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gcc-6.3.0: fatal error: stdlib.h: No such file or directory
Hi David, I am trying to stitch together a fast5 package for Gentoo Linux but it fails to compile with 6.3.0 here:
>>> Emerging (2 of 3) sci-libs/fast5-9999::science
>>> Unpacking source...
* Fetching https://github.com/mateidavid/fast5.git ...
git fetch https://github.com/mateidavid/fast5.git +HEAD:refs/git-r3/HEAD
git symbolic-ref refs/git-r3/sci-libs/fast5/0/__main__ refs/git-r3/HEAD
* Checking out https://github.com/mateidavid/fast5.git to /apps/gentoo/var/tmp/portage/sci-libs/fast5-9999/work/fast5-9999 ...
git checkout --quiet refs/git-r3/HEAD
GIT update -->
repository: https://github.com/mateidavid/fast5.git
at the commit: 8a48fd7d70d64225ac349135dcf5734b9f452125
>>> Source unpacked in /apps/gentoo/var/tmp/portage/sci-libs/fast5-9999/work
>>> Preparing source in /apps/gentoo/var/tmp/portage/sci-libs/fast5-9999/work/fast5-9999 ...
>>> Source prepared.
>>> Configuring source in /apps/gentoo/var/tmp/portage/sci-libs/fast5-9999/work/fast5-9999 ...
>>> Source configured.
>>> Compiling source in /apps/gentoo/var/tmp/portage/sci-libs/fast5-9999/work/fast5-9999 ...
make -j25 -C python develop-user HDF5_DIR=/apps/gentoo/usr HDF5_LIB_DIR=/apps/gentoo/usr/lib64
make: Entering directory '/apps/gentoo/var/tmp/portage/sci-libs/fast5-9999/work/fast5-9999/python'
/apps/gentoo/usr/bin/python setup.py develop --user
Compiling fast5/fast5.pyx because it changed.
[1/1] Cythonizing fast5/fast5.pyx
running develop
running egg_info
creating fast5.egg-info
writing fast5.egg-info/PKG-INFO
writing top-level names to fast5.egg-info/top_level.txt
writing dependency_links to fast5.egg-info/dependency_links.txt
writing manifest file 'fast5.egg-info/SOURCES.txt'
reading manifest file 'fast5.egg-info/SOURCES.txt'
writing manifest file 'fast5.egg-info/SOURCES.txt'
running build_ext
building 'fast5' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/fast5
x86_64-pc-linux-gnu-g++ -pthread -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -fPIC -I../include -I../src -I/apps/gentoo/usr/include/python2.7 -c fast5/fast5.cpp -o build/temp.linux-x86_64-2.7/fast5/fast5.o -std=c++11 -Wall -Wextra -Wpedantic -isystem /apps/gentoo/usr/include
In file included from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include/g++-v6/ext/string_conversions.h:41:0,
from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include/g++-v6/bits/basic_string.h:5402,
from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include/g++-v6/string:52,
from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include/g++-v6/bits/locale_classes.h:40,
from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include/g++-v6/bits/ios_base.h:41,
from /apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include/g++-v6/ios:42,
from fast5/fast5.cpp:536:
/apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include/g++-v6/cstdlib:75:25: fatal error: stdlib.h: No such file or directory
#include_next <stdlib.h>
^
compilation terminated.
error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1
make: *** [Makefile:41: develop-user] Error 1
make: Leaving directory '/apps/gentoo/var/tmp/portage/sci-libs/fast5-9999/work/fast5-9999/python'
It works with gcc-5.4.0.