STAN 2.4.0
Benedikt Zacher
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/STAN | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings STAN_2.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/STAN.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.4.0’
* 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 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 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getAvgSignal 30.648 0.156 3.795
viterbi2GRanges 29.156 0.160 3.999
DirScore 9.328 0.088 1.968
* 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, 1 NOTE
See
‘/home/biocbuild/bbs-3.5-bioc/meat/STAN.Rcheck/00check.log’
for details.
* installing *source* package ‘STAN’ ...
** libs
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Bernoulli.cpp -o Bernoulli.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c EmissionFactory.cpp -o EmissionFactory.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c EmissionFunction.cpp -o EmissionFunction.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c HMM.cpp -o HMM.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c InitialProbability.cpp -o InitialProbability.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c JointlyIndependent.cpp -o JointlyIndependent.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c MemoryAllocation.cpp -o MemoryAllocation.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Multinomial.cpp -o Multinomial.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c MultivariateGaussian.cpp -o MultivariateGaussian.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c NegativeBinomial.cpp -o NegativeBinomial.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Poisson.cpp -o Poisson.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c PoissonLogNormal.cpp -o PoissonLogNormal.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c RAccessUtils.cpp -o RAccessUtils.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c RWrapper.cpp -o RWrapper.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c TransitionMatrix.cpp -o TransitionMatrix.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -w -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c matUtils.cpp -o matUtils.o
g++ -shared -L/home/biocbuild/bbs-3.5-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-3.5-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/STAN.Rcheck/STAN/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (STAN)