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BioC 3.5: CHECK report for STAN on tokay2

This page was generated on 2017-10-18 14:23:45 -0400 (Wed, 18 Oct 2017).

Package 1274/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.4.0
Benedikt Zacher
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/STAN
Branch: RELEASE_3_5
Last Commit: 82298ef
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: STAN
Version: 2.4.0
Command: rm -rf STAN.buildbin-libdir STAN.Rcheck && mkdir STAN.buildbin-libdir STAN.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=STAN.buildbin-libdir STAN_2.4.0.tar.gz >STAN.Rcheck\00install.out 2>&1 && cp STAN.Rcheck\00install.out STAN-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=STAN.buildbin-libdir --install="check:STAN-install.out" --force-multiarch --no-vignettes --timings STAN_2.4.0.tar.gz
StartedAt: 2017-10-18 03:14:53 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 03:22:20 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 447.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: STAN.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf STAN.buildbin-libdir STAN.Rcheck && mkdir STAN.buildbin-libdir STAN.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=STAN.buildbin-libdir STAN_2.4.0.tar.gz >STAN.Rcheck\00install.out 2>&1 && cp STAN.Rcheck\00install.out STAN-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=STAN.buildbin-libdir --install="check:STAN-install.out" --force-multiarch --no-vignettes --timings STAN_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/STAN.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'STAN/DESCRIPTION' ... OK
* this is package 'STAN' version '2.4.0'
* 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 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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
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 ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
  -w
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/STAN.buildbin-libdir/STAN/libs/i386/STAN.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/STAN.Rcheck/00check.log'
for details.

STAN.Rcheck/00install.out:


install for i386

* installing *source* package 'STAN' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Bernoulli.cpp -o Bernoulli.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c EmissionFactory.cpp -o EmissionFactory.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c EmissionFunction.cpp -o EmissionFunction.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c HMM.cpp -o HMM.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c InitialProbability.cpp -o InitialProbability.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c JointlyIndependent.cpp -o JointlyIndependent.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c MemoryAllocation.cpp -o MemoryAllocation.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Multinomial.cpp -o Multinomial.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c MultivariateGaussian.cpp -o MultivariateGaussian.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c NegativeBinomial.cpp -o NegativeBinomial.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Poisson.cpp -o Poisson.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c PoissonLogNormal.cpp -o PoissonLogNormal.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c RAccessUtils.cpp -o RAccessUtils.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c RWrapper.cpp -o RWrapper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c TransitionMatrix.cpp -o TransitionMatrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c matUtils.cpp -o matUtils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o STAN.dll tmp.def 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 -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/STAN.buildbin-libdir/STAN/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'STAN' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Bernoulli.cpp -o Bernoulli.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c EmissionFactory.cpp -o EmissionFactory.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c EmissionFunction.cpp -o EmissionFunction.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c HMM.cpp -o HMM.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c InitialProbability.cpp -o InitialProbability.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c JointlyIndependent.cpp -o JointlyIndependent.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c MemoryAllocation.cpp -o MemoryAllocation.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Multinomial.cpp -o Multinomial.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c MultivariateGaussian.cpp -o MultivariateGaussian.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c NegativeBinomial.cpp -o NegativeBinomial.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c Poisson.cpp -o Poisson.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c PoissonLogNormal.cpp -o PoissonLogNormal.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c RAccessUtils.cpp -o RAccessUtils.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c RWrapper.cpp -o RWrapper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c TransitionMatrix.cpp -o TransitionMatrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -w -D_RDLL_ -fopenmp    -O2 -Wall  -mtune=core2 -c matUtils.cpp -o matUtils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o STAN.dll tmp.def 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 -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/STAN.buildbin-libdir/STAN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'STAN' as STAN_2.4.0.zip
* DONE (STAN)

STAN.Rcheck/examples_i386/STAN-Ex.timings:

nameusersystemelapsed
DimNames000
DirScore1.240.141.39
Emission000
EmissionParams0.020.000.02
HMM-class0.010.000.01
HMM0.020.000.02
HMMEmission-class0.020.000.01
HMMEmission000
InitProb000
LogLik0.140.020.16
StateNames000
Transitions000
bdHMM-class0.040.000.05
bdHMM0.020.000.01
binarizeData0.050.010.07
call_dpoilog000
fitHMM0.120.030.15
getAvgSignal2.170.072.17
getLogLik0.060.030.09
getPosterior0.050.060.11
getSizeFactors0.060.000.06
getViterbi0.230.010.29
initBdHMM0.000.020.01
initHMM0.000.020.02
runningMean0.080.000.08
viterbi2GRanges2.580.262.59

STAN.Rcheck/examples_x64/STAN-Ex.timings:

nameusersystemelapsed
DimNames000
DirScore1.780.031.79
Emission000
EmissionParams0.020.000.01
HMM-class000
HMM0.030.000.03
HMMEmission-class000
HMMEmission000
InitProb000
LogLik0.110.020.16
StateNames000
Transitions000
bdHMM-class0.060.000.06
bdHMM0.010.000.01
binarizeData0.030.010.05
call_dpoilog000
fitHMM0.160.020.36
getAvgSignal2.020.112.03
getLogLik0.060.000.25
getPosterior0.030.010.10
getSizeFactors0.060.030.09
getViterbi0.260.000.31
initBdHMM0.020.000.01
initHMM0.020.020.03
runningMean0.100.000.11
viterbi2GRanges2.210.132.25