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This page was generated on 2023-04-12 11:06:28 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

BUILD BIN results for STAN on lconway


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 1970/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STAN 2.26.2  (landing page)
Rafael Campos-Martin
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/STAN
git_branch: RELEASE_3_16
git_last_commit: a982cef
git_last_commit_date: 2023-01-19 11:18:47 -0400 (Thu, 19 Jan 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: STAN
Version: 2.26.2
Command: rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh STAN_2.26.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R STAN.buildbin-libdir
StartedAt: 2023-04-11 00:07:27 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 00:08:48 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 80.6 seconds
RetCode: 0
Status:   OK  
PackageFile: STAN_2.26.2.tgz
PackageFileSize: 1.442 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf STAN.buildbin-libdir && mkdir STAN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh STAN_2.26.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R STAN.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=STAN.buildbin-libdir STAN_2.26.2.tar.gz'
>>>>>>> 

* installing *source* package ‘STAN’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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++14 -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++14 -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++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D_RDLL_   -fPIC  -Wall -g -O2  -c HMM.cpp -o HMM.o
HMM.cpp:967:12: warning: variable 'allT' set but not used [-Wunused-but-set-variable]
    double allT = 0;
           ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13)
installing to /Users/biocbuild/bbs-3.16-bioc/meat/STAN.buildbin-libdir/00LOCK-STAN/00new/STAN/libs
** R
** data
** inst
** 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)


>>>>>>> 
>>>>>>> FIXING LINKS FOR STAN.buildbin-libdir/STAN/libs/STAN.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "STAN.buildbin-libdir/STAN/libs/STAN.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "STAN.buildbin-libdir/STAN/libs/STAN.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "STAN.buildbin-libdir/STAN/libs/STAN.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "STAN.buildbin-libdir/STAN/libs/STAN.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "STAN.buildbin-libdir/STAN/libs/STAN.so"