Can't Use ggpubr

General
, ,
1

I have the latest version of R, I have tried updating it but it says I have the latest version. Version 1.4.1106

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I downloaded ggpubr correctly and when I try to load ggpubr on my script, it tells me:

library(ggpubr)
Error: package or namespace load failed for ‘ggpubr’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘car’.

After I download and load "car" package, it tells me "Error in library(car) : there is no package called ‘car’"

This is part of the error is tells me when downloading car:
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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/vrest011/Library/R/4.0/library/Rcpp/include' -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/vrest011/Library/R/4.0/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o 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-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
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 ‘/Users/vrest011/Library/R/4.0/library/RcppEigen’
    Warning in install.packages :
    installation of package ‘RcppEigen’ had non-zero exit status
  • installing source package ‘quantreg’ ...
    ** package ‘quantreg’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -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 ‘/Users/vrest011/Library/R/4.0/library/quantreg’
    Warning in install.packages :
    installation of package ‘quantreg’ had non-zero exit status
    ERROR: dependencies ‘nloptr’, ‘RcppEigen’ are not available for package ‘lme4’
  • removing ‘/Users/vrest011/Library/R/4.0/library/lme4’
    Warning in install.packages :
    installation of package ‘lme4’ had non-zero exit status
    ERROR: dependencies ‘quantreg’, ‘lme4’ are not available for package ‘car’
  • removing ‘/Users/vrest011/Library/R/4.0/library/car’
    Warning in install.packages :
    installation of package ‘car’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/f0/dpk2b5sx3r1g09mfncfw_qtjr1pt89/T/RtmpWlFrBW/downloaded_packages’

library(car)
Error in library(car) : there is no package called ‘car’

2

Hi @Vrest

You need install library(car)

install.packages("car")
#next
library(car)
3

Thank you, I have been trying to download it and load it but after I download it I get this message:

18 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/vrest011/Library/R/4.0/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o 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-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
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 ‘/Users/vrest011/Library/R/4.0/library/RcppEigen’
    Warning in install.packages :
    installation of package ‘RcppEigen’ had non-zero exit status
  • installing source package ‘quantreg’ ...
    ** package ‘quantreg’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -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 ‘/Users/vrest011/Library/R/4.0/library/quantreg’
    Warning in install.packages :
    installation of package ‘quantreg’ had non-zero exit status
    ERROR: dependencies ‘nloptr’, ‘RcppEigen’ are not available for package ‘lme4’
  • removing ‘/Users/vrest011/Library/R/4.0/library/lme4’
    Warning in install.packages :
    installation of package ‘lme4’ had non-zero exit status
    ERROR: dependencies ‘quantreg’, ‘lme4’ are not available for package ‘car’
  • removing ‘/Users/vrest011/Library/R/4.0/library/car’
    Warning in install.packages :
    installation of package ‘car’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/f0/dpk2b5sx3r1g09mfncfw_qtjr1pt89/T/RtmpWlFrBW/downloaded_packages’

When I load the package it gives me this message:
library(car)
Error in library(car) : there is no package called ‘car’
>

4

First, I want to clarify this, you have old versions of both RStudio (1.4.1106) and R (4.0.0). RStudio is an IDE (Integrated Development Environment) for the R programming language but it doesn't come with R bundled.
To update R you can download the latest version from here
https://cran.r-project.org/bin/macosx/
And to update RStudio you can download it from here

Now about your specific issue, since you are using an old R version, there are no precompiled binaries available for it and you need to compile packages from source but you are missing the required compilers in your system (not in R). If you do not want or can't update R, the only solution to this is installing the recommended development tools for macOS systems as described here:

https://cran.r-project.org/bin/macosx/tools

5

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