Rafael Campos-Martin
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/STAN |
| Branch: RELEASE_3_9 |
| Last Commit: b9f2e86 |
| Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:30:40 -0400 (Wed, 16 Oct 2019).
| Package 1592/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| STAN 2.12.0 Rafael Campos-Martin
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: STAN |
| Version: 2.12.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:STAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings STAN_2.12.0.tar.gz |
| StartedAt: 2019-10-16 07:22:18 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:29:24 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 426.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: STAN.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:STAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings STAN_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/STAN.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'STAN/DESCRIPTION' ... OK * this is package 'STAN' version '2.12.0' * 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 'STAN' can be installed ... OK * 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 * 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 ... NOTE initBdClust: warning in initBdHMM(obs, dStates = dStates, uStates = uStates, method = method, directedObs = directedObs, sizeFactor = sizeFactors, sharedCov = sharedCov, dirFlags = dirFlags): partial argument match of 'sizeFactor' to 'sizeFactors' binarizeData :: no visible global function definition for 'ppois' clusterMat : : no visible global function definition for 'ppois' clusterMat: no visible global function definition for 'kmeans' myQNBinom: no visible global function definition for 'dnbinom' optimizeNB : : no visible global function definition for 'optim' optimizeNBInit: no visible global function definition for 'optim' optimizePoiLog : : no visible global function definition for 'optim' optimizePoiLogInit: no visible global function definition for 'optim' Undefined global functions or variables: dnbinom kmeans optim ppois Consider adding importFrom("stats", "dnbinom", "kmeans", "optim", "ppois") to your NAMESPACE file. * 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-3.9-bioc/R/library/STAN/libs/i386/STAN.dll': 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-3.9-bioc/R/library/STAN/libs/x64/STAN.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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/STAN.Rcheck/00check.log' for details.
STAN.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/STAN_2.12.0.tar.gz && rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=STAN.buildbin-libdir STAN_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL STAN_2.12.0.zip && rm STAN_2.12.0.tar.gz STAN_2.12.0.zip
###
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install for i386
* installing *source* package 'STAN' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c Bernoulli.cpp -o Bernoulli.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c EmissionFactory.cpp -o EmissionFactory.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c EmissionFunction.cpp -o EmissionFunction.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c HMM.cpp -o HMM.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c InitialProbability.cpp -o InitialProbability.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c JointlyIndependent.cpp -o JointlyIndependent.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c MemoryAllocation.cpp -o MemoryAllocation.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c Multinomial.cpp -o Multinomial.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c MultivariateGaussian.cpp -o MultivariateGaussian.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c NegativeBinomial.cpp -o NegativeBinomial.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c Poisson.cpp -o Poisson.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c PoissonLogNormal.cpp -o PoissonLogNormal.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c RAccessUtils.cpp -o RAccessUtils.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -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:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c TransitionMatrix.cpp -o TransitionMatrix.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c matUtils.cpp -o matUtils.o
C:/Rtools/mingw_32/bin/g++ -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-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c Bernoulli.cpp -o Bernoulli.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c EmissionFactory.cpp -o EmissionFactory.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c EmissionFunction.cpp -o EmissionFunction.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c HMM.cpp -o HMM.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c InitialProbability.cpp -o InitialProbability.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c JointlyIndependent.cpp -o JointlyIndependent.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c MemoryAllocation.cpp -o MemoryAllocation.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c Multinomial.cpp -o Multinomial.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c MultivariateGaussian.cpp -o MultivariateGaussian.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c NegativeBinomial.cpp -o NegativeBinomial.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c Poisson.cpp -o Poisson.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c PoissonLogNormal.cpp -o PoissonLogNormal.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c RAccessUtils.cpp -o RAccessUtils.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -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:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c TransitionMatrix.cpp -o TransitionMatrix.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D_RDLL_ -fopenmp -O2 -Wall -mtune=generic -c matUtils.cpp -o matUtils.o
C:/Rtools/mingw_64/bin/g++ -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-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/STAN.buildbin-libdir/STAN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'STAN' as STAN_2.12.0.zip
* DONE (STAN)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'STAN' successfully unpacked and MD5 sums checked
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STAN.Rcheck/examples_i386/STAN-Ex.timings
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STAN.Rcheck/examples_x64/STAN-Ex.timings
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