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BioC 3.4: CHECK report for STAN on zin1

This page was generated on 2016-09-21 03:39:08 -0700 (Wed, 21 Sep 2016).

Package 1166/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.1.3
Benedikt Zacher
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/STAN
Last Changed Rev: 117964 / Revision: 121152
Last Changed Date: 2016-05-30 02:58:47 -0700 (Mon, 30 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: STAN
Version: 2.1.3
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings STAN_2.1.3.tar.gz
StartedAt: 2016-09-20 13:00:36 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:04:25 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 228.9 seconds
RetCode: 0
Status:  OK 
CheckDir: STAN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings STAN_2.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/STAN.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.1.3’
* 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 ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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
viterbi2GRanges 7.752  0.056   3.185
getAvgSignal    7.628  0.044   3.060
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/STAN.Rcheck/00check.log’
for details.


STAN.Rcheck/00install.out:

* installing *source* package ‘STAN’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)

STAN.Rcheck/STAN-Ex.timings:

nameusersystemelapsed
DimNames0.0080.0000.006
DirScore1.7960.0600.739
Emission0.0000.0040.004
EmissionParams0.0040.0000.003
HMM-class0.0040.0000.004
HMM0.0040.0000.003
HMMEmission-class0.0000.0000.002
HMMEmission0.0000.0000.002
InitProb0.0040.0000.002
LogLik0.6280.0200.244
StateNames0.0000.0000.003
Transitions0.0000.0000.002
bdHMM-class0.0120.0000.012
bdHMM0.0080.0000.011
binarizeData0.0320.0000.034
call_dpoilog0.0000.0000.001
fitHMM0.6720.0120.241
getAvgSignal7.6280.0443.060
getLogLik0.6320.0280.247
getPosterior0.6640.0160.262
getSizeFactors0.0240.0000.024
getViterbi0.7040.0160.241
initBdHMM0.0080.0000.010
initHMM0.0080.0000.009
runningMean0.0280.0000.026
viterbi2GRanges7.7520.0563.185