Angr installation failed in RPI3 - pip

I am trying to install Angr tool on Raspberry pi 3, OS Ubuntu mate 16.04. Git link Angr tool
I isolated problem while installing pyvex getting this error, git link Pyvex
running install
running bdist_egg
running build
Building libVEX
cc -Ipub -Ipriv -Wall -Wmissing-prototypes -Wstrict-prototypes -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wmissing-declarations -Wwrite-strings -Wformat -Wformat-security -std=gnu99 -fstrict-aliasing -fPIC -g -malign-double -o auxprogs/genoffsets auxprogs/genoffsets.c
cc: error: unrecognized command line option ‘-malign-double’
Makefile-gcc:72: recipe for target 'pub/libvex_guest_offsets.h' failed
make: *** [pub/libvex_guest_offsets.h] Error 1
error: Unable to build libVEX.
-malign-double is for X86 architecture as per GCC documentation but i have arm architecture. How do I fix this issue.

During build PyVEX downloads VEX. I think you have to download it yourself, fix Makefile and build. Then return to building PyVEX.
Report the problem to the angr team.

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Couldn't install gem - extconf.rb failed

I upgraded the macos to Mojave and reinstalled xcode, xcode CLT, ruby, etc. Then when I tried:
gem install nokogiri
I got the following error (installing other gems gave similar error):
ERROR: Failed to build gem native extension.
current directory: /usr/local/lib/ruby/gems/2.5.0/gems/nokogiri-1.8.5/ext/nokogiri
/usr/local/opt/ruby/bin/ruby -r ./siteconf20181209-20884-etfc5r.rb extconf.rb
checking if the C compiler accepts ... *** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers. Check the mkmf.log file for more details. You may
need configuration options.
I checked the mkmf.log, which contains the following:
"clang -o conftest -I/usr/local/Cellar/ruby/2.5.3_1/include/ruby-2.5.0/x86_64-darwin18 -I/usr/local/Cellar/ruby/2.5.3_1/include/ruby-2.5.0/ruby/backward -I/usr/local/Cellar/ruby/2.5.3_1/include/ruby-2.5.0 -I. -I/usr/local/opt/libyaml/include -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT -O3 -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wno-tautological-compare -Wno-parentheses-equality -Wno-constant-logical-operand -Wno-self-assign -Wunused-variable -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens -fno-common -pipe conftest.c -L. -L/usr/local/Cellar/ruby/2.5.3_1/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L. -fstack-protector -L/usr/local/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -lruby.2.5.3 -lpthread -ldl -lobjc "
In file included from conftest.c:1:
In file included from /usr/local/Cellar/ruby/2.5.3_1/include/ruby-2.5.0/ruby.h:33:
In file included from /usr/local/Cellar/ruby/2.5.3_1/include/ruby-2.5.0/ruby/ruby.h:29:
The text went on like this for a while. I also cd to the nokogiri folder and directly run extconf.rb, and got the following error:
checking if the C compiler accepts ... *** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers. Check the mkmf.log file for more details. You may
need configuration options.`
Provided configuration options:
--with-opt-dir
--with-opt-include
... (skipped similar content for brevity and continued below)
usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/mkmf.rb:456:in 'try_do': The compiler failed to generate an executable file. (RuntimeError)
You have to install development tools first.
I tried to install xcode. I also installed the header and acknowledged the license. I at first thought it has to do with GCC, but the mkmf file showed that the problem is with Clang.
Hope someone can help.
I had to run the following cryptic commands to get nokogiri installed. Basically this entails getting my C compiler working in mac osx Mojave, after having everything working fine in a previous OS (Yosemite I think it was...)
This is an (somewhat) obvious step when upgrading osx:
xcode-select --install
I also had to do this, which I never would've known how to do without google and this post
sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /
Finally, I had to agree to the xcode license (found I had to do this via the makefile logs when install of nokogiri failed...)
sudo xcodebuild -licence
It'll prompt you to eventually type "agree"
Finally, continuing with bundle works as expected for a new rails project that includes nokogiri. Success!

Rstudio unable to install package devtools: gcc error

I want to install package devtools. But after successful downloading of all dependencies, it gives error while installing of the form:
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rawmatch.c -o rawmatch.o
gcc: error: unrecognized command line option ‘-fstack-protector-strong’
gcc: error: unrecognized command line option ‘-Wdate-time’
/usr/lib/R/etc/Makeconf:159: recipe for target 'rawmatch.o' failed
make: *** [rawmatch.o] Error 1
ERROR: compilation failed for package ‘mime’
* removing ‘/usr/local/lib/R/site-library/mime’
I have checked gcc. I am able to run a sample c program file from terminal.
It seems you'll need to use a more recent gcc version, 4.9 at least.
Both unrecognized options, -fstack-protector-strong and -Wdate-time, were introduced in gcc 4.9 (release notes).

Platypus installation error message

I am trying to install Platypus and have gotten the following error message:
building 'htslibWrapper' extension
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c htslibWrapper.c -o build/temp.linux-x86_64-2.7/htslibWrapper.o -msse2 -msse3 -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC
htslibWrapper.c:243:25: fatal error: htslib/bgzf.h: No such file or directory
#include "htslib/bgzf.h"
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
I am new to Bioinformatics and cannot seem to find a working solution online.
Sometimes the bioinformatics applications don't describe thier dependencies all that well. See this link for a possible solution
Install htslib from http://www.htslib.org/download/ and copy c headers to Platypus root folder:
cp -r htslib-x.x.x/htslib platypus_folder/
Build again

MySqlDB: llvm-gcc-4.2: error. Even after installing XCode 4.6.3 and storing MySQL include folder in XAMPP

I took the following steps after reading suggestions from http://andhikalegawa.wordpress.com/2012/01/05/installing-mysql-python-on-snow-leopard-using-xampp-mysql/
Downloaded MySQL-python-1.2.4b4 and unzipped
Changed the mysql_config = /Applications/XAMPP/xamppfiles/bin/mysql_config (as I am using XAMPP 1.7.3)
Downloaded mysql-5.1.70-osx10.6-x86 (I could not find 5.1.55 which is the version used in XAMPP) kept the include folder at /Applications/XAMPP/xamppfiles/
I am new to development so, downloaded XCode 4.6.3 with command line tools.
Logically it should have worked I am getting the following error
running build
running build_py
copying MySQLdb/release.py -> build/lib.macosx-10.7-intel-2.7/MySQLdb
running build_ext
building '_mysql' extension
creating build/temp.macosx-10.7-intel-2.7
llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -pipe -Dversion_info=(1,2,4,'beta',4) -D_version_=1.2.4b4 -I/Applications/XAMPP/xamppfiles/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _mysql.c -o build/temp.macosx-10.7-intel-2.7/_mysql.o -mmacosx-version-min=10.4 -arch i386 -arch ppc -D_P1003_1B_VISIBLE -DSIGNAL_WITH_VIO_CLOSE -DSIGNALS_DONT_BREAK_READ -DIGNORE_SIGHUP_SIGQUIT -DDONT_DECLARE_CXA_PURE_VIRTUAL
In file included from _mysql.c:44:
/Applications/XAMPP/xamppfiles/include/my_config.h:1088:1: warning: "HAVE_WCSCOLL" redefined
In file included from /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:8,
from _mysql.c:29:
/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/pyconfig.h:891:1: warning: this is the location of the previous definition
llvm-gcc-4.2: error trying to exec '/usr/bin/../llvm-gcc-4.2/bin/powerpc-apple-darwin11-llvm-gcc-4.2': execvp: No such file or directory
lipo: can't figure out the architecture type of: /var/folders/6p/8bxdl12d2nq05dmwbmdzttt40000gn/T//cc0v0ehE.out
error: command 'llvm-gcc-4.2' failed with exit status 255
Looks like it's trying to compile universal for PowerPC, which you probably don't have?
error trying to exec '/usr/bin/../llvm-gcc-4.2/bin/powerpc-apple-darwin11-llvm-gcc-4.2'
I would suggest setting the ARCHFLAGS:
shell> rm -Rf build/
shell> ARCHFLAGS="-arch i386" /usr/bin/python setup.py build
Or instead of i386, on 64-bit x86_64. But since you are downloading 32-bit MySQL, might be good to use i386.
Good luck! (Shameless advert: you can always try MySQL Connector/Python)

gcc cannot find bits/predefs.h on i686

Okay, so, I switched from ubuntu 12.04 64-bit to 32-bit and installed build-essential.
I then compiled and installed GMP-5.0.5, MPFR-3.1.1, MPC-1.0, ISL-0.10 and CLOOG-0.17.0. I checked out a copy of the main gcc trunk and attempted to build it with the following configure line (from a separate directory):
../svnsrc/configure --prefix=/usr/GCC/svn --enable-__cxa_atexit --with-plugin-ld=/usr/bin/ld.gold --enable-threads=posix --enable-werror --enable-build-with-cxx --with-gmp=/usr/GCC/prereq/svn --with-mpfr=/usr/GCC/prereq/svn --with-mpc=/usr/GCC/prereq/svn --with-isl=/usr/GCC/prereq/svn --with-cloog=/usr/GCC/prereq/svn --enable-languages=c,c++
Configure ran fine and so I ran make && make check. This ran fine for a while, but then it failed with the following error:
/home/matt/GCC/svnbuild/./gcc/xgcc -B/home/matt/GCC/svnbuild/./gcc/ -B/usr/GCC/svn/i686-pc-linux-gnu/bin/ -B/usr/GCC/svn/i686-pc-linux-gnu/lib/ -isystem /usr/GCC/svn/i686-pc-linux-gnu/include -isystem /usr/GCC/svn/i686-pc-linux-gnu/sys-include -g -O2 -O2 -g -O2 -DIN_GCC -W -Wall -Wwrite-strings -Wcast-qual -Wstrict-prototypes -Wmissing-prototypes -Wold-style-definition -isystem ./include -fpic -mlong-double-80 -g -DIN_LIBGCC2 -fbuilding-libgcc -fno-stack-protector -fpic -mlong-double-80 -I. -I. -I../.././gcc -I../../../svnsrc/libgcc -I../../../svnsrc/libgcc/. -I../../../svnsrc/libgcc/../gcc -I../../../svnsrc/libgcc/../include -I../../../svnsrc/libgcc/config/libbid -DENABLE_DECIMAL_BID_FORMAT -DHAVE_CC_TLS -DUSE_TLS -o _muldi3.o -MT _muldi3.o -MD -MP -MF _muldi3.dep -DL_muldi3 -c ../../../svnsrc/libgcc/libgcc2.c -fvisibility=hidden -DHIDE_EXPORTS
In file included from /usr/include/stdio.h:28:0,
from ../../../svnsrc/libgcc/../gcc/tsystem.h:88,
from ../../../svnsrc/libgcc/libgcc2.c:29:
/usr/include/features.h:324:26: fatal error: bits/predefs.h: No such file or directory
#include <bits/predefs.h>
^
compilation terminated.
make[3]: *** [_muldi3.o] Error 1
make[3]: Leaving directory `/home/matt/GCC/svnbuild/i686-pc-linux-gnu/libgcc
I looked around, but everything I seemed to find was that this error was caused on x86_64, by not installing gcc-multilib, because Ubuntu and Debian use the mutiarch system, separating the libraries. Okay, fine...but I'm using i686, so why would I need the 64-bit libraries? Any help would be appreciated. Thanks.
Try doing a
sudo apt-get install gcc-multilib
I don't think that installing a 32-bit system changes the architecture of your computer, because your computer will always be a 64-bit machine. Installing the 64-bit version of Ubuntu should only give better multi-core performance. Since your computer is still a 64-bit computer, you probably need a C compiler that will compile on 64-bit machines. Hence the gcc-multilib. I think.
the gcc-multilib trick didn't work out for me. Instead, setting this in the build environment did the trick:
C_INCLUDE_PATH=/usr/include/$(gcc -print-multiarch)

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