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) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:00 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (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 | ||||
|
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. |
| Package 1884/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| STAN 2.22.0 (landing page) Rafael Campos-Martin
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| 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 |
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### Running command:
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### /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
###
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* 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.
STAN.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL STAN
###
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* 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)
STAN.Rcheck/STAN-Ex.timings
| name | user | system | elapsed | |
| DimNames | 0.005 | 0.000 | 0.005 | |
| DirScore | 0.175 | 0.011 | 0.139 | |
| Emission | 0.003 | 0.000 | 0.002 | |
| EmissionParams | 0.002 | 0.000 | 0.002 | |
| HMM-class | 0.002 | 0.000 | 0.002 | |
| HMM | 0.002 | 0.000 | 0.002 | |
| HMMEmission-class | 0.001 | 0.000 | 0.001 | |
| HMMEmission | 0.001 | 0.000 | 0.001 | |
| InitProb | 0.001 | 0.000 | 0.001 | |
| LogLik | 0.022 | 0.010 | 0.023 | |
| StateNames | 0.004 | 0.001 | 0.001 | |
| Transitions | 0.001 | 0.000 | 0.002 | |
| bdHMM-class | 0.01 | 0.00 | 0.01 | |
| bdHMM | 0.006 | 0.000 | 0.006 | |
| binarizeData | 0.059 | 0.000 | 0.059 | |
| call_dpoilog | 0.001 | 0.000 | 0.000 | |
| fitBdClust | 0.100 | 0.013 | 0.074 | |
| fitHMM | 0.026 | 0.000 | 0.020 | |
| getAvgSignal | 1.209 | 0.012 | 0.752 | |
| getLogLik | 0.036 | 0.000 | 0.026 | |
| getPosterior | 0.040 | 0.000 | 0.026 | |
| getSizeFactors | 0.026 | 0.000 | 0.019 | |
| getViterbi | 0.035 | 0.000 | 0.027 | |
| initBdHMM | 0.011 | 0.000 | 0.010 | |
| initHMM | 0.007 | 0.000 | 0.007 | |
| runningMean | 1.020 | 0.020 | 1.039 | |
| viterbi2GRanges | 1.304 | 0.004 | 0.843 | |