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 12:04:58 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:STAN.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings STAN_2.12.0.tar.gz |
| StartedAt: 2019-10-16 05:16:42 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:21:54 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 312.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: STAN.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:STAN.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings STAN_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/STAN.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * 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 for sufficient/correct file permissions ... 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 * 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed viterbi2GRanges 18.682 0.170 3.246 getAvgSignal 18.668 0.173 3.327 fitBdClust 11.874 0.095 1.821 DirScore 9.847 0.138 1.818 * 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 ‘/home/biocbuild/bbs-3.9-bioc/meat/STAN.Rcheck/00check.log’ for details.
STAN.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL STAN
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘STAN’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Bernoulli.cpp -o Bernoulli.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c EmissionFactory.cpp -o EmissionFactory.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c EmissionFunction.cpp -o EmissionFunction.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c HMM.cpp -o HMM.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c InitialProbability.cpp -o InitialProbability.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c JointlyIndependent.cpp -o JointlyIndependent.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c MemoryAllocation.cpp -o MemoryAllocation.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Multinomial.cpp -o Multinomial.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c MultivariateGaussian.cpp -o MultivariateGaussian.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c NegativeBinomial.cpp -o NegativeBinomial.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Poisson.cpp -o Poisson.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c PoissonLogNormal.cpp -o PoissonLogNormal.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c RAccessUtils.cpp -o RAccessUtils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -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;
^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c TransitionMatrix.cpp -o TransitionMatrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c matUtils.cpp -o matUtils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o STAN.so 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 -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-STAN/00new/STAN/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (STAN)
STAN.Rcheck/STAN-Ex.timings
| name | user | system | elapsed | |
| DimNames | 0.005 | 0.001 | 0.005 | |
| DirScore | 9.847 | 0.138 | 1.818 | |
| Emission | 0.003 | 0.000 | 0.004 | |
| EmissionParams | 0.004 | 0.000 | 0.004 | |
| HMM-class | 0.004 | 0.000 | 0.003 | |
| HMM | 0.000 | 0.003 | 0.004 | |
| HMMEmission-class | 0.002 | 0.001 | 0.002 | |
| HMMEmission | 0.002 | 0.000 | 0.002 | |
| InitProb | 0.003 | 0.000 | 0.002 | |
| LogLik | 3.480 | 0.078 | 0.563 | |
| StateNames | 0.002 | 0.000 | 0.003 | |
| Transitions | 0.003 | 0.000 | 0.003 | |
| bdHMM-class | 0.018 | 0.000 | 0.018 | |
| bdHMM | 0.012 | 0.000 | 0.012 | |
| binarizeData | 1.064 | 0.137 | 1.200 | |
| call_dpoilog | 0.000 | 0.000 | 0.001 | |
| fitBdClust | 11.874 | 0.095 | 1.821 | |
| fitHMM | 3.612 | 0.082 | 0.617 | |
| getAvgSignal | 18.668 | 0.173 | 3.327 | |
| getLogLik | 3.446 | 0.070 | 0.522 | |
| getPosterior | 3.471 | 0.049 | 0.548 | |
| getSizeFactors | 0.035 | 0.012 | 0.046 | |
| getViterbi | 3.754 | 0.073 | 0.679 | |
| initBdHMM | 0.020 | 0.004 | 0.024 | |
| initHMM | 0.009 | 0.004 | 0.013 | |
| runningMean | 0.036 | 0.008 | 0.044 | |
| viterbi2GRanges | 18.682 | 0.170 | 3.246 | |