Hello,I'm on ubuntu 20.04 and I try to install a package in Rstudio after installing Rstudio, but I always get this error :
R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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> install.packages("FactoMineR")
Installing package into ‘/home/lilia/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
also installing the dependencies ‘nloptr’, ‘pbkrtest’, ‘lme4’, ‘car’
trying URL 'https://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 'https://cloud.r-project.org/src/contrib/pbkrtest_0.5.2.tar.gz'
Content type 'application/x-gzip' length 75295 bytes (73 KB)
==================================================
downloaded 73 KB
trying URL 'https://cloud.r-project.org/src/contrib/lme4_1.1-31.tar.gz'
Content type 'application/x-gzip' length 2947739 bytes (2.8 MB)
==================================================
downloaded 2.8 MB
trying URL 'https://cloud.r-project.org/src/contrib/car_3.1-1.tar.gz'
Content type 'application/x-gzip' length 578902 bytes (565 KB)
==================================================
downloaded 565 KB
trying URL 'https://cloud.r-project.org/src/contrib/FactoMineR_2.7.tar.gz'
Content type 'application/x-gzip' length 2831910 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
* 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 g++ -std=gnu++14 accepts -g... yes
checking for g++ -std=gnu++14 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++14 accepts -g... (cached) yes
checking for g++ -std=gnu++14 option to enable C++11 features... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... yes
checking for pkg-config checking NLopt version... insufficient: NLopt 2.7.0 or later is preferred.
checking for cmake... /usr/bin/cmake
using NLopt via local cmake build on x86_64
set CMAKE_BIN=/usr/bin/cmake
set CC=gcc
set CFLAGS= -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
set CXX=g++
set CXXFLAGS=-std=gnu++11 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
set LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro
-- The C compiler identification is GNU 9.4.0
-- The CXX compiler identification is GNU 9.4.0
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- NLopt version 2.7.1
-- Looking for getopt.h
-- Looking for getopt.h - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for getpid
-- Looking for getpid - found
-- Looking for syscall
-- Looking for syscall - found
-- Looking for isinf
-- Looking for isinf - found
-- Looking for isnan
-- Looking for isnan - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for qsort_r
-- Looking for qsort_r - found
-- Looking for time
-- Looking for time - found
-- Looking for copysign
-- Looking for copysign - found
-- Looking for getopt
-- Looking for getopt - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of uint32_t
-- Check size of uint32_t - done
-- Check size of unsigned int
-- Check size of unsigned int - done
-- Check size of unsigned long
-- Check size of unsigned long - done
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Looking for fpclassify
-- Looking for fpclassify - TRUE
-- Performing Test HAVE_THREAD_LOCAL_STORAGE
-- Performing Test HAVE_THREAD_LOCAL_STORAGE - Success
-- Performing Test HAVE_THREAD_LOCAL_STORAGE
-- Performing Test HAVE_THREAD_LOCAL_STORAGE - Failed
-- Looking for __cplusplus
-- Looking for __cplusplus - found
-- Performing Test SUPPORTS_STDCXX11
-- Performing Test SUPPORTS_STDCXX11 - Success
-- Performing Test HAS_FPIC
-- Performing Test HAS_FPIC - Success
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt-build
Scanning dependencies of target generate-cpp
Scanning dependencies of target generate-fortran
[ 1%] Generating nlopt.hpp
[ 3%] Generating nlopt.f
[ 3%] Built target generate-fortran
[ 3%] Built target generate-cpp
Scanning dependencies of target nlopt
[ 5%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/direct_wrap.c.o
[ 7%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/DIRect.c.o
[ 9%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/DIRserial.c.o
[ 11%] Building C object CMakeFiles/nlopt.dir/src/algs/direct/DIRsubrout.c.o
[ 13%] Building C object CMakeFiles/nlopt.dir/src/algs/cdirect/cdirect.c.o
[ 15%] Building C object CMakeFiles/nlopt.dir/src/algs/cdirect/hybrid.c.o
[ 17%] Building C object CMakeFiles/nlopt.dir/src/algs/praxis/praxis.c.o
[ 19%] Building C object CMakeFiles/nlopt.dir/src/algs/luksan/plis.c.o
[ 21%] Building C object CMakeFiles/nlopt.dir/src/algs/luksan/plip.c.o
[ 23%] Building C object CMakeFiles/nlopt.dir/src/algs/luksan/pnet.c.o
[ 25%] Building C object CMakeFiles/nlopt.dir/src/algs/luksan/mssubs.c.o
[ 27%] Building C object CMakeFiles/nlopt.dir/src/algs/luksan/pssubs.c.o
[ 29%] Building C object CMakeFiles/nlopt.dir/src/algs/crs/crs.c.o
[ 31%] Building C object CMakeFiles/nlopt.dir/src/algs/mlsl/mlsl.c.o
[ 33%] Building C object CMakeFiles/nlopt.dir/src/algs/mma/mma.c.o
[ 35%] Building C object CMakeFiles/nlopt.dir/src/algs/mma/ccsa_quadratic.c.o
[ 37%] Building C object CMakeFiles/nlopt.dir/src/algs/cobyla/cobyla.c.o
[ 39%] Building C object CMakeFiles/nlopt.dir/src/algs/newuoa/newuoa.c.o
[ 41%] Building C object CMakeFiles/nlopt.dir/src/algs/neldermead/nldrmd.c.o
[ 43%] Building C object CMakeFiles/nlopt.dir/src/algs/neldermead/sbplx.c.o
[ 45%] Building C object CMakeFiles/nlopt.dir/src/algs/auglag/auglag.c.o
[ 47%] Building C object CMakeFiles/nlopt.dir/src/algs/bobyqa/bobyqa.c.o
[ 49%] Building C object CMakeFiles/nlopt.dir/src/algs/isres/isres.c.o
[ 50%] Building C object CMakeFiles/nlopt.dir/src/algs/slsqp/slsqp.c.o
[ 52%] Building C object CMakeFiles/nlopt.dir/src/algs/esch/esch.c.o
[ 54%] Building C object CMakeFiles/nlopt.dir/src/api/general.c.o
[ 56%] Building C object CMakeFiles/nlopt.dir/src/api/options.c.o
[ 58%] Building C object CMakeFiles/nlopt.dir/src/api/optimize.c.o
[ 60%] Building C object CMakeFiles/nlopt.dir/src/api/deprecated.c.o
[ 62%] Building C object CMakeFiles/nlopt.dir/src/api/f77api.c.o
[ 64%] Building C object CMakeFiles/nlopt.dir/src/util/mt19937ar.c.o
[ 66%] Building C object CMakeFiles/nlopt.dir/src/util/sobolseq.c.o
[ 68%] Building C object CMakeFiles/nlopt.dir/src/util/timer.c.o
[ 70%] Building C object CMakeFiles/nlopt.dir/src/util/stop.c.o
[ 72%] Building C object CMakeFiles/nlopt.dir/src/util/redblack.c.o
[ 74%] Building C object CMakeFiles/nlopt.dir/src/util/qsort_r.c.o
[ 76%] Building C object CMakeFiles/nlopt.dir/src/util/rescale.c.o
[ 80%] Building CXX object CMakeFiles/nlopt.dir/src/algs/stogo/global.cc.o
[ 80%] Building CXX object CMakeFiles/nlopt.dir/src/algs/stogo/linalg.cc.o
[ 82%] Building CXX object CMakeFiles/nlopt.dir/src/algs/stogo/local.cc.o
[ 84%] Building CXX object CMakeFiles/nlopt.dir/src/algs/stogo/stogo.cc.o
[ 86%] Building CXX object CMakeFiles/nlopt.dir/src/algs/stogo/tools.cc.o
[ 88%] Building CXX object CMakeFiles/nlopt.dir/src/algs/ags/evolvent.cc.o
[ 90%] Building CXX object CMakeFiles/nlopt.dir/src/algs/ags/solver.cc.o
[ 92%] Building CXX object CMakeFiles/nlopt.dir/src/algs/ags/local_optimizer.cc.o
[ 94%] Building CXX object CMakeFiles/nlopt.dir/src/algs/ags/ags.cc.o
[ 96%] Linking CXX static library libnlopt.a
[100%] Built target nlopt
[ 1%] Built target generate-cpp
[ 98%] Built target nlopt
[100%] Built target generate-fortran
Install the project...
-- Install configuration: "Release"
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/lib/pkgconfig/nlopt.pc
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/include/nlopt.h
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/include/nlopt.hpp
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/include/nlopt.f
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/lib/libnlopt.a
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/lib/cmake/nlopt/NLoptLibraryDepends.cmake
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/lib/cmake/nlopt/NLoptLibraryDepends-release.cmake
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/lib/cmake/nlopt/NLoptConfig.cmake
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/lib/cmake/nlopt/NLoptConfigVersion.cmake
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/share/man/man3/nlopt.3
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/share/man/man3/nlopt_minimize.3
-- Installing: /tmp/RtmpqxNfAU/R.INSTALL1aa6f68976f05/nloptr/src/nlopt/share/man/man3/nlopt_minimize_constrained.3
mv: cannot move 'nlopt/lib' to a subdirectory of itself, 'nlopt/lib/lib'
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/lilia/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init_nloptr.c -o init_nloptr.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/lilia/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nloptr.c -o nloptr.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/lilia/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c test-C-API.cpp -o test-C-API.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/lilia/R/x86_64-pc-linux-gnu-library/4.2/testthat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o nloptr.so init_nloptr.o nloptr.o test-C-API.o test-runner.o -llapack -lblas -lgfortran -lm -lquadmath nlopt/lib/libnlopt.a -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/home/lilia/R/x86_64-pc-linux-gnu-library/4.2/nloptr’
Warning in install.packages :
installation of package ‘nloptr’ had non-zero exit status
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/home/lilia/R/x86_64-pc-linux-gnu-library/4.2/lme4’
Warning in install.packages :
installation of package ‘lme4’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/lilia/R/x86_64-pc-linux-gnu-library/4.2/pbkrtest’
Warning in install.packages :
installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/lilia/R/x86_64-pc-linux-gnu-library/4.2/car’
Warning in install.packages :
installation of package ‘car’ had non-zero exit status
ERROR: dependency ‘car’ is not available for package ‘FactoMineR’
* removing ‘/home/lilia/R/x86_64-pc-linux-gnu-library/4.2/FactoMineR’
Warning in install.packages :
installation of package ‘FactoMineR’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmptBvDiz/downloaded_packages’
>
Thanks in advance for your help.