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CHECK report for STAN on malbec1

This page was generated on 2019-04-16 11:50:43 -0400 (Tue, 16 Apr 2019).

Package 1512/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.10.1
Rafael Campos-Martin
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/STAN
Branch: RELEASE_3_8
Last Commit: b0dc295
Last Changed Date: 2019-01-04 13:17:56 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: STAN
Version: 2.10.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:STAN.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings STAN_2.10.1.tar.gz
StartedAt: 2019-04-16 03:16:45 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:21:45 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 300.6 seconds
RetCode: 0
Status:  OK 
CheckDir: STAN.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:STAN.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings STAN_2.10.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/STAN.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.10.1’
* 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 ... 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 22.240  0.260   5.135
getAvgSignal    21.004  0.140   3.868
fitBdClust      13.384  0.104   2.087
DirScore        10.664  0.120   1.847
* 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-3.8-bioc/meat/STAN.Rcheck/00check.log’
for details.



Installation output

STAN.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL STAN
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘STAN’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-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-3.8-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-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)

Tests output


Example timings

STAN.Rcheck/STAN-Ex.timings

nameusersystemelapsed
DimNames0.0080.0000.008
DirScore10.664 0.120 1.847
Emission0.0000.0040.004
EmissionParams0.0040.0000.003
HMM-class0.0040.0000.004
HMM0.0040.0000.003
HMMEmission-class0.0000.0000.001
HMMEmission0.0040.0000.002
InitProb0.0040.0000.003
LogLik3.9560.0560.701
StateNames0.0040.0000.001
Transitions0.0000.0000.002
bdHMM-class0.0120.0040.013
bdHMM0.0080.0000.009
binarizeData0.0560.0120.068
call_dpoilog000
fitBdClust13.384 0.104 2.087
fitHMM4.0160.0480.695
getAvgSignal21.004 0.140 3.868
getLogLik4.1200.0600.708
getPosterior4.0080.0600.622
getSizeFactors0.0640.0000.059
getViterbi3.8640.0480.686
initBdHMM0.0240.0040.026
initHMM0.0080.0040.014
runningMean0.0440.0120.057
viterbi2GRanges22.240 0.260 5.135