbiSequence.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c consensusRejectionControlled.cpp -o consensusRejectionControlled.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c differentialRejectionControlled.cpp -o differentialRejectionControlled.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c expStep.cpp -o expStep.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c getMarginalProbability.cpp -o getMarginalProbability.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c innerMaxStepProb.cpp -o innerMaxStepProb.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c maxStepProb.cpp -o maxStepProb.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rbinomVectorized.cpp -o rbinomVectorized.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c reweight.cpp -o reweight.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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 -LD:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -fopenmp -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-epigraHMM/00new/epigraHMM/libs/x64
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'epigraHMM'
    finding HTML links ... done
    addOffsets                              html  
    callPatterns                            html  
    callPeaks                               html  
    cleanCounts                             html  
    controlEM                               html  
    epigraHMM                               html  
    epigraHMMDataSetFromBam                 html  
    epigraHMMDataSetFromMatrix              html  
    estimateTransitionProb                  html  
    expStep                                 html  
    helas3                                  html  
    info                                    html  
    initializer                             html  
    maxStepProb                             html  
    normalizeCounts                         html  
    plotCounts                              html  
    plotPatterns                            html  
    segmentGenome                           html  
    simulateMarkovChain                     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
* DONE (epigraHMM)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'svaNUMT' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'svaRetro' is missing or broken
 done