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This page was generated on 2022-04-13 12:06:00 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for STAN on nebbiolo2


To the developers/maintainers of the STAN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/STAN.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1884/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.22.0  (landing page)
Rafael Campos-Martin
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/STAN
git_branch: RELEASE_3_14
git_last_commit: 3fab9c3
git_last_commit_date: 2021-10-26 12:14:57 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: STAN
Version: 2.22.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:STAN.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings STAN_2.22.0.tar.gz
StartedAt: 2022-04-12 09:33:24 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 09:38:07 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 283.8 seconds
RetCode: 0
Status:   OK  
CheckDir: STAN.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:STAN.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings STAN_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/STAN.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘2.22.0’
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/STAN.Rcheck/00check.log’
for details.



Installation output

STAN.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL STAN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘STAN’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c Bernoulli.cpp -o Bernoulli.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c EmissionFactory.cpp -o EmissionFactory.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c EmissionFunction.cpp -o EmissionFunction.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c HMM.cpp -o HMM.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c InitialProbability.cpp -o InitialProbability.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c JointlyIndependent.cpp -o JointlyIndependent.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c MemoryAllocation.cpp -o MemoryAllocation.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c Multinomial.cpp -o Multinomial.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c MultivariateGaussian.cpp -o MultivariateGaussian.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c NegativeBinomial.cpp -o NegativeBinomial.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c Poisson.cpp -o Poisson.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c PoissonLogNormal.cpp -o PoissonLogNormal.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c RAccessUtils.cpp -o RAccessUtils.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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]
  350 |         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]
 1157 |         return sexpemissionParam;
      |                ^~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c TransitionMatrix.cpp -o TransitionMatrix.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_ -fopenmp  -fpic  -g -O2  -Wall -c matUtils.cpp -o matUtils.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-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-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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)

Tests output


Example timings

STAN.Rcheck/STAN-Ex.timings

nameusersystemelapsed
DimNames0.0050.0000.005
DirScore0.1750.0110.139
Emission0.0030.0000.002
EmissionParams0.0020.0000.002
HMM-class0.0020.0000.002
HMM0.0020.0000.002
HMMEmission-class0.0010.0000.001
HMMEmission0.0010.0000.001
InitProb0.0010.0000.001
LogLik0.0220.0100.023
StateNames0.0040.0010.001
Transitions0.0010.0000.002
bdHMM-class0.010.000.01
bdHMM0.0060.0000.006
binarizeData0.0590.0000.059
call_dpoilog0.0010.0000.000
fitBdClust0.1000.0130.074
fitHMM0.0260.0000.020
getAvgSignal1.2090.0120.752
getLogLik0.0360.0000.026
getPosterior0.0400.0000.026
getSizeFactors0.0260.0000.019
getViterbi0.0350.0000.027
initBdHMM0.0110.0000.010
initHMM0.0070.0000.007
runningMean1.0200.0201.039
viterbi2GRanges1.3040.0040.843