Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:11 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the methimpute package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methimpute.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. |
Package 1098/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methimpute 1.14.0 (landing page) Aaron Taudt
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: methimpute |
Version: 1.14.0 |
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/methimpute_1.14.0.tar.gz && rm -rf methimpute.buildbin-libdir && mkdir methimpute.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methimpute.buildbin-libdir methimpute_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL methimpute_1.14.0.zip && rm methimpute_1.14.0.tar.gz methimpute_1.14.0.zip |
StartedAt: 2021-10-14 08:22:28 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 08:24:47 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 138.6 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/methimpute_1.14.0.tar.gz && rm -rf methimpute.buildbin-libdir && mkdir methimpute.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methimpute.buildbin-libdir methimpute_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL methimpute_1.14.0.zip && rm methimpute_1.14.0.tar.gz methimpute_1.14.0.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 66 1279k 66 855k 0 0 1202k 0 0:00:01 --:--:-- 0:00:01 1203k 100 1279k 100 1279k 0 0 1366k 0 --:--:-- --:--:-- --:--:-- 1366k install for i386 * installing *source* package 'methimpute' ... ** 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:/extsoft/include" -fopenmp -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:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o densities.cpp: In member function 'virtual void BinomialTestContext::calc_densities(Rcpp::Matrix<14>::Row&)': densities.cpp:614:31: 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:/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:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitHMM.cpp -o fitHMM.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:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitHMM_context.cpp -o fitHMM_context.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:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_context.cpp -o hmm_context.o hmm_context.cpp: In destructor 'HMM_context::~HMM_context()': hmm_context.cpp:68:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Density*>::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i<this->emissionDensities.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c methimpute_init.c -o methimpute_init.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:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o scalehmm.cpp: In destructor 'ScaleHMM::~ScaleHMM()': scalehmm.cpp:311:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Density*>::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i<this->emissionDensities.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw32/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:/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/methimpute.buildbin-libdir/00LOCK-methimpute/00new/methimpute/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'methimpute' finding HTML links ... done arabidopsis_TEs html arabidopsis_chromosomes html arabidopsis_genes html arabidopsis_toydata html binning html 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 inflateMethylome html loadFromFiles html methimpute-objects html methimpute-package html methimputeBinomialHMM html methimputeData html parameterScan html plotting html print.methimputeBinomialHMM html transCoord 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 'methimpute' ... ** 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:/extsoft/include" -fopenmp -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:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o densities.cpp: In member function 'virtual void BinomialTestContext::calc_densities(Rcpp::Matrix<14>::Row&)': densities.cpp:614:31: 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:/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:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitHMM.cpp -o fitHMM.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:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitHMM_context.cpp -o fitHMM_context.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:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmm_context.cpp -o hmm_context.o hmm_context.cpp: In destructor 'HMM_context::~HMM_context()': hmm_context.cpp:68:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Density*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i=0; i<this->emissionDensities.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c methimpute_init.c -o methimpute_init.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:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o scalehmm.cpp: In destructor 'ScaleHMM::~ScaleHMM()': scalehmm.cpp:311:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Density*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i=0; i<this->emissionDensities.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw64/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:/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/methimpute.buildbin-libdir/methimpute/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'methimpute' as methimpute_1.14.0.zip * DONE (methimpute) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'methimpute' successfully unpacked and MD5 sums checked