Rafael Campos-Martin
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/STAN |
| Branch: RELEASE_3_10 |
| Last Commit: 2d374bb |
| Last Changed Date: 2019-10-29 13:09:02 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:08:57 -0400 (Wed, 15 Apr 2020).
| Package 1669/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| STAN 2.14.0 Rafael Campos-Martin
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: STAN |
| Version: 2.14.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:STAN.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings STAN_2.14.0.tar.gz |
| StartedAt: 2020-04-15 02:22:00 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:28:04 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 364.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: STAN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:STAN.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings STAN_2.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/STAN.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.14.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
viterbi2GRanges 20.732 0.200 4.477
getAvgSignal 20.652 0.160 4.292
fitBdClust 13.856 0.120 3.228
DirScore 10.400 0.188 2.379
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/STAN.Rcheck/00check.log’
for details.
STAN.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL STAN
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘STAN’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Bernoulli.cpp -o Bernoulli.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c EmissionFactory.cpp -o EmissionFactory.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c EmissionFunction.cpp -o EmissionFunction.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c HMM.cpp -o HMM.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c InitialProbability.cpp -o InitialProbability.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c JointlyIndependent.cpp -o JointlyIndependent.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c MemoryAllocation.cpp -o MemoryAllocation.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Multinomial.cpp -o Multinomial.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c MultivariateGaussian.cpp -o MultivariateGaussian.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c NegativeBinomial.cpp -o NegativeBinomial.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c Poisson.cpp -o Poisson.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c PoissonLogNormal.cpp -o PoissonLogNormal.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c RAccessUtils.cpp -o RAccessUtils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c RWrapper.cpp -o RWrapper.o
RWrapper.cpp: In function ‘EmissionFunction** RGETEMISSION(SEXP, int, SEXP, int*, const char*, double***, int*, int, SEXP, int*, int*, int*)’:
RWrapper.cpp:350:16: warning: ‘HMMEmissionFunctions’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return HMMEmissionFunctions;
^~~~~~~~~~~~~~~~~~~~
RWrapper.cpp: In function ‘SEXPREC* prepareEmission(const char*, SEXP, SEXP, EmissionFunction**, int)’:
RWrapper.cpp:1157:16: warning: ‘sexpemissionParam’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return sexpemissionParam;
^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c TransitionMatrix.cpp -o TransitionMatrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fopenmp -fpic -g -O2 -Wall -c matUtils.cpp -o matUtils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-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-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/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)
STAN.Rcheck/STAN-Ex.timings
| name | user | system | elapsed | |
| DimNames | 0.008 | 0.000 | 0.009 | |
| DirScore | 10.400 | 0.188 | 2.379 | |
| Emission | 0.004 | 0.000 | 0.004 | |
| EmissionParams | 0.004 | 0.000 | 0.004 | |
| HMM-class | 0.004 | 0.000 | 0.004 | |
| HMM | 0.000 | 0.004 | 0.003 | |
| HMMEmission-class | 0.004 | 0.000 | 0.002 | |
| HMMEmission | 0.000 | 0.000 | 0.002 | |
| InitProb | 0.004 | 0.000 | 0.002 | |
| LogLik | 4.056 | 0.088 | 1.037 | |
| StateNames | 0.004 | 0.000 | 0.002 | |
| Transitions | 0.000 | 0.000 | 0.002 | |
| bdHMM-class | 0.012 | 0.004 | 0.018 | |
| bdHMM | 0.012 | 0.000 | 0.011 | |
| binarizeData | 1.104 | 0.132 | 1.244 | |
| call_dpoilog | 0.000 | 0.000 | 0.001 | |
| fitBdClust | 13.856 | 0.120 | 3.228 | |
| fitHMM | 4.008 | 0.072 | 0.943 | |
| getAvgSignal | 20.652 | 0.160 | 4.292 | |
| getLogLik | 4.024 | 0.048 | 0.751 | |
| getPosterior | 4.132 | 0.060 | 0.807 | |
| getSizeFactors | 0.064 | 0.004 | 0.068 | |
| getViterbi | 3.928 | 0.064 | 0.760 | |
| initBdHMM | 0.012 | 0.000 | 0.014 | |
| initHMM | 0.004 | 0.004 | 0.009 | |
| runningMean | 0.020 | 0.004 | 0.026 | |
| viterbi2GRanges | 20.732 | 0.200 | 4.477 | |