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pythonモジュールのインストールが失敗する-"limits.h"がない？

コンパイルを必要とするpython 3つのモジュール（例：regex、cytoolsz、spacy））をインストールしようとしていますが、これらはすべて以下と同じエラーで失敗します（下）。以下のgrepを使用して「limits.h」の存在を確認するには、gcc、g ++ build-essentials、python3-devなどを再インストールしましたが、役に立ちませんでした。

私はUbuntu 18.10を使用しています。

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]>

小切手：

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'

小切手：

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

エラー：

    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/

両方とも linux-libc-devおよびlibc6-devはすでにインストールされており、両方を再インストールしてみました。私のPATHは：

$ 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

以前のカーネルである4.18.0での起動も試みましたが、結果は同じでした。

pythoncompilinggcc
2
mac

分析（スキップできますが、将来同様の問題を診断するのに役立つ可能性があります）

limits.hから参照されている/usr/include/limits.hファイルが欠落しているというGCCの不満（anotherlimits.h file）：

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

/usr/include/limits.hで確認すると、次のことがわかります。

$ 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

つまり、libcのlimits.hには、コンパイラー自体によって提供されるanotherlimits.hが含まれます。 apt-fileツールと少し常識を使用して、必要なパッケージがlibgcc-8-devであると判断できます。

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

dpkgクエリは、インストールされているパッケージとファイルをリストします。

$ dpkg -S limits.h | grep linux
libgcc-8-dev:AMD64: /usr/lib/gcc/x86_64-linux-gnu/8/include-fixed/limits.h
...

ただし、GCCはディレクトリが不足していると文句を言います。

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

結論と修正

これはすべて、おそらくlibgcc-8-devパッケージがシステムで破損したことを意味します。復元するには、次を実行：

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

（8を適切なメジャーGCCバージョンに置き換える必要がある場合があります）

一般に、システムからlimits.hを手動で削除したり、他の方法でGCCインストールをいじったりしたことを覚えていない場合は、ファイルシステムの整合性とハードドライブの状態を確認することをお勧めします。

2
undercat applauds Monica