R can't install packages, gcc and g++ fatal error - r

Question

I haven't been able to install any packages (such as randomForest, devtools, etc.)
I have also updated my R to 4.2 recently (not sure if they are related). I am also running Ubuntu.
I suspect it was something to do with the C++ compiler, such as the g++ and GCC.
things that I have done:
I have edit the Makevars to include:
CC=/usr/bin/gcc
CXX=/usr/bin/g++
FC=/usr/bin/gfortran
F77=/usr/bin/gfortran
Is there anyone facing the same problem? or any hints and guidance are really appreciated. Thank you in advance. If you need more information, please kindly let me know.
One of the errors is (installing devtools):
* installing *source* package ‘sourcetools’ ...
** package ‘sourcetools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Reader.cpp -o Reader.o
g++: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:177: Reader.o] Error 1
ERROR: compilation failed for package ‘sourcetools’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/sourcetools’
Warning in install.packages :
installation of package ‘sourcetools’ had non-zero exit status
* installing *source* package ‘systemfonts’ ...
** package ‘systemfonts’ successfully unpacked and MD5 sums checked
** using staged installation
Package fontconfig was not found in the pkg-config search path.
Perhaps you should add the directory containing `fontconfig.pc'
to the PKG_CONFIG_PATH environment variable
No package 'fontconfig' found
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
No package 'freetype2' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lfontconfig -lfreetype
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the fontconfig freetype2 library. Try installing:
* deb: libfontconfig1-dev (Debian, Ubuntu, etc)
* rpm: fontconfig-devel (Fedora, EPEL)
* csw: fontconfig_dev (Solaris)
* brew: freetype (OSX)
If fontconfig freetype2 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a fontconfig freetype2.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:10: fatal error: fontconfig/fontconfig.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘systemfonts’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/systemfonts’
Warning in install.packages :
installation of package ‘systemfonts’ had non-zero exit status
* installing *source* package ‘gert’ ...
** package ‘gert’ successfully unpacked and MD5 sums checked
** using staged installation
> curl::curl_download("https://r-lib.github.io/gert/get-libgit2-linux.sh","get-libgit2-linux.sh")
>
>
Using static libgit2-1.1.0 for Linux x86_64
Using PKG_CFLAGS=-DSTATIC_LIBGIT2 -I/tmp/RtmpNHz5pp/R.INSTALL48c6b475a68c2/gert/libgit2/include
Using PKG_LIBS=-L/tmp/RtmpNHz5pp/R.INSTALL48c6b475a68c2/gert/libgit2/lib -lgit2 -lrt -lpthread -lssh2 -lssl -lcrypto -ldl -lpcre -lz
Configuration OK!
** libs
rm -f gert.so branch.o clone.o commit.o config.o conflicts.o files.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o
gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpNHz5pp/R.INSTALL48c6b475a68c2/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c branch.c -o branch.o
gcc: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: branch.o] Error 1
ERROR: compilation failed for package ‘gert’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/gert’
Warning in install.packages :
installation of package ‘gert’ had non-zero exit status
* installing *source* package ‘commonmark’ ...
** package ‘commonmark’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
rm -f cmark/cmark.o cmark/node.o cmark/iterator.o cmark/blocks.o cmark/inlines.o cmark/scanners.o cmark/utf8.o cmark/buffer.o cmark/references.o cmark/render.o cmark/man.o cmark/xml.o cmark/html.o cmark/commonmark.o cmark/latex.o cmark/houdini_href_e.o cmark/houdini_html_e.o cmark/houdini_html_u.o cmark/cmark_ctype.o cmark/arena.o cmark/html.o cmark/linked_list.o cmark/plugin.o cmark/registry.o cmark/syntax_extension.o cmark/plaintext.o cmark/footnotes.o cmark/map.o extensions/autolink.o extensions/core-extensions.o extensions/ext_scanners.o extensions/strikethrough.o extensions/table.o extensions/tagfilter.o extensions/tasklist.o extensions.o init.o wrapper.o commonmark.so cmark/libstatcmark.a
gcc -I"/usr/share/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c extensions.c -o extensions.o
gcc: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: extensions.o] Error 1
ERROR: compilation failed for package ‘commonmark’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/commonmark’
Warning in install.packages :
installation of package ‘commonmark’ had non-zero exit status
* installing *source* package ‘profvis’ ...
** package ‘profvis’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pause.c -o pause.o
gcc: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: pause.o] Error 1
ERROR: compilation failed for package ‘profvis’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/profvis’
Warning in install.packages :
installation of package ‘profvis’ had non-zero exit status
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c capture.c -o capture.o
gcc: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: capture.o] Error 1
ERROR: compilation failed for package ‘rlang’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/rlang’
* restoring previous ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/rlang’
Warning in install.packages :
installation of package ‘rlang’ had non-zero exit status
* installing *source* package ‘later’ ...
** package ‘later’ successfully unpacked and MD5 sums checked
** using staged installation
Running configure script
-latomic linker flag needed.
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o
g++: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:177: RcppExports.o] Error 1
ERROR: compilation failed for package ‘later’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/later’
Warning in install.packages :
installation of package ‘later’ had non-zero exit status
ERROR: dependency ‘systemfonts’ is not available for package ‘textshaping’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/textshaping’
Warning in install.packages :
installation of package ‘textshaping’ had non-zero exit status
* installing *source* package ‘cachem’ ...
** package ‘cachem’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cache.c -o cache.o
gcc: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: cache.o] Error 1
ERROR: compilation failed for package ‘cachem’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/cachem’
Warning in install.packages :
installation of package ‘cachem’ had non-zero exit status
ERROR: dependency ‘gert’ is not available for package ‘usethis’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/usethis’
Warning in install.packages :
installation of package ‘usethis’ had non-zero exit status
* installing *source* package ‘pkgload’ ...
** package ‘pkgload’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace ‘rlang’ 1.0.2 is being loaded, but >= 1.0.3 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘pkgload’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/pkgload’
* restoring previous ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/pkgload’
Warning in install.packages :
installation of package ‘pkgload’ had non-zero exit status
ERROR: dependency ‘later’ is not available for package ‘promises’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/promises’
Warning in install.packages :
installation of package ‘promises’ had non-zero exit status
ERROR: dependencies ‘systemfonts’, ‘textshaping’ are not available for package ‘ragg’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/ragg’
Warning in install.packages :
installation of package ‘ragg’ had non-zero exit status
ERROR: dependency ‘cachem’ is not available for package ‘memoise’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/memoise’
Warning in install.packages :
installation of package ‘memoise’ had non-zero exit status
ERROR: dependency ‘commonmark’ is not available for package ‘roxygen2’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/roxygen2’
Warning in install.packages :
installation of package ‘roxygen2’ had non-zero exit status
ERROR: dependencies ‘promises’, ‘later’ are not available for package ‘httpuv’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/httpuv’
Warning in install.packages :
installation of package ‘httpuv’ had non-zero exit status
ERROR: dependency ‘memoise’ is not available for package ‘downlit’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/downlit’
Warning in install.packages :
installation of package ‘downlit’ had non-zero exit status
ERROR: dependencies ‘httpuv’, ‘sourcetools’, ‘later’, ‘promises’, ‘commonmark’, ‘cachem’ are not available for package ‘shiny’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/shiny’
Warning in install.packages :
installation of package ‘shiny’ had non-zero exit status
ERROR: dependencies ‘downlit’, ‘memoise’, ‘ragg’ are not available for package ‘pkgdown’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/pkgdown’
Warning in install.packages :
installation of package ‘pkgdown’ had non-zero exit status
ERROR: dependency ‘shiny’ is not available for package ‘miniUI’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/miniUI’
Warning in install.packages :
installation of package ‘miniUI’ had non-zero exit status
ERROR: dependencies ‘usethis’, ‘memoise’, ‘miniUI’, ‘pkgdown’, ‘profvis’, ‘roxygen2’ are not available for package ‘devtools’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/devtools’
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpITL0q0/downloaded_packages’