Mac R package install error

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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’

trying URL ‘http://cloud.r-project.org/src/contrib/RcppEigen_0.3.3.9.2.tar.gz’
Content type ‘application/x-gzip’ length 1476004 bytes (1.4 MB)

downloaded 1.4 MB

trying URL ‘http://cloud.r-project.org/src/contrib/quantreg_5.93.tar.gz’
Content type ‘application/x-gzip’ length 1025022 bytes (1000 KB)

downloaded 1000 KB

trying URL ‘http://cloud.r-project.org/src/contrib/TMB_1.9.0.tar.gz’
Content type ‘application/x-gzip’ length 742353 bytes (724 KB)

downloaded 724 KB

trying URL ‘http://cloud.r-project.org/src/contrib/RcppArmadillo_0.11.1.1.0.tar.gz’
Content type ‘application/x-gzip’ length 1371134 bytes (1.3 MB)

downloaded 1.3 MB

trying URL ‘http://cloud.r-project.org/src/contrib/sf_1.0-7.tar.gz’
Content type ‘application/x-gzip’ length 3529597 bytes (3.4 MB)

downloaded 3.4 MB

trying URL ‘http://cloud.r-project.org/src/contrib/units_0.8-0.tar.gz’
Content type ‘application/x-gzip’ length 866695 bytes (846 KB)

downloaded 846 KB

trying URL ‘http://cloud.r-project.org/src/contrib/lme4_1.1-29.tar.gz’
Content type ‘application/x-gzip’ length 3306026 bytes (3.2 MB)

downloaded 3.2 MB

trying URL ‘http://cloud.r-project.org/src/contrib/car_3.0-13.tar.gz’
Content type ‘application/x-gzip’ length 494341 bytes (482 KB)

downloaded 482 KB

trying URL ‘http://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz’
Content type ‘application/x-gzip’ length 2219877 bytes (2.1 MB)

downloaded 2.1 MB

trying URL ‘http://cloud.r-project.org/src/contrib/glmmTMB_1.1.3.tar.gz’
Content type ‘application/x-gzip’ length 3959196 bytes (3.8 MB)

downloaded 3.8 MB

trying URL ‘http://cloud.r-project.org/src/contrib/rstanarm_2.21.3.tar.gz’
Content type ‘application/x-gzip’ length 3767563 bytes (3.6 MB)

downloaded 3.6 MB

trying URL ‘http://cloud.r-project.org/src/contrib/rstan_2.21.5.tar.gz’
Content type ‘application/x-gzip’ length 1189130 bytes (1.1 MB)

downloaded 1.1 MB

trying URL ‘http://cloud.r-project.org/src/contrib/shinystan_2.6.0.tar.gz’
Content type ‘application/x-gzip’ length 2399890 bytes (2.3 MB)

downloaded 2.3 MB

trying URL ‘http://cloud.r-project.org/src/contrib/projpred_2.1.2.tar.gz’
Content type ‘application/x-gzip’ length 472165 bytes (461 KB)

downloaded 461 KB

trying URL ‘http://cloud.r-project.org/src/contrib/spdep_1.2-4.tar.gz’
Content type ‘application/x-gzip’ length 4046582 bytes (3.9 MB)

downloaded 3.9 MB

trying URL ‘http://cloud.r-project.org/src/contrib/ape_5.6-2.tar.gz’
Content type ‘application/x-gzip’ length 1754486 bytes (1.7 MB)

downloaded 1.7 MB

trying URL ‘http://cloud.r-project.org/src/contrib/afex_1.1-1.tar.gz’
Content type ‘application/x-gzip’ length 2929555 bytes (2.8 MB)

downloaded 2.8 MB

trying URL ‘http://cloud.r-project.org/src/contrib/brms_2.17.0.tar.gz’
Content type ‘application/x-gzip’ length 5679524 bytes (5.4 MB)

downloaded 5.4 MB

  • 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: https://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

2

Hi JW,

Try installing gfortran (brew install gfortran).

There might be other packages needed, too, though…

  • rick
3

Thank you Rick! Even after installing gfortran, it shows the below message.

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!

I didn’t see a list of packages that need to be installed in the install instruction. Is the issue related to the R package?

Best,
JW

4

JW,

Those three R packages are only needed for the following AFNI programs

‘afex’ for 3dMVM
‘brms’ for RBA, TRR, MBA
‘metafor’ for 3dICC

So, if you’re not going to run any of those programs above, you can ignore the warnings. In case you want to use 3dMVM, try installing ‘afex’ inside R:

install.packages(‘afex’, dependencies = NA)

5

Hi Gang,

Thank you for the suggestion. Right, I need to use 3dMVM. I installed afex in R as you suggested and ran 3dMVM, but showed the below error message.

Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
Error in library(“afex”) : there is no package called ‘afex’

I am not sure why it can’t detect afex even after I installed it. Any suggestions will be appreciated.

Best,
Jun

6

Hi Jun,

If you would like to, please run:

rPkgsInstall -pkgs afex

and send me email with the complete text output.

  • rick
7

Hi Jun,

Thanks for the output.
Unfortunately, my own testing is showing the same problem, which we will need to track down a bit.

It looks like perhaps homebrew has moved the location of the gfortran directory, and now the R package building code is looking in the wrong direction. Maybe the R or homebrew folks will need to resolve this.

We will look into it more…

  • rick
8

Hi Rick,

Thank you for the update. Please keep me posted.

Best,
JW

9

Hi,

Here are a few things you can try:

For gfortran you can install a version that R 3.6 uses.
Run this at the terminal:


curl -s -L -o gfortran-6.1.pkg "[https://cloud.r-project.org/bin/macosx/tools/gfortran-6.1.pkg](https://cloud.r-project.org/bin/macosx/tools/gfortran-6.1.pkg)"
sudo installer -pkg gfortran-6.1.pkg -target /
rm gfortran-6.1.pkg

You need this to your path before you try to use it


/usr/local/gfortran/bin

For 3dMVM, you need afex. Try to install it directly using this at the terminal:


Rscript -e "install.packages(c('afex'),repos='[https://cloud.r-project.org](https://cloud.r-project.org)')"

You also may need cmake, but I am not certrain for afex.
If you do need it, you can install it with homebrew:


brew install cmake

Let me know how it goes!

Thanks, Justin

10

Hi Justin,

Thank you so much!

I tried Rscript -e “install.packages(c(‘afex’),repos=‘https://cloud.r-project.org’)” first prior to installing cmake, which failed. But, after installing cmake and running the Rscript, 3dMVM works. It still shows in afni_system_check that missing R packages though. I really appreciate your help!

Best,
JW

11

Hi,
Glad it works.
There will be some packages missing from afni_system_check.
This should get most of them, but not all:


Rscript -e "install.packages(c('phia','snow','nlme','lmerTest'),repos='[https://cloud.r-project.org](https://cloud.r-project.org)')"

Some of the packages are not available on mac with R 3.6.3.
We are working on compiling for R 4.

Thanks, Justin

12

Thank you Justin. I really appreciate your help!

JW

13

No problem.
This is what we are here for.
Let me know if you have any more questions.
thanks, Justin

14

Hello! I am having a similar issue to JW on my Mac M2 (OS 13.6). I need to run 3dLME but cannot get the necessary R packages to load with the latest version of R (4.3.2). I also tried using R version 3.6.3 but had some trouble with downloading outdated versions of the packages. I will paste the output of afni_system_check.py -check_all. Can you please let me know if you have any solutions for this?

Thanks,
kelly

COSGRKEL% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 22.6.0
version: Darwin Kernel Version 22.6.0: Fri Sep 15 13:41:28 PDT 2023; root:xnu-8796.141.3.700.8~1/RELEASE_ARM64_T6020
distribution: 13.6
number of CPUs: 10
apparent login shell: zsh (current shell is csh)
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/COSGRKEL/abin/afni
afni version : Precompiled binary macos_10.12_local: Jan 22 2024
: AFNI_24.0.02 'Caracalla'
AFNI_version.txt : AFNI_24.0.02, macos_10.12_local, Jan 22 2024, official
which python : /Users/COSGRKEL/anaconda3/bin/python
python version : 3.11.4
which R : /usr/local/bin/R
R version : R version 4.3.2 (aarch64-apple-darwin20)

instances of various programs found in PATH:
afni : 1 (/Users/COSGRKEL/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R)
python : 2
/Users/COSGRKEL/anaconda3/bin/python3.11
/opt/homebrew/Cellar/python@3.11/3.11.7_1/Frameworks/Python.framework/Versions/3.11/bin/python3.11
python2 : 0
python3 : 3
/Users/COSGRKEL/anaconda3/bin/python3.11
/opt/homebrew/Cellar/python@3.11/3.11.7_1/Frameworks/Python.framework/Versions/3.11/bin/python3.11
/usr/bin/python3

** have python3 but not python2

testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/COSGRKEL/abin/R_io.so':
dlopen(/Users/COSGRKEL/abin/R_io.so, 0x0006): tried: '/Users/COSGRKEL/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/COSGRKEL/abin/R_io.so' (no such file), '/Users/COSGRKEL/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

------------------------ dependent program tests -------------------------
checking for dependent programs...

which tcsh : /bin/tcsh
which Xvfb : /opt/X11/bin/Xvfb

checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/COSGRKEL/abin/R_io.so':
dlopen(/Users/COSGRKEL/abin/R_io.so, 0x0006): tried: '/Users/COSGRKEL/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/COSGRKEL/abin/R_io.so' (no such file), '/Users/COSGRKEL/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

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

------------------------------ python libs -------------------------------

++ module loaded: matplotlib.pyplot
module file : /Users/COSGRKEL/anaconda3/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.7.1

++ module loaded: flask
module file : /Users/COSGRKEL/anaconda3/lib/python3.11/site-packages/flask/init.py
flask version : 2.2.2

** failed to load module flask_cors
-- flask_cors is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH = /Users/COSGRKEL/anaconda3/bin:/Users/COSGRKEL/anaconda3/condabin:/Users/COSGRKEL/fsl/share/fsl/bin:/Users/COSGRKEL/fsl/share/fsl/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/homebrew/opt/python/libexec/bin:/Library/Frameworks/R.framework/Resources:/usr/local/gfortran/bin:/Users/COSGRKEL/abin:/Users/COSGRKEL/abin:/Users/COSGRKEL/abin

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

----------------------------- eval dot files -----------------------------

----------- AFNI $HOME files -----------

.afnirc                   : found
.sumarc                   : found
.afni/help/all_progs.COMP : found

--------- shell startup files ----------

-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, flatdir, apsearch

-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)

dot file test : want 1 modifications across 3 files:

  file             path  flatdir  apsearch        follower
  ---------------  ----  -------  --------        --------
  .cshrc           0     0        1               0     
  .tcshrc          0     0        0               1     
  .zshrc           0     0        0               0

------------------------------ 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 .

------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5

which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.2.5

++ 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:/opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

  • just be aware: login shell 'zsh', but our code examples use 'tcsh'
  • AFNI programs show FAILURE
  • missing R packages (see rPkgsInstall)
  • dot file test : want 1 modifications across 3 files:
  • insufficient data for AFNI bootcamp
    (see "Prepare for Bootcamp" on install pages)
  • consider installing gcc under homebrew
  • consider installing glib under homebrew

Also this is the output of file afni R_io.so:

afni: Mach-O 64-bit executable x86_64
R_io.so: Mach-O 64-bit dynamically linked shared library x86_64

15

Hi Kelly,

Since you have an ARM mac with R 4.3 and homebrew, it seems like you have gone through some of the current installation steps. If so, it would be better to go down the route of building your own AFNI binaries (which is included in those instructions).

Have you gone through some of that? If so, do you know exactly how much? For example, is the homebrew installation complete, by running that first script?

zsh OS_notes.macos_12_ARM_a_admin_pt1.zsh
  • rick
16

Hi Rick,

I just redid all of those installation steps. After that, I tried running 'rPkgsInstall -pkgs ALL' and got the same error message about being unable to load the R_io.so file.

Thanks,
K

17

I just did a total redownload of afni and everything seems to be working now :) Thanks for your help!

18

Oh, that is great news, Kelly! Thanks for the update!

  • rick