Apache Thrift installation failed on AIX7.2 server - gcc

Somehow, there is no "Issues" tab available at "https://github.com/apache/thrift" so I will ask question here to see if someone can help me with Apache Thrift installation issue.
I tried to following the instruction of Apache Thrift installation on my AIX7.2 server. ./bootstrap.sh step has been finished without issue. Although there are some fatal errors in ./configure --with-boost=/usr/local step, the last line of config.log file shows configure: exit 0 so I would expect the configure step is ok. My issue is the make step. It failed with the following error:
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I/usr/local/include -I/usr/include -I./src -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -Wall -Wextra -pedantic -g -O2 -MT src/thrift/TApplicationException.lo -MD -MP -MF src/thrift/.deps/TApplicationException.Tpo -c src/thrift/TApplicationException.cpp -fPIC -DPIC -o src/thrift/.libs/TApplicationException.o
In file included from /opt/freeware/lib/gcc/powerpc-ibm-aix7.2.0.0/8.3.0/include/c++/ext/string_conversions.h:41,
from /opt/freeware/lib/gcc/powerpc-ibm-aix7.2.0.0/8.3.0/include/c++/bits/basic_string.h:6400,
from /opt/freeware/lib/gcc/powerpc-ibm-aix7.2.0.0/8.3.0/include/c++/string:52,
from ./src/thrift/Thrift.h:37,
from ./src/thrift/TApplicationException.h:23,
from src/thrift/TApplicationException.cpp:20:
/opt/freeware/lib/gcc/powerpc-ibm-aix7.2.0.0/8.3.0/include/c++/cstdlib:151:11: error: '::malloc' has not been declared
using ::malloc;
^~~~~~
/opt/freeware/lib/gcc/powerpc-ibm-aix7.2.0.0/8.3.0/include/c++/cstdlib:164:11: error: '::realloc' has not been declared
using ::realloc;
^~~~~~~
As far as I can see, line 151 & line 164 in /opt/freeware/lib/gcc/powerpc-ibm-aix7.2.0.0/8.3.0/include/c++/cstdlib have using ::malloc; and using ::realloc; along with lots of other using statements. Below is copied from line 151 to line 164.
using ::malloc;
#ifdef _GLIBCXX_HAVE_MBSTATE_T
using ::mblen;
using ::mbstowcs;
using ::mbtowc;
#endif // _GLIBCXX_HAVE_MBSTATE_T
using ::qsort;
#if __cplusplus >= 201103L
# ifdef _GLIBCXX_HAVE_QUICK_EXIT
using ::quick_exit;
# endif
#endif
using ::rand;
using ::realloc;
What's wrong with it and how to fix it?
Thanks.

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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).

yocto: failing to find Python.h and cross compiling fails

Im using poky version of yocto, and adding zbar library in my yocto build. I found a readymade recipe at http://cgit.openembedded.org/meta-openembedded/tree/meta-oe/recipes-support/zbar/zbar_0.10.bb and modified it a bit to get working with poky. I got it working fine with imagemagick, and the compiled zbarimg works on the target board.
The modified recipe is available here: http://paste.ubuntu.com/25725000/
When I proceed configuring python support (--with-python) to the build, some dependency issues crept up, which Im unable to resolve.
It appears as if the compiler doesn't find the appropriate headers, since the include paths don't contain appropriate folder.
The full compiler command is:
arm-poky-linux-gnueabi-libtool: compile: arm-poky-linux-gnueabi-gcc -march=armv7-a -mfloat-abi=hard -mfpu=neon -mtune=cortex-a7 --sysroot=/home/jlumme/imx_build/build-x11-pico-imx6ul/tmp/sysroots/pico-imx6ul-emmc -DHAVE_CONFIG_H -I. -I/home/jlumme/imx_build/build-x11-pico-imx6ul/tmp/work/cortexa7hf-vfp-neon-poky-linux-gnueabi/zbar/0.10-r0/zbar-0.10 -I./include -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -I/usr/include/python2.7 -I/usr/include/python2.7 -I/home/jlumme/imx_build/build-x11-pico-imx6ul/tmp/work/cortexa7hf-vfp-neon-poky-linux-gnueabi/zbar/0.10-r0/zbar-0.10/include -Wall -Wno-parentheses -O2 -pipe -g -feliminate-unused-debug-types -c /home/jlumme/imx_build/build-x11-pico-imx6ul/tmp/work/cortexa7hf-vfp-neon-poky-linux-gnueabi/zbar/0.10-r0/zbar-0.10/python/symbol.c -fPIC -DPIC -o python/.libs/python_zbar_la-symbol.o
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There is a warning from compiler: cc1: warning: include location "/usr/include/python2.7" is unsafe for cross-compilation [-Wpoison-system-directories] which I don't know why it happens, but it seems like the python2.7 folder is appropriately looked at, just not under the sysroot (my host system doesn't have /usr/lib/python2.7)
If I go to the sysroot include (/home/jlumme/imx_build/build-x11-pico-imx6ul/tmp/sysroots/pico-imx6ul-emmc/usr/include/) folder, I can see that it has a subfolder python2.7. If under this usr/include folder I add a symlink Python.h -> python2.7/Python.h, the compiler will complain about the next header file which is not found.
So to me it seems, all I should do is add the appropriate 'sysroot' + usr/include/python2.7 as include search folder it would compile happily - but Im not sure how..
The full compilation log is available here: http://paste.ubuntu.com/25725014/
This is a bug in the zbar configure script.
Try inheriting pythonnative so the configure script can run a compatible Python to know where to look.

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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:
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Build again

ld cannot find -l<library>

I am having trouble installing pyipopt on ubuntu 12.04. During linking, I receive the error:
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Even though I know that this library is installed and the .so and .la files are available in /home/mostafa/MyBuilds/CoinIpopt/build/lib/
does anyone have a solution for this?
below is the complete return of running setup.py build:
root#ubuntu:~/MyBuilds/pyipopt# sudo python setup.py build
running build
running build_ext
building 'pyipopt' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/home/mostafa/MyBuilds/CoinIpopt/build/include/coin/ -I/usr/include/python2.7 -c src/callback.c -o build/temp.linux-x86_64-2.7/src/callback.o
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/home/mostafa/MyBuilds/CoinIpopt/build/include/coin/ -I/usr/include/python2.7 -c src/pyipopt.c -o build/temp.linux-x86_64-2.7/src/pyipopt.o
src/pyipopt.c: In function ‘set_intermediate_callback’:
src/pyipopt.c:452:15: warning: variable ‘myowndata’ set but not used [-Wunused-but-set-variable]
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relrobuild/temp.linux-x86_64-2.7/src/callback.o build/temp.linux-x86_64-2.7/src/pyipopt.o -L/home/mostafa/MyBuilds/CoinIpopt/build/lib/ -lipopt -lblas -lcoinhsl -lcoinmetis -llapack -ldl -lm -o build/lib.linux-x86_64-2.7/pyipopt.so -Wl,--rpath -Wl,/home/mostafa/MyBuilds/CoinIpopt/build/lib/
/usr/bin/ld: cannot find -lcoinhsl
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
-Ldir
Add directory dir to the list of directories to be searched for -l.
You may install your coinhsl library in one of your standard libraries directories and run 'ldconfig` before doing your ppyipopt install
I had a similar problem with another library and the reason why it didn't found it, was that I didn't run the make install (after running ./configure and make) for that library. The make install may require root privileges (in this case use: sudo make install). After running the make install you should have the so files in the correct folder, i.e. here /usr/local/lib and not in the folder mentioned by you.
you can add the Path to coinhsl lib to LD_LIBRARY_PATH variable. May be that will help.
export LD_LIBRARY_PATH=/xx/yy/zz:$LD_LIBRARY_PATH
where /xx/yy/zz represent the path to coinhsl lib.

Having difficulty to install git using Homebrew

I am watching this video to install git using Homebrew. I already got Homebrew installed. The problem i have is installing git using Homebrew. I typed brew install git and have certain error message.
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./generate-cmdlist.sh > common-cmds.h+ && mv common-cmds.h+ common-cmds.h
/usr/bin/xcrun clang -o hex.o -c -MF ./.depend/hex.o.d -MMD -MP -Os -w -pipe -march=native -Qunused-arguments -I. -DUSE_ST_TIMESPEC -DNO_GETTEXT -DHAVE_DEV_TTY -DSHA1_HEADER='<openssl/sha.h>' -DNO_MEMMEM hex.c
/usr/bin/xcrun clang -o ident.o -c -MF ./.depend/ident.o.d -MMD -MP -Os -w -pipe -march=native -Qunused-arguments -I. -DUSE_ST_TIMESPEC -DNO_GETTEXT -DHAVE_DEV_TTY -DSHA1_HEADER='<openssl/sha.h>' -DNO_MEMMEM ident.c
/usr/bin/xcrun clang -o kwset.o -c -MF ./.depend/kwset.o.d -MMD -MP -Os -w -pipe -march=native -Qunused-arguments -I. -DUSE_ST_TIMESPEC -DNO_GETTEXT -DHAVE_DEV_TTY -DSHA1_HEADER='<openssl/sha.h>' -DNO_MEMMEM kwset.c
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In file included from ./cache.h:4:
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#include <unistd.h>
^
In file included from hex.c:1:
In file included from ./cache.h:4:
./git-compat-util.h:93:10: fatal error: 'unistd.h' file not found
#include <unistd.h>
^
In file included from kwset.c:37:
In file included from ./cache.h:4:
./git-compat-util.h:93:10: fatal error: 'unistd.h' file not found
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1 error generated.
make: *** [hex.o] Error 1
1 error generated.
make: *** Waiting for unfinished jobs....
make: *** [ident.o] Error 1
1 error generated.
make: *** [kwset.o] Error 1
==> Build Environment
CPU: quad-core 64-bit sandybridge
MacOS: 10.7.4-x86_64
Xcode: 4.3.2
CC: /usr/bin/xcrun clang => /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang
CXX: /usr/bin/xcrun clang++ => /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
LD: /usr/bin/xcrun clang => /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang
CFLAGS: -Os -w -pipe -march=native -Qunused-arguments
CXXFLAGS: -Os -w -pipe -march=native -Qunused-arguments
MAKEFLAGS: -j4
Error: Failed executing: make prefix=/usr/local/Cellar/git/1.7.10.3 CC=/usr/bin/xcrun\ clang CFLAGS=-Os\ -w\ -pipe\ -march=native\ -Qunused-arguments LDFLAGS= install (git.rb:49)
These existing issues may help you:
https://github.com/mxcl/homebrew/issues/8643
https://github.com/mxcl/homebrew/issues/9023
https://github.com/mxcl/homebrew/issues/9618
https://github.com/mxcl/homebrew/issues/10544
https://github.com/mxcl/homebrew/issues/11481
https://github.com/mxcl/homebrew/issues/12325
https://github.com/mxcl/homebrew/issues/12344
https://github.com/mxcl/homebrew/issues/12400
https://github.com/mxcl/homebrew/issues/12478
Otherwise, please report the bug:
https://github.com/mxcl/homebrew/wiki/reporting-bugs
How do i solve this error? Need some help
You must install the command-line tools through Xcode to get the needed headers.
I suggest you to download it. Also, if you use github, I suggest you to just read this page. One year ago I started in this way.

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