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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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Package 1261/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miloR 2.2.0  (landing page)
Mike Morgan
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/miloR
git_branch: RELEASE_3_20
git_last_commit: 5e1d958
git_last_commit_date: 2024-10-29 10:59:29 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

BUILD BIN results for miloR on kjohnson3

To the developers/maintainers of the miloR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miloR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: miloR
Version: 2.2.0
Command: rm -rf miloR.buildbin-libdir && mkdir miloR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh miloR_2.2.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R miloR.buildbin-libdir
StartedAt: 2024-11-09 16:58:48 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 16:59:27 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 38.6 seconds
RetCode: 0
Status:   OK  
PackageFile: miloR_2.2.0.tgz
PackageFileSize: 7.205 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf miloR.buildbin-libdir && mkdir miloR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh miloR_2.2.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R miloR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=miloR.buildbin-libdir miloR_2.2.0.tar.gz'
>>>>>>> 

* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp:246:9: warning: variable 'stot' set but not used [-Wunused-but-set-variable]
    int stot = 0;
        ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
fitGeneticPLGlmm.cpp:113:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
    double _intercept = constval; // intercept for HE regression
           ^
fitGeneticPLGlmm.cpp:200:10: warning: unused variable '_phi_est' [-Wunused-variable]
    bool _phi_est = true; // control if we re-estimate phi or not
         ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c fitPLGlmm.cpp -o fitPLGlmm.o
fitPLGlmm.cpp:106:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
    double _intercept = constval; // intercept for HE regression?? need a better estimate.
           ^
fitPLGlmm.cpp:172:10: warning: unused variable '_phi_est' [-Wunused-variable]
    bool _phi_est = true; // control if we re-estimate phi or not
         ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c inference.cpp -o inference.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c invertPseudoVar.cpp -o invertPseudoVar.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c multiP.cpp -o multiP.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c paramEst.cpp -o paramEst.o
paramEst.cpp:36:33: warning: left operand of comma operator has no effect [-Wunused-value]
        double rhs = 0.5 * mid1[0, 0];
                                ^
paramEst.cpp:172:12: warning: unused variable 'lambda' [-Wunused-variable]
    double lambda = 1e-1;
           ^
paramEst.cpp:173:12: warning: unused variable 'lambda_step' [-Wunused-variable]
    double lambda_step = 10;
           ^
paramEst.cpp:174:12: warning: unused variable '_illcond_eps' [-Wunused-variable]
    double _illcond_eps = 1e-6;
           ^
paramEst.cpp:175:12: warning: unused variable '_lcond_target' [-Wunused-variable]
    double _lcond_target = 1e-5;
           ^
paramEst.cpp:241:19: warning: unused variable 'nsq' [-Wunused-variable]
    unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix, no diag
                  ^
paramEst.cpp:242:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:242:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:243:12: warning: unused variable '_ycovij' [-Wunused-variable]
    double _ycovij; // Declare temp_value
           ^
paramEst.cpp:276:19: warning: unused variable 'nsq' [-Wunused-variable]
    unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
                  ^
paramEst.cpp:277:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:277:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:278:12: warning: unused variable '_ycovij' [-Wunused-variable]
    double _ycovij; // Declare temp_value
           ^
paramEst.cpp:342:19: warning: unused variable 'nsq' [-Wunused-variable]
    unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
                  ^
paramEst.cpp:409:19: warning: unused variable 'nsq' [-Wunused-variable]
    unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
                  ^
paramEst.cpp:410:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:410:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:442:19: warning: unused variable 'nsq' [-Wunused-variable]
    unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
                  ^
paramEst.cpp:443:18: warning: unused variable 'i' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                 ^
paramEst.cpp:443:21: warning: unused variable 'j' [-Wunused-variable]
    unsigned int i, j;      // Declare loop variables i and j for OpenMP
                    ^
paramEst.cpp:774:12: warning: unused variable 'half_logli' [-Wunused-variable]
    double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
           ^
paramEst.cpp:779:10: warning: unused variable 'comp_vals' [-Wunused-variable]
    bool comp_vals = false;
         ^
22 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c pseudovarPartial.cpp -o pseudovarPartial.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c solveQP.cpp -o solveQP.o
In file included from solveQP.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include/RcppMLCommon.hpp:36:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from solveQP.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include/RcppMLCommon.hpp:36:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from solveQP.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include/RcppMLCommon.hpp:36:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from solveQP.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include/RcppMLCommon.hpp:36:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppML/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -std=gnu++11  -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o miloR.so RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o solveQP.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/miloR.buildbin-libdir/00LOCK-miloR/00new/miloR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘graph’ in package ‘miloR’
** 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 (miloR)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR miloR.buildbin-libdir/miloR/libs/miloR.so
>>>>>>> 

>>>>>>> Paths before fix:
miloR.buildbin-libdir/miloR/libs/miloR.so:
	miloR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"

>>>>>>> Paths after fix:
miloR.buildbin-libdir/miloR/libs/miloR.so:
	miloR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)