Cfrgtkky

I am trying to install a number of python 3 modules (e.g. regex, cytoolsz, spacy) that require compilation, but they all fail with an error identical to the below (bottom). I have tried to check for the presence of "limits.h" using the the grep below. I have reinstalled gcc, g++ build-essentials, python3-dev etc, but to no avail.

x86_64-linux-gnu-gcc -xc -E -v /dev/null



Using built-in specs.

COLLECT_GCC=x86_64-linux-gnu-gcc

OFFLOAD_TARGET_NAMES=nvptx-none

OFFLOAD_TARGET_DEFAULT=1

Target: x86_64-linux-gnu

Configured with: ../src/configure -v --with-pkgversion='Ubuntu 8.2.0-7ubuntu1' --with-bugurl=file:///usr/share/doc/gcc-8/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-8 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu

Thread model: posix

gcc version 8.2.0 (Ubuntu 8.2.0-7ubuntu1) 

COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'

 /usr/lib/gcc/x86_64-linux-gnu/8/cc1 -E -quiet -v -imultiarch x86_64-linux-gnu /dev/null -mtune=generic -march=x86-64 -fstack-protector-strong -Wformat -Wformat-security

ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"

ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed"

ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/8/../../../../x86_64-linux-gnu/include"

#include "..." search starts here:

#include <...> search starts here:

 /usr/lib/gcc/x86_64-linux-gnu/8/include

 /usr/local/include

 /usr/include/x86_64-linux-gnu

 /usr/include

End of search list.

# 1 "/dev/null"

# 1 "<built-in>"

# 1 "<command-line>"

# 31 "<command-line>"

# 1 "/usr/include/stdc-predef.h" 1 3 4

# 32 "<command-line>" 2

# 1 "/dev/null"

COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/8/:/usr/lib/gcc/x86_64-linux-gnu/8/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/8/:/usr/lib/gcc/x86_64-linux-gnu/

LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/8/:/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/8/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/8/../../../:/lib/:/usr/lib/

COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'

Check:

dpkg -S limits.h | grep linux

linux-headers-4.18.0-15: /usr/src/linux-headers-4.18.0-15/include/linux/dynamic_queue_limits.h

linux-libc-dev:amd64: /usr/include/linux/limits.h

linux-headers-4.19.0-041900rc8: /usr/src/linux-headers-4.19.0-041900rc8/include/uapi/linux/limits.h

linux-headers-4.18.0-14: /usr/src/linux-headers-4.18.0-14/include/linux/drbd_limits.h

linux-headers-4.18.0-15: /usr/src/linux-headers-4.18.0-15/arch/arm/include/asm/limits.h

linux-headers-4.18.0-14: /usr/src/linux-headers-4.18.0-14/include/uapi/linux/limits.h

linux-headers-4.18.0-14: /usr/src/linux-headers-4.18.0-14/include/linux/dynamic_queue_limits.h

libgcc-8-dev:amd64: /usr/lib/gcc/x86_64-linux-gnu/8/include-fixed/limits.h

linux-headers-4.18.0-14: /usr/src/linux-headers-4.18.0-14/arch/arm/include/asm/limits.h

linux-headers-4.18.0-15: /usr/src/linux-headers-4.18.0-15/include/linux/drbd_limits.h

linux-headers-4.19.0-041900rc8: /usr/src/linux-headers-4.19.0-041900rc8/include/linux/drbd_limits.h

linux-headers-4.18.0-15: /usr/src/linux-headers-4.18.0-15/include/uapi/linux/limits.h

linux-headers-4.19.0-041900rc8: /usr/src/linux-headers-4.19.0-041900rc8/include/linux/dynamic_queue_limits.h

linux-headers-4.19.0-041900rc8: /usr/src/linux-headers-4.19.0-041900rc8/arch/arm/include/asm/limits.h

libgcc-8-dev:amd64: /usr/lib/gcc/x86_64-linux-gnu/8/include-fixed/syslimits.h

Error:

    sudo pip3 install regex                   

The directory '/home/mac/.cache/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.

The directory '/home/mac/.cache/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.

Collecting regex

  Downloading https://files.pythonhosted.org/packages/9a/6f/8c1479c781bbc94394f9c4e33ad4139068bcc6a1b018c5a5525471262b8a/regex-2019.02.18.tar.gz (643kB)

    100% |████████████████████████████████| 645kB 813kB/s 

Installing collected packages: regex

  Running setup.py install for regex ... error

    Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-n16bk3y6/regex/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('rn', 'n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-z1rqj4ab-record/install-record.txt --single-version-externally-managed --compile:

    /home/mac/.local/lib/python3.6/site-packages/setuptools/dist.py:475: UserWarning: Normalizing '2019.02.18' to '2019.2.18'

      normalized_version,

    running install

    running build

    running build_py

    creating build

    creating build/lib.linux-x86_64-3.6

    copying regex_3/regex.py -> build/lib.linux-x86_64-3.6

    copying regex_3/_regex_core.py -> build/lib.linux-x86_64-3.6

    copying regex_3/test_regex.py -> build/lib.linux-x86_64-3.6

    running build_ext

    building '_regex' extension

    creating build/temp.linux-x86_64-3.6

    creating build/temp.linux-x86_64-3.6/regex_3

    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c regex_3/_regex.c -o build/temp.linux-x86_64-3.6/regex_3/_regex.o

    In file included from /usr/include/python3.6m/Python.h:11,

                     from regex_3/_regex.c:48:

    /usr/include/limits.h:124:26: error: no include path in which to search for limits.h

     # include_next <limits.h>

                              ^

    In file included from regex_3/_regex.c:48:

    /usr/include/python3.6m/Python.h:14:2: error: #error "Something's broken.  UCHAR_MAX should be defined in limits.h."

     #error "Something's broken.  UCHAR_MAX should be defined in limits.h."

      ^~~~~

    /usr/include/python3.6m/Python.h:18:2: error: #error "Python's source code assumes C's unsigned char is an 8-bit type."

     #error "Python's source code assumes C's unsigned char is an 8-bit type."

      ^~~~~

    In file included from /usr/include/python3.6m/Python.h:25,

                     from regex_3/_regex.c:48:

    /usr/include/stdio.h:33:10: fatal error: stddef.h: No such file or directory

     #include <stddef.h>

              ^~~~~~~~~~

    compilation terminated.

    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1



    ----------------------------------------

Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-n16bk3y6/regex/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('rn', 'n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-z1rqj4ab-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-n16bk3y6/regex/

First and foremost to address your question completely. The file limits.h in /usr/include/linux/ is provided by the linux-libc-dev package. So to have the header files in this location you simply have to install it by:

sudo apt install linux-libc-dev

to have header files provided in /usr/include/ which are occasionally used as well you need the libc6-dev package which provides them. Install it by:

sudo apt install libc6-dev

Furthermore it is bad practice to use pip3 with sudo as it tends to create root owned folders in your home directory. To fix this, I assume you already did a couple of installs that way simply take back ownership of /home/$USER/.cache/pip by:

sudo chown -Rv <your-username>:<your-username> /home/<your-username>/.cache/pip