Dear AFNI experts,

I am having an issue installing R packages and below is the output of sudo rPkgsInstall -pkgs ALL.

updating R_LD_LIBRARY_PATH ...
Warning: dependencies ‘jtools’, ‘cmdstanr’ are not available
also installing the dependencies ‘RcppEigen’, ‘quantreg’, ‘TMB’, ‘RcppArmadillo’, ‘sf’, ‘units’, ‘lme4’, ‘car’, ‘nloptr’, ‘glmmTMB’, ‘rstanarm’, ‘rstan’, ‘shinystan’, ‘projpred’, ‘spdep’, ‘ape’


There are binary versions available but the source versions are later:
binary source needs_compilation
RcppEigen 0.3.3.9.1 0.3.3.9.2 TRUE
quantreg 5.85 5.93 TRUE
TMB 1.7.22 1.9.0 TRUE
RcppArmadillo 0.10.7.3.0 0.11.1.1.0 TRUE
sf 1.0-5 1.0-7 TRUE
units 0.7-2 0.8-0 TRUE
lme4 1.1-28 1.1-29 TRUE
car 3.0-10 3.0-13 FALSE
nloptr 1.2.2.3 2.0.3 TRUE
rstanarm 2.19.2 2.21.3 TRUE
rstan 2.21.3 2.21.5 TRUE
shinystan 2.5.0 2.6.0 FALSE
projpred 2.0.2 2.1.2 TRUE
spdep 1.1-12 1.2-4 TRUE
ape 5.6-1 5.6-2 TRUE
afex 0.28-1 1.1-1 FALSE
brms 2.15.0 2.17.0 FALSE

Package which is only available in source form, and may need
compilation of C/C++/Fortran: ‘glmmTMB’
installing the source packages ‘RcppEigen’, ‘quantreg’, ‘TMB’, ‘RcppArmadillo’, ‘sf’, ‘units’, ‘lme4’, ‘car’, ‘nloptr’, ‘glmmTMB’, ‘rstanarm’, ‘rstan’, ‘shinystan’, ‘projpred’, ‘spdep’, ‘ape’, ‘afex’, ‘brms’

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* installing *source* package ‘RcppEigen’ ...
** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c RcppEigen.cpp -o RcppEigen.o
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:1:
In file included from ../inst/include/Eigen/Core:540:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:2:
In file included from ../inst/include/Eigen/LU:47:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:3:
In file included from ../inst/include/Eigen/Cholesky:12:
In file included from ../inst/include/Eigen/Jacobi:29:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:3:
In file included from ../inst/include/Eigen/Cholesky:43:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:4:
In file included from ../inst/include/Eigen/QR:15:
In file included from ../inst/include/Eigen/Householder:27:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:4:
In file included from ../inst/include/Eigen/QR:48:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:5:
In file included from ../inst/include/Eigen/SVD:48:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:6:
In file included from ../inst/include/Eigen/Geometry:58:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:7:
In file included from ../inst/include/Eigen/Eigenvalues:58:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:26:
In file included from ../inst/include/Eigen/SparseCore:66:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:27:
In file included from ../inst/include/Eigen/OrderingMethods:71:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:29:
In file included from ../inst/include/Eigen/SparseCholesky:43:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:32:
In file included from ../inst/include/Eigen/SparseQR:34:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:33:
In file included from ../inst/include/Eigen/IterativeLinearSolvers:46:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:32:
In file included from ../inst/include/Eigen/CholmodSupport:45:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:35:
In file included from ../inst/include/unsupported/Eigen/KroneckerProduct:34:
../inst/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma
diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:39:
In file included from ../inst/include/unsupported/Eigen/Polynomials:135:
../inst/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma
diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppEigen.cpp:22:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:40:
In file included from ../inst/include/unsupported/Eigen/SparseExtra:51:
../inst/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma
diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
18 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:1:
In file included from ../inst/include/Eigen/Core:540:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:2:
In file included from ../inst/include/Eigen/LU:47:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:3:
In file included from ../inst/include/Eigen/Cholesky:12:
In file included from ../inst/include/Eigen/Jacobi:29:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:3:
In file included from ../inst/include/Eigen/Cholesky:43:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:4:
In file included from ../inst/include/Eigen/QR:15:
In file included from ../inst/include/Eigen/Householder:27:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:4:
In file included from ../inst/include/Eigen/QR:48:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:5:
In file included from ../inst/include/Eigen/SVD:48:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:6:
In file included from ../inst/include/Eigen/Geometry:58:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:7:
In file included from ../inst/include/Eigen/Eigenvalues:58:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:26:
In file included from ../inst/include/Eigen/SparseCore:66:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:27:
In file included from ../inst/include/Eigen/OrderingMethods:71:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:29:
In file included from ../inst/include/Eigen/SparseCholesky:43:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:32:
In file included from ../inst/include/Eigen/SparseQR:34:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:33:
In file included from ../inst/include/Eigen/IterativeLinearSolvers:46:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:32:
In file included from ../inst/include/Eigen/CholmodSupport:45:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:35:
In file included from ../inst/include/unsupported/Eigen/KroneckerProduct:34:
../inst/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma
diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:39:
In file included from ../inst/include/unsupported/Eigen/Polynomials:135:
../inst/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma
diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:40:
In file included from ../inst/include/unsupported/Eigen/SparseExtra:51:
../inst/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma
diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
18 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c fastLm.cpp -o fastLm.o
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:1:
In file included from ../inst/include/Eigen/Core:540:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:2:
In file included from ../inst/include/Eigen/LU:47:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:3:
In file included from ../inst/include/Eigen/Cholesky:12:
In file included from ../inst/include/Eigen/Jacobi:29:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:3:
In file included from ../inst/include/Eigen/Cholesky:43:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:4:
In file included from ../inst/include/Eigen/QR:15:
In file included from ../inst/include/Eigen/Householder:27:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:4:
In file included from ../inst/include/Eigen/QR:48:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:5:
In file included from ../inst/include/Eigen/SVD:48:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:6:
In file included from ../inst/include/Eigen/Geometry:58:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:30:
In file included from ../inst/include/Eigen/Dense:7:
In file included from ../inst/include/Eigen/Eigenvalues:58:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:26:
In file included from ../inst/include/Eigen/SparseCore:66:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:27:
In file included from ../inst/include/Eigen/OrderingMethods:71:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:29:
In file included from ../inst/include/Eigen/SparseCholesky:43:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:32:
In file included from ../inst/include/Eigen/SparseQR:34:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:31:
In file included from ../inst/include/Eigen/Sparse:33:
In file included from ../inst/include/Eigen/IterativeLinearSolvers:46:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:32:
In file included from ../inst/include/Eigen/CholmodSupport:45:
../inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not
pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:35:
In file included from ../inst/include/unsupported/Eigen/KroneckerProduct:34:
../inst/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma
diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:39:
In file included from ../inst/include/unsupported/Eigen/Polynomials:135:
../inst/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma
diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from fastLm.cpp:23:
In file included from ./fastLm.h:25:
In file included from ../inst/include/RcppEigen.h:25:
In file included from ../inst/include/RcppEigenForward.h:40:
In file included from ../inst/include/unsupported/Eigen/SparseExtra:51:
../inst/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma
diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
18 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang++ -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 RcppEigen.so RcppEigen.o RcppExports.o fastLm.o init.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-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppEigen.so] Error 1
ERROR: compilation failed for package ‘RcppEigen’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen’
* installing *source* package ‘quantreg’ ...
** package ‘quantreg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fPIC -Wall -g -O2 -c akj.f -o akj.o
make: gfortran: No such file or directory
make: *** [akj.o] Error 1
ERROR: compilation failed for package ‘quantreg’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/quantreg’
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ -std=gnu++11 accepts -g... (cached) yes
checking whether we have a suitable tempdir... /tmp
checking whether R CMD SHLIB can already compile programs using OpenMP... no
checking whether g++ version is sufficient... almost
configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++.
checking for macOS... found
checking for macOS Apple compiler... not found
checking for clang compiler... found
checking for OpenMP compatible version of clang... not found
configure: WARNING: OpenMP unavailable and turned off.
checking LAPACK_LIBS... R-supplied partial LAPACK found
configure: WARNING: Some complex-valued LAPACK functions may not be available
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c fastLm.cpp -o fastLm.o
clang++ -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 RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.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-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo’
* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
** using staged installation
configure: units: 0.8-0
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -std=gnu++11 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for error_at_line... no
checking for gcc... clang
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for XML_ParserCreate in -lexpat... yes
checking udunits2.h usability... no
checking udunits2.h presence... no
checking for udunits2.h... no
checking udunits2/udunits2.h usability... no
checking udunits2/udunits2.h presence... no
checking for udunits2/udunits2.h... no
checking for ut_read_xml in -ludunits2... no
configure: error: in `/private/tmp/RtmpZErXaI/R.INSTALLe70417f70c25/units':
configure: error:
--------------------------------------------------------------------------------
Configuration failed because libudunits2.so was not found. Try installing:
* deb: libudunits2-dev (Debian, Ubuntu, ...)
* rpm: udunits2-devel (Fedora, EPEL, ...)
* brew: udunits (OSX)
If udunits2 is already installed in a non-standard location, use:
--configure-args='--with-udunits2-lib=/usr/local/lib'
if the library was not found, and/or:
--configure-args='--with-udunits2-include=/usr/include/udunits2'
if the header was not found, replacing paths with appropriate values.
You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually.
--------------------------------------------------------------------------------

See `config.log' for more details
ERROR: configuration failed for package ‘units’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/units’
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
checking for clang++ -std=gnu++11 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... clang++ -std=gnu++11 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether clang++ -std=gnu++11 accepts -g... (cached) yes
checking for clang++ -std=gnu++11 option to enable C++11 features... (cached) none needed
checking for pkg-config... no
checking for cmake... no

------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

- sudo yum install cmake (Fedora/CentOS; inside a terminal)
- sudo apt install cmake (Debian/Ubuntu; inside a terminal).
- sudo pacman -S cmake (Arch Linux; inside a terminal).
- sudo brew install cmake (MacOS; inside a terminal with Homebrew)
- sudo port install cmake (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: [cmake.org]

-------------------------------------------------------

ERROR: configuration failed for package ‘nloptr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nloptr’
* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BIONJ.c -o BIONJ.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c NNI.c -o NNI.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c SPR.c -o SPR.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c additive.c -o additive.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ape.c -o ape.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c bNNI.c -o bNNI.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c bionjs.c -o bionjs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c bipartition.c -o bipartition.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c bitsplits.c -o bitsplits.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c delta_plot.c -o delta_plot.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c dist_dna.c -o dist_dna.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c dist_nodes.c -o dist_nodes.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ewLasso.c -o ewLasso.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c heap.c -o heap.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mat_expo.c -o mat_expo.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c me.c -o me.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c me_balanced.c -o me_balanced.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c me_ols.c -o me_ols.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mvr.c -o mvr.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mvrs.c -o mvrs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nj.c -o nj.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c njs.c -o njs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pic.c -o pic.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c plot_phylo.c -o plot_phylo.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c prop_part.cpp -o prop_part.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c rTrait.c -o rTrait.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c read_dna.c -o read_dna.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c reorder_Rcpp.cpp -o reorder_Rcpp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c reorder_phylo.c -o reorder_phylo.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c treePop.c -o treePop.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c tree_build.c -o tree_build.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c tree_phylo.c -o tree_phylo.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c triangMtd.c -o triangMtd.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c triangMtds.c -o triangMtds.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ultrametric.c -o ultrametric.o
clang++ -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 ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.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-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [ape.so] Error 1
ERROR: compilation failed for package ‘ape’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ape’
ERROR: dependency ‘RcppEigen’ is not available for package ‘TMB’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/TMB’
ERROR: dependency ‘units’ is not available for package ‘sf’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sf’
ERROR: dependencies ‘nloptr’, ‘RcppEigen’ are not available for package ‘lme4’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/lme4’
ERROR: dependency ‘RcppEigen’ is not available for package ‘rstan’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan’
ERROR: dependencies ‘quantreg’, ‘lme4’ are not available for package ‘car’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/car’
ERROR: dependencies ‘TMB’, ‘lme4’, ‘RcppEigen’ are not available for package ‘glmmTMB’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/glmmTMB’
ERROR: dependency ‘rstan’ is not available for package ‘shinystan’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/shinystan’
ERROR: dependencies ‘lme4’, ‘RcppArmadillo’ are not available for package ‘projpred’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/projpred’
ERROR: dependencies ‘sf’, ‘units’ are not available for package ‘spdep’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/spdep’
ERROR: dependencies ‘lme4’, ‘rstan’, ‘shinystan’, ‘RcppEigen’ are not available for package ‘rstanarm’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstanarm’
ERROR: dependencies ‘lme4’, ‘car’ are not available for package ‘afex’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/afex’
ERROR: dependencies ‘rstan’, ‘shinystan’ are not available for package ‘brms’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/brms’

The downloaded source packages are in
‘/private/tmp/RtmpYdczUK/downloaded_packages’

++ Note: @ 10:27:40
This package has been installed on the computer: afex
This package has been installed on the computer: brms
This package has been installed on the computer: metafor























Output of afni_system_check.py -check_all is below.

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Mon Apr 18 21:50:40 PDT 2022; root:xnu-6153.141.62~1/RELEASE_X86_64
distribution: 10.15.7
number of CPUs: 24
apparent login shell: tcsh (current shell is csh)
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/cvas/abin/afni
afni version : Precompiled binary macos_10.12_local: May 20 2022
: AFNI_22.1.10 'Antoninus Pius'
AFNI_version.txt : AFNI_22.1.10, macos_10.12_local, May 20 2022
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/cvas/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 2
/usr/local/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/bin/python3.9
/usr/bin/python3


testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : success

checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE

oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: metafor!


R RHOME : /Library/Frameworks/R.framework/Resources

checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc
matplotlib version : 1.3.1
** need maptplotlib version 2.2+ for APQC


-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/bin/python3.9)
/usr/local/bin/python3.9 (sym link to /usr/local/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/bin/python3.9)

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/cvas/abin:/Users/cvas/abin:/Users/cvas/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/cvas/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.8.1

which brew : /usr/local/bin/brew
brew version : Homebrew 3.4.11

-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
-- consider installing gcc under homebrew
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.72.1/lib/libglib-2.0.dylib
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'csh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================
* missing R packages (see rPkgsInstall)
* check for partial install of PyQt4
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)





Could you please let me know what is an issue here?

Best,
JW