Rafael Campos-Martin
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/STAN |
| Branch: RELEASE_3_12 |
| Last Commit: efe18e3 |
| Last Changed Date: 2020-10-27 10:57:53 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:36:58 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the STAN package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1796/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| STAN 2.18.0 (landing page) Rafael Campos-Martin
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: STAN |
| Version: 2.18.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:STAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings STAN_2.18.0.tar.gz |
| StartedAt: 2021-05-06 06:37:59 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:44:43 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 404.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: STAN.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:STAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings STAN_2.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/STAN.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STAN/DESCRIPTION’ ... OK
* this is package ‘STAN’ version ‘2.18.0’
* 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 ... WARNING
Found the following significant warnings:
matUtils.cpp:114:10: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
matUtils.cpp:115:14: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
matUtils.cpp:125:10: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/STAN.Rcheck/00install.out’ for details.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/STAN.Rcheck/00check.log’
for details.
STAN.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL STAN
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘STAN’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c Bernoulli.cpp -o Bernoulli.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c EmissionFactory.cpp -o EmissionFactory.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c EmissionFunction.cpp -o EmissionFunction.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c HMM.cpp -o HMM.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c InitialProbability.cpp -o InitialProbability.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c JointlyIndependent.cpp -o JointlyIndependent.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c MemoryAllocation.cpp -o MemoryAllocation.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c Multinomial.cpp -o Multinomial.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c MultivariateGaussian.cpp -o MultivariateGaussian.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c NegativeBinomial.cpp -o NegativeBinomial.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c ParamContainerEmissions.cpp -o ParamContainerEmissions.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c Poisson.cpp -o Poisson.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c PoissonLogNormal.cpp -o PoissonLogNormal.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c RAccessUtils.cpp -o RAccessUtils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c RWrapper.cpp -o RWrapper.o
RWrapper.cpp:343:17: warning: variable 'HMMEmissionFunctions' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(strcmp(type,poissonlognormal) == 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RWrapper.cpp:350:16: note: uninitialized use occurs here
return HMMEmissionFunctions;
^~~~~~~~~~~~~~~~~~~~
RWrapper.cpp:343:14: note: remove the 'if' if its condition is always true
else if(strcmp(type,poissonlognormal) == 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RWrapper.cpp:311:48: note: initialize the variable 'HMMEmissionFunctions' to silence this warning
EmissionFunction **HMMEmissionFunctions;
^
= nullptr
RWrapper.cpp:1140:21: warning: variable 'sexpemissionParam' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(strcmp(type, multinomial) == 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RWrapper.cpp:1157:16: note: uninitialized use occurs here
return sexpemissionParam;
^~~~~~~~~~~~~~~~~
RWrapper.cpp:1140:18: note: remove the 'if' if its condition is always true
else if(strcmp(type, multinomial) == 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RWrapper.cpp:1123:31: note: initialize the variable 'sexpemissionParam' to silence this warning
SEXP sexpemissionParam;
^
= nullptr
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c TransitionMatrix.cpp -o TransitionMatrix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -D_RDLL_ -fPIC -Wall -g -O2 -c matUtils.cpp -o matUtils.o
matUtils.cpp:114:10: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
for (register int i = 0 ; i < myN ; i++)
^~~~~~~~~
matUtils.cpp:115:14: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
for (register int j = i ; j < myldz ; j++)
^~~~~~~~~
matUtils.cpp:125:10: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
for (register int i = 0 ; i < myNCol ; i++)
^~~~~~~~~
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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 | 0.210 | 0.014 | 0.228 | |
| Emission | 0.002 | 0.001 | 0.003 | |
| EmissionParams | 0.003 | 0.000 | 0.004 | |
| HMM-class | 0.005 | 0.001 | 0.006 | |
| HMM | 0.004 | 0.001 | 0.006 | |
| HMMEmission-class | 0.003 | 0.001 | 0.003 | |
| HMMEmission | 0.003 | 0.000 | 0.003 | |
| InitProb | 0.002 | 0.000 | 0.003 | |
| LogLik | 0.033 | 0.007 | 0.040 | |
| StateNames | 0.003 | 0.000 | 0.003 | |
| Transitions | 0.001 | 0.000 | 0.002 | |
| bdHMM-class | 0.014 | 0.000 | 0.015 | |
| bdHMM | 0.009 | 0.000 | 0.009 | |
| binarizeData | 0.028 | 0.005 | 0.033 | |
| call_dpoilog | 0.000 | 0.000 | 0.001 | |
| fitBdClust | 0.093 | 0.006 | 0.101 | |
| fitHMM | 0.030 | 0.007 | 0.037 | |
| getAvgSignal | 0.804 | 0.019 | 0.825 | |
| getLogLik | 0.035 | 0.005 | 0.041 | |
| getPosterior | 0.034 | 0.005 | 0.040 | |
| getSizeFactors | 0.034 | 0.007 | 0.041 | |
| getViterbi | 0.042 | 0.007 | 0.048 | |
| initBdHMM | 0.016 | 0.002 | 0.017 | |
| initHMM | 0.009 | 0.001 | 0.011 | |
| runningMean | 0.027 | 0.005 | 0.032 | |
| viterbi2GRanges | 0.910 | 0.021 | 0.931 | |