Rafael Campos-Martin
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/STAN |
| git_branch: RELEASE_3_13 |
| git_last_commit: 9c7a3b4 |
| git_last_commit_date: 2021-05-19 12:06:26 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:24 -0400 (Fri, 15 Oct 2021).
|
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. |
| Package 1852/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| STAN 2.20.0 (landing page) Rafael Campos-Martin
| 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 | WARNINGS | OK | | ||||||||
| Package: STAN |
| Version: 2.20.0 |
| Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/STAN_2.20.0.tar.gz && rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=STAN.buildbin-libdir STAN_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL STAN_2.20.0.zip && rm STAN_2.20.0.tar.gz STAN_2.20.0.zip |
| StartedAt: 2021-10-14 10:55:51 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 10:58:04 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 132.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/STAN_2.20.0.tar.gz && rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=STAN.buildbin-libdir STAN_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL STAN_2.20.0.zip && rm STAN_2.20.0.tar.gz STAN_2.20.0.zip
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install for i386
* installing *source* package 'STAN' ...
** 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:/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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 -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 -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/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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"C:/Users/BIOCBU~1/BBS-3~1.13-/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 -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 -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/STAN.buildbin-libdir/STAN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'STAN' as STAN_2.20.0.zip
* DONE (STAN)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'STAN' successfully unpacked and MD5 sums checked