Rafael Campos-Martin
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/STAN |
| Branch: RELEASE_3_7 |
| Last Commit: f2bc4a6 |
| Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:26:27 -0400 (Wed, 17 Oct 2018).
| Package 1434/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| STAN 2.8.0 Rafael Campos-Martin
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: STAN |
| Version: 2.8.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:STAN.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings STAN_2.8.0.tar.gz |
| StartedAt: 2018-10-16 04:01:06 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 04:04:52 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 226.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: STAN.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:STAN.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings STAN_2.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/STAN.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.8.0’
* 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 : <anonymous>: no visible global function definition for
'ppois'
clusterMat : <anonymous>: no visible global function definition for
'ppois'
clusterMat: no visible global function definition for 'kmeans'
myQNBinom: no visible global function definition for 'dnbinom'
optimizeNB : <anonymous>: no visible global function definition for
'optim'
optimizeNBInit: no visible global function definition for 'optim'
optimizePoiLog : <anonymous>: 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 ... NOTE
Error in .requirePackage(package) :
unable to find required package 'Gviz'
Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
Execution halted
* 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 18.600 0.224 3.331
getAvgSignal 17.960 0.116 2.313
fitBdClust 9.928 0.048 1.061
DirScore 8.096 0.096 0.977
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.7-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-3.7-bioc/R/bin/R CMD INSTALL STAN
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘STAN’ ...
** libs
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Bernoulli.cpp -o Bernoulli.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c EmissionFactory.cpp -o EmissionFactory.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c EmissionFunction.cpp -o EmissionFunction.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c HMM.cpp -o HMM.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c InitialProbability.cpp -o InitialProbability.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c JointlyIndependent.cpp -o JointlyIndependent.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c MemoryAllocation.cpp -o MemoryAllocation.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Multinomial.cpp -o Multinomial.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c MultivariateGaussian.cpp -o MultivariateGaussian.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c NegativeBinomial.cpp -o NegativeBinomial.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Poisson.cpp -o Poisson.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c PoissonLogNormal.cpp -o PoissonLogNormal.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c RAccessUtils.cpp -o RAccessUtils.o
g++ -I"/home/biocbuild/bbs-3.7-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++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c TransitionMatrix.cpp -o TransitionMatrix.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c matUtils.cpp -o matUtils.o
g++ -shared -L/home/biocbuild/bbs-3.7-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-3.7-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/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
* DONE (STAN)
STAN.Rcheck/STAN-Ex.timings
| name | user | system | elapsed | |
| DimNames | 0.004 | 0.000 | 0.005 | |
| DirScore | 8.096 | 0.096 | 0.977 | |
| Emission | 0.004 | 0.000 | 0.004 | |
| EmissionParams | 0.000 | 0.004 | 0.004 | |
| HMM-class | 0.004 | 0.000 | 0.005 | |
| HMM | 0.004 | 0.000 | 0.003 | |
| HMMEmission-class | 0.004 | 0.000 | 0.002 | |
| HMMEmission | 0.000 | 0.000 | 0.002 | |
| InitProb | 0.000 | 0.000 | 0.002 | |
| LogLik | 3.352 | 0.044 | 0.388 | |
| StateNames | 0.004 | 0.000 | 0.004 | |
| Transitions | 0.004 | 0.000 | 0.004 | |
| bdHMM-class | 0.016 | 0.008 | 0.021 | |
| bdHMM | 0.016 | 0.000 | 0.016 | |
| binarizeData | 0.068 | 0.016 | 0.085 | |
| call_dpoilog | 0.000 | 0.000 | 0.001 | |
| fitBdClust | 9.928 | 0.048 | 1.061 | |
| fitHMM | 2.672 | 0.044 | 0.293 | |
| getAvgSignal | 17.960 | 0.116 | 2.313 | |
| getLogLik | 3.212 | 0.036 | 0.384 | |
| getPosterior | 2.956 | 0.048 | 0.346 | |
| getSizeFactors | 0.068 | 0.008 | 0.057 | |
| getViterbi | 2.660 | 0.060 | 0.326 | |
| initBdHMM | 0.028 | 0.000 | 0.027 | |
| initHMM | 0.008 | 0.008 | 0.015 | |
| runningMean | 0.056 | 0.008 | 0.062 | |
| viterbi2GRanges | 18.600 | 0.224 | 3.331 | |