3

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.

I am on Ubuntu 18.10.

dpkg -s gcc  
Package: gcc
Status: install ok installed
Priority: optional
Section: devel
Installed-Size: 50
Maintainer: Ubuntu Developers <[email protected]>
Architecture: amd64
Source: gcc-defaults (1.179ubuntu1)
Version: 4:8.2.0-1ubuntu1
Provides: c-compiler, gcc-x86-64-linux-gnu (= 4:8.2.0-1ubuntu1)
Depends: cpp (= 4:8.2.0-1ubuntu1), gcc-8 (>= 8.2.0-4~)
Recommends: libc6-dev | libc-dev
Suggests: gcc-multilib, make, manpages-dev, autoconf, automake, libtool, flex, bison, gdb, gcc-doc
Conflicts: gcc-doc (<< 1:2.95.3)
Description: GNU C compiler
 This is the GNU C compiler, a fairly portable optimizing compiler for C.
 .
 This is a dependency package providing the default GNU C compiler.
Original-Maintainer: Debian GCC Maintainers <[email protected]>

Check:

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('\r\n', '\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('\r\n', '\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/

Both linux-libc-dev and libc6-dev are already installed and I have also tried reinstalling both. My PATH is:

$ echo $PATH
/home/mac/.opam/system/bin:/home/mac/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

I also tried booting into an earlier kernel, 4.18.0, but the results were the same.

Improve this question
16
  • 3
    /usr/include/limits.h should be provided by the libc6-dev package - is it installed? Commented Mar 3, 2019 at 19:22
  • Yes, it is installed. I also tried reinstalling. But from the check above it looks like it is in /usr/include/linux instead of /usr/include/. Commented Mar 3, 2019 at 19:25
  • The file in /usr/include/linux comes from package linux-libc-dev (which is for kernel development rather than user-space development I think) Commented Mar 3, 2019 at 19:30
  • OK, got. The limits.h from libc6-dev is in fact in /usr/include. Commented Mar 3, 2019 at 19:34
  • 1
    Does running echo '#include <limits.h>' | x86_64-linux-gnu-gcc -E - produce an error? Commented Mar 3, 2019 at 21:46

1 Answer 1

Reset to default
4

Analysis (you can skip it, but it may help diagnose similar problems in the future)

Your GCC complains about a missing limits.h file referenced from /usr/include/limits.h (another limits.h file):

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

Checking with /usr/include/limits.h we can see the following:

$ sed -n 117,125p /usr/include/limits.h
 /* Get the compiler's limits.h, which defines almost all the ISO constants.

    We put this #include_next outside the double inclusion check because
    it should be possible to include this file more than once and still get
    the definitions from gcc's header.  */
#if defined __GNUC__ && !defined _GCC_LIMITS_H_
/* `_GCC_LIMITS_H_' is what GCC's file defines.  */
# include_next <limits.h>
#endif

In other words, libc's limits.h includes another limits.h provided by the compiler itself. Using the apt-file tool and a bit of common sense we can determine that the package you need is libgcc-8-dev:

$ apt-file search /limits.h | grep gcc-8
libgcc-8-dev: /usr/lib/gcc/x86_64-linux-gnu/8/include-fixed/limits.h
...

Your dpkg query lists the package and file as installed:

$ dpkg -S limits.h | grep linux
libgcc-8-dev:amd64: /usr/lib/gcc/x86_64-linux-gnu/8/include-fixed/limits.h
...

However, GCC complains about a missing directory:

$ x86_64-linux-gnu-gcc -xc -E -v /dev/null
...
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed"

Conclusion and fix

All this likely means that libgcc-8-dev package somehow got corrupted on your system. To restore it, run:

$ sudo apt-get install --reinstall libgcc-8-dev

(you may need to replace 8 with the appropriate major GCC version you have)

In general, if you don't remember manually deleting limits.h from your system or tinkering with the GCC install in any other way, it may be a good idea to check your file system's consistency and hard drive health.

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