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CHECK report for STAN on celaya2

This page was generated on 2019-04-09 13:11:16 -0400 (Tue, 09 Apr 2019).

Package 1560/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.11.0
Rafael Campos-Martin
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/STAN
Branch: master
Last Commit: 123b152
Last Changed Date: 2018-11-30 12:12:22 -0400 (Fri, 30 Nov 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: STAN
Version: 2.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:STAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings STAN_2.11.0.tar.gz
StartedAt: 2019-04-09 05:46:56 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:54:19 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 443.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: STAN.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:STAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings STAN_2.11.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/STAN.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STAN/DESCRIPTION’ ... OK
* this is package ‘STAN’ version ‘2.11.0’
* 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 ... WARNING
Found the following significant warnings:
  matUtils.cpp:114:10: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
  matUtils.cpp:115:14: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
  matUtils.cpp:125:10: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/STAN.Rcheck/00install.out’ for details.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getAvgSignal    5.471  3.819   2.257
viterbi2GRanges 3.850  2.807   1.388
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/STAN.Rcheck/00check.log’
for details.



Installation output

STAN.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL STAN
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘STAN’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c Bernoulli.cpp -o Bernoulli.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c EmissionFactory.cpp -o EmissionFactory.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c EmissionFunction.cpp -o EmissionFunction.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c HMM.cpp -o HMM.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c InitialProbability.cpp -o InitialProbability.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c JointlyIndependent.cpp -o JointlyIndependent.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c MemoryAllocation.cpp -o MemoryAllocation.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c Multinomial.cpp -o Multinomial.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c MultivariateGaussian.cpp -o MultivariateGaussian.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c NegativeBinomial.cpp -o NegativeBinomial.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c Poisson.cpp -o Poisson.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c PoissonLogNormal.cpp -o PoissonLogNormal.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c RAccessUtils.cpp -o RAccessUtils.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c RWrapper.cpp -o RWrapper.o
RWrapper.cpp:343:17: warning: variable 'HMMEmissionFunctions' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if(strcmp(type,poissonlognormal) == 0)
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:350:16: note: uninitialized use occurs here
        return HMMEmissionFunctions;
               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:343:14: note: remove the 'if' if its condition is always true
        else if(strcmp(type,poissonlognormal) == 0)
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:311:48: note: initialize the variable 'HMMEmissionFunctions' to silence this warning
        EmissionFunction **HMMEmissionFunctions;
                                               ^
                                                = nullptr
RWrapper.cpp:1140:21: warning: variable 'sexpemissionParam' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
            else if(strcmp(type, multinomial) == 0)
                    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:1157:16: note: uninitialized use occurs here
        return sexpemissionParam;
               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:1140:18: note: remove the 'if' if its condition is always true
            else if(strcmp(type, multinomial) == 0)
                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
RWrapper.cpp:1123:31: note: initialize the variable 'sexpemissionParam' to silence this warning
        SEXP sexpemissionParam;
                              ^
                               = nullptr
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c TransitionMatrix.cpp -o TransitionMatrix.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -D_RDLL_ -fopenmp  -fPIC  -Wall -g -O2  -c matUtils.cpp -o matUtils.o
matUtils.cpp:114:10: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    for (register int i = 0 ; i < myN ; i++)
         ^˜˜˜˜˜˜˜˜
matUtils.cpp:115:14: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
        for (register int j = i ; j < myldz ; j++)
             ^˜˜˜˜˜˜˜˜
matUtils.cpp:125:10: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    for (register int i = 0 ; i < myNCol ; i++)
         ^˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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)

Tests output


Example timings

STAN.Rcheck/STAN-Ex.timings

nameusersystemelapsed
DimNames0.0100.0010.010
DirScore0.7860.5900.305
Emission0.0160.0130.005
EmissionParams0.0180.0140.006
HMM-class0.0190.0160.006
HMM0.0160.0130.005
HMMEmission-class0.0090.0070.004
HMMEmission0.0090.0080.004
InitProb0.0090.0070.004
LogLik0.2240.1880.072
StateNames0.0100.0070.003
Transitions0.0130.0100.004
bdHMM-class0.0640.0560.020
bdHMM0.0510.0400.015
binarizeData0.5030.3620.185
call_dpoilog0.0000.0000.002
fitBdClust4.0030.4040.388
fitHMM0.2620.2820.072
getAvgSignal5.4713.8192.257
getLogLik0.1640.1170.067
getPosterior0.2370.2400.068
getSizeFactors0.2660.2810.079
getViterbi0.2560.2320.071
initBdHMM0.0670.0620.022
initHMM0.0490.0420.016
runningMean0.3680.3890.106
viterbi2GRanges3.8502.8071.388