Cannot install packages in R: fatal error: bits/functional_hash.h: No such file or directory #include <bits/functional_hash.h>

I am not able to install any packages.

/usr/include/c++/7/bits/basic_string.h:6587:10: fatal error: bits/functional_hash.h: No such file or directory
#include <bits/functional_hash.h>
^~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:181: recipe for target 'test-catch.o' failed
make: *** [test-catch.o] Error 1
ERROR: compilation failed for package ‘testthat’

  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/testthat’
    Warning in install.packages :
    installation of package ‘testthat’ had non-zero exit status
  • installing source package ‘farver’ ...
    ** package ‘farver’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ColorSpace.cpp -o ColorSpace.o
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Comparison.cpp -o Comparison.o
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Conversion.cpp -o Conversion.o
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c encode.cpp -o encode.o
    In file included from /usr/include/c++/7/string:52:0,
    from /usr/include/c++/7/stdexcept:39,
    from /usr/include/c++/7/array:39,
    from /usr/include/c++/7/tuple:39,
    from /usr/include/c++/7/unordered_map:41,
    from encode.h:4,
    from encode.cpp:1:
    /usr/include/c++/7/bits/basic_string.h:6587:10: fatal error: bits/functional_hash.h: No such file or directory
    #include <bits/functional_hash.h>
    ^~~~~~~~~~~~~~~~~~~~~~~~
    compilation terminated.
    /usr/lib/R/etc/Makeconf:181: recipe for target 'encode.o' failed
    make: *** [encode.o] Error 1
    ERROR: compilation failed for package ‘farver’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/farver’
    Warning in install.packages :
    installation of package ‘farver’ had non-zero exit status
  • installing source package ‘Rcpp’ ...
    ** package ‘Rcpp’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o
    In file included from /usr/include/c++/7/string:52:0,
    from /usr/include/c++/7/stdexcept:39,
    from /usr/include/c++/7/array:39,
    from /usr/include/c++/7/tuple:39,
    from /usr/include/c++/7/unordered_map:41,
    from ../inst/include/Rcpp/platform/compiler.h:153,
    from ../inst/include/Rcpp/r/headers.h:67,
    from ../inst/include/RcppCommon.h:29,
    from ../inst/include/Rcpp.h:27,
    from api.cpp:24:
    /usr/include/c++/7/bits/basic_string.h:6587:10: fatal error: bits/functional_hash.h: No such file or directory
    #include <bits/functional_hash.h>
    ^~~~~~~~~~~~~~~~~~~~~~~~
    compilation terminated.
    /usr/lib/R/etc/Makeconf:181: recipe for target 'api.o' failed
    make: *** [api.o] Error 1
    ERROR: compilation failed for package ‘Rcpp’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/Rcpp’
    Warning in install.packages :
    installation of package ‘Rcpp’ had non-zero exit status
  • installing source package ‘fs’ ...
    ** package ‘fs’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.38.1/include -I. -pthread -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c id.cc -o id.o
    In file included from /usr/include/c++/7/string:52:0,
    from utils.h:5,
    from id.cc:1:
    /usr/include/c++/7/bits/basic_string.h:6587:10: fatal error: bits/functional_hash.h: No such file or directory
    #include <bits/functional_hash.h>
    ^~~~~~~~~~~~~~~~~~~~~~~~
    compilation terminated.
    /usr/lib/R/etc/Makeconf:179: recipe for target 'id.o' failed
    make: *** [id.o] Error 1
    ERROR: compilation failed for package ‘fs’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/fs’
    Warning in install.packages :
    installation of package ‘fs’ had non-zero exit status
  • installing source package ‘stringi’ ...
    ** package ‘stringi’ successfully unpacked and MD5 sums checked
    ** using staged installation
    checking for R_HOME... /usr/lib/R
    checking for R... /usr/lib/R/bin/R
    checking for endianness... little
    checking for R >= 3.1.0 for C++11 use... yes
    checking for R < 3.4.0 for CXX1X flag use... no
    checking for cat... /bin/cat
    checking for local ICUDT_DIR... icu61/data
    checking for gcc... gcc -std=gnu99
    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 gcc -std=gnu99 accepts -g... yes
    checking for gcc -std=gnu99 option to accept ISO C89... none needed
    checking how to run the C preprocessor... gcc -std=gnu99 -E
    checking for grep that handles long lines and -e... /bin/grep
    checking for egrep... /bin/grep -E
    checking for ANSI C header files... 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 elf.h usability... yes
    checking elf.h presence... yes
    checking for elf.h... yes
    checking whether we are using the GNU C++ compiler... yes
    checking whether g++ -std=gnu++11 accepts -g... yes
    checking whether the C++ compiler supports the long long type... no
    *** trying with C++11 compiler disabled
    checking for local ICUDT_DIR... icu55/data
    checking for gcc... gcc -std=gnu99
    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 gcc -std=gnu99 accepts -g... yes
    checking for gcc -std=gnu99 option to accept ISO C89... none needed
    checking how to run the C preprocessor... gcc -std=gnu99 -E
    checking for grep that handles long lines and -e... (cached) /bin/grep
    checking for egrep... (cached) /bin/grep -E
    checking for ANSI C header files... yes
    checking for sys/types.h... (cached) yes
    checking for sys/stat.h... (cached) yes
    checking for stdlib.h... (cached) yes
    checking for string.h... (cached) yes
    checking for memory.h... (cached) yes
    checking for strings.h... (cached) yes
    checking for inttypes.h... (cached) yes
    checking for stdint.h... (cached) yes
    checking for unistd.h... (cached) yes
    checking for elf.h... (cached) yes
    checking whether we are using the GNU C++ compiler... yes
    checking whether g++ -std=gnu++11 accepts -g... yes
    checking whether the C++ compiler supports the long long type... no
    *** stringi cannot be built. Check your compiler flags (Makeconf, Makevars, etc.).
    *** also, verify your C++ compiler's abilities (long long, STL, etc. support)
    ERROR: configuration failed for package ‘stringi’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/stringi’
    Warning in install.packages :
    installation of package ‘stringi’ had non-zero exit status
  • installing source package ‘dplyr’ ...
    ** package ‘dplyr’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chop.cpp -o chop.o
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filter.cpp -o filter.o
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c funs.cpp -o funs.o
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c group_by.cpp -o group_by.o
    In file included from /usr/include/c++/7/vector:65:0,
    from group_by.cpp:2:
    /usr/include/c++/7/bits/stl_bvector.h:1281:10: fatal error: bits/functional_hash.h: No such file or directory
    #include <bits/functional_hash.h>
    ^~~~~~~~~~~~~~~~~~~~~~~~
    compilation terminated.
    /usr/lib/R/etc/Makeconf:181: recipe for target 'group_by.o' failed
    make: *** [group_by.o] Error 1
    ERROR: compilation failed for package ‘dplyr’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/dplyr’
    Warning in install.packages :
    installation of package ‘dplyr’ had non-zero exit status
  • installing source package ‘readr’ ...
    ** package ‘readr’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/vb/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/vb/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Collector.cpp -o Collector.o
    In file included from /usr/include/c++/7/string:52:0,
    from /home/vb/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include/cpp11/attribute_proxy.hpp:4,
    from /home/vb/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include/cpp11/list.hpp:6,
    from Collector.cpp:1:
    /usr/include/c++/7/bits/basic_string.h:6587:10: fatal error: bits/functional_hash.h: No such file or directory
    #include <bits/functional_hash.h>
    ^~~~~~~~~~~~~~~~~~~~~~~~
    compilation terminated.
    /usr/lib/R/etc/Makeconf:181: recipe for target 'Collector.o' failed
    make: *** [Collector.o] Error 1
    ERROR: compilation failed for package ‘readr’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/readr’
    Warning in install.packages :
    installation of package ‘readr’ had non-zero exit status
  • installing source package ‘xml2’ ...
    ** package ‘xml2’ successfully unpacked and MD5 sums checked
    ** using staged installation
    Found pkg-config cflags and libs!
    Using PKG_CFLAGS=-I/usr/include/libxml2
    Using PKG_LIBS=-lxml2
    ** libs
    g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-7BvS0x/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c connection.cpp -o connection.o
    In file included from /usr/include/c++/7/vector:65:0,
    from connection.cpp:2:
    /usr/include/c++/7/bits/stl_bvector.h:1281:10: fatal error: bits/functional_hash.h: No such file or directory
    #include <bits/functional_hash.h>
    ^~~~~~~~~~~~~~~~~~~~~~~~
    compilation terminated.
    /usr/lib/R/etc/Makeconf:181: recipe for target 'connection.o' failed
    make: *** [connection.o] Error 1
    ERROR: compilation failed for package ‘xml2’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/xml2’
    Warning in install.packages :
    installation of package ‘xml2’ had non-zero exit status
    ERROR: dependency ‘testthat’ is not available for package ‘isoband’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/isoband’
    Warning in install.packages :
    installation of package ‘isoband’ had non-zero exit status
    ERROR: dependency ‘farver’ is not available for package ‘scales’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/scales’
    Warning in install.packages :
    installation of package ‘scales’ had non-zero exit status
    ERROR: dependency ‘dplyr’ is not available for package ‘dbplyr’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/dbplyr’
    Warning in install.packages :
    installation of package ‘dbplyr’ had non-zero exit status
    ERROR: dependencies ‘Rcpp’, ‘readr’ are not available for package ‘haven’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/haven’
    Warning in install.packages :
    installation of package ‘haven’ had non-zero exit status
    ERROR: dependency ‘Rcpp’ is not available for package ‘lubridate’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/lubridate’
    Warning in install.packages :
    installation of package ‘lubridate’ had non-zero exit status
    ERROR: dependency ‘Rcpp’ is not available for package ‘readxl’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/readxl’
    Warning in install.packages :
    installation of package ‘readxl’ had non-zero exit status
    ERROR: dependency ‘stringi’ is not available for package ‘stringr’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/stringr’
    Warning in install.packages :
    installation of package ‘stringr’ had non-zero exit status
    ERROR: dependency ‘dplyr’ is not available for package ‘tidyr’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/tidyr’
    Warning in install.packages :
    installation of package ‘tidyr’ had non-zero exit status
    ERROR: dependency ‘stringr’ is not available for package ‘knitr’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/knitr’
    Warning in install.packages :
    installation of package ‘knitr’ had non-zero exit status
    ERROR: dependency ‘stringr’ is not available for package ‘selectr’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/selectr’
    Warning in install.packages :
    installation of package ‘selectr’ had non-zero exit status
    ERROR: dependencies ‘dplyr’, ‘stringr’, ‘tidyr’ are not available for package ‘broom’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/broom’
    Warning in install.packages :
    installation of package ‘broom’ had non-zero exit status
    ERROR: dependencies ‘isoband’, ‘scales’ are not available for package ‘ggplot2’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/ggplot2’
    Warning in install.packages :
    installation of package ‘ggplot2’ had non-zero exit status
    ERROR: dependencies ‘knitr’, ‘stringr’ are not available for package ‘rmarkdown’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/rmarkdown’
    Warning in install.packages :
    installation of package ‘rmarkdown’ had non-zero exit status
    ERROR: dependencies ‘broom’, ‘tidyr’ are not available for package ‘modelr’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/modelr’
    Warning in install.packages :
    installation of package ‘modelr’ had non-zero exit status
    ERROR: dependencies ‘xml2’, ‘selectr’ are not available for package ‘rvest’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/rvest’
    Warning in install.packages :
    installation of package ‘rvest’ had non-zero exit status
    ERROR: dependencies ‘fs’, ‘knitr’, ‘rmarkdown’ are not available for package ‘reprex’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/reprex’
    Warning in install.packages :
    installation of package ‘reprex’ had non-zero exit status
    ERROR: dependencies ‘broom’, ‘dbplyr’, ‘dplyr’, ‘ggplot2’, ‘haven’, ‘lubridate’, ‘modelr’, ‘readr’, ‘readxl’, ‘reprex’, ‘rvest’, ‘stringr’, ‘tidyr’, ‘xml2’ are not available for package ‘tidyverse’
  • removing ‘/home/vb/R/x86_64-pc-linux-gnu-library/4.0/tidyverse’
    Warning in install.packages :
    installation of package ‘tidyverse’ had non-zero exit status

The downloaded source packages are in
‘/tmp/Rtmpbt60wV/downloaded_packages’

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.