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CHECK report for STAN on celaya2

This page was generated on 2019-10-16 12:53:38 -0400 (Wed, 16 Oct 2019).

Package 1592/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.12.0
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)
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

Summary

Package: STAN
Version: 2.12.0
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_2.12.0.tar.gz
StartedAt: 2019-10-16 07:10:06 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:17:40 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 454.3 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_2.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/STAN.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.12.0’
* 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 ... 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 : : 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 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    6.196  1.824   1.268
viterbi2GRanges 6.031  1.508   1.666
* 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
###
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##############################################################################


* 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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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
DimNames0.0120.0020.013
DirScore0.7720.3240.457
Emission0.0130.0090.005
EmissionParams0.0090.0060.005
HMM-class0.0140.0100.006
HMM0.0120.0080.005
HMMEmission-class0.0080.0050.003
HMMEmission0.0080.0050.003
InitProb0.0080.0050.003
LogLik0.1650.1290.074
StateNames0.0090.0070.004
Transitions0.0080.0070.004
bdHMM-class0.0540.0350.022
bdHMM0.0400.0240.016
binarizeData1.2420.2041.097
call_dpoilog0.0010.0000.003
fitBdClust0.3750.2120.180
fitHMM0.1550.1180.069
getAvgSignal6.1961.8241.268
getLogLik0.1580.1350.061
getPosterior0.1930.1720.083
getSizeFactors0.2700.2480.111
getViterbi0.2220.2010.065
initBdHMM0.0620.0420.027
initHMM0.0410.0260.017
runningMean0.2610.3030.081
viterbi2GRanges6.0311.5081.666