I am trying to install a software package called HYPRE on my Macbook (High Sierra 10.13.6). I follow the install instructions, which require me to first navigate to the appropriate folder and type ./configure in the terminal. This generates the error:
checking how to run the C preprocessor... /lib/cpp
configure: error: in /Users/Tilton/FVM/HYPRE/hypre-master/src': configure: error: C preprocessor "/lib/cpp" fails sanity check See config.log' for more details
I searched around and saw some similar error issues reported online, but could not understand the issue. I am happy to share the config.log file, but it's very long ...
Related
I cannot install Xdebug on Homestead because I get some sort of compile error.
I am following the Xdebug Wizard (https://xdebug.org/wizard) and when I input the ./configure command I get this error:
configure: error: in /home/vagrant/code/xdebug-2.7.2:
configure: error: cannot run C compiled programs.
If you meant to cross compile, use '--host'.
See 'config.log' for more details
This points at that you don't have a C compiler installed at all. You will have better luck after installing the php-dev package first, which should pull in the compilers that PHP extensions will need.
I'm trying to upgrade my Vim to MacVim by running:
$ brew install macvim --with--override-system-vim
I'm getting this error message saying that the package cannot be compiled:
configure: creating cache auto/config.cache
checking whether make sets $(MAKE)... yes
checking for gcc... clang
checking whether the C compiler works... no
configure: error: in `/private/tmp/macvim-20161028-10122-1pp1odr/macvim-snapshot-113/src':
configure: error: C compiler cannot create executables
See `config.log' for more details
I have Xcode 8.1 installed on my machine. But brew seems to think it's a pre-release version:
Warning: You are using a pre-release version of Xcode.
You may encounter build failures or other breakages.
Please create pull-requests instead of filing issues.
I have been following the instructions here to compile an avr cross compiler toolchain on my x86 PC. I had to do some searching on the step for compiling gcc because it was complaining about some missing dependencies, turns out there was a a script I could just run which downloaded the pre-requisites.
Now however, I am stuck on the step where I'm supposed to compile avr-libc. I get this error:
blah#blah-computer:~/avr/avr-libc-1.8.0$ ./configure --prefix=$PREFIX --build='./config.guess' --host=avr
checking build system type... Invalid configuration `./config.guess': machine `./config.guess' not recognized
configure: error: /bin/bash ./config.sub ./config.guess failed
From my googling of this problem, it seems there might be something wrong with my installation of autotools, and I actually remember seeing some warning about autotools when I was compiling gcc but as far as I could tell that step was actually successful.
Could anybody give me a good quick explanation of what autotools is and maybe help me fix my problem?
I don't see why you would need to specify --build at all. Just set the environment variable: CC=avr-gcc (the AVR cross compiler), and use --prefix=... and --host=avr as before. AVR-libc will set the CFLAGS to the 'best' values as it builds each ISA version in the multi-lib.
However, if you want to specify --build, use the backtick characters rather than the single-quote characters to execute the script: --build=`./config.guess`
Not sure if this is the correct place for this kind of question. If not, please point me in the right direction.
I'm using OSX 10.5.8 on a white 13" macbook with Xcode 3.1.4. When installing py27-bottleneck through macports, I get the following error
---> Building py27-bottleneck
running build
running build_py
package init file 'bottleneck/tests/__init__.py' not found (or not a regular file)
package init file 'bottleneck/src/func/__init__.py' not found (or not a regular file)
package init file 'bottleneck/src/move/__init__.py' not found (or not a regular file)
package init file 'bottleneck/tests/__init__.py' not found (or not a regular file)
package init file 'bottleneck/src/func/__init__.py' not found (or not a regular file)
package init file 'bottleneck/src/move/__init__.py' not found (or not a regular file)
running build_ext
building 'func' extension
/usr/bin/gcc-4.2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c bottleneck/src/func/func.c -o build/temp.macosx-10.5-i386-2.7/bottleneck/src/func/func.o
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760,
from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from bottleneck/src/func/func.c:314:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:242: warning: ?_import_umath? defined but not used
cc1(53864) malloc: *** mmap(size=298745856) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
cc1: out of memory allocating 298742336 bytes after a total of 0 bytes
error: command '/usr/bin/gcc-4.2' failed with exit status 1
Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py-bottleneck/py27-bottleneck/work/Bottleneck-0.8.0" && /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 setup.py --no-user-cfg build
Exit code: 1
Error: org.macports.build for port py27-bottleneck returned: command execution failed
Warning: targets not executed for py27-bottleneck: org.macports.activate org.macports.build org.macports.destroot org.macports.install
Please see the log file for port py27-bottleneck for details:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py-bottleneck/py27-bottleneck/main.log
Error: Problem while installing py27-bottleneck
I don't really know what the problem is and why this had happened, but what I noticed was that macports is still using an old compiler.
So does anybody know how I can fix this problem?
Also, why is macports still using gcc-4.2, while I have all my symlinks pointing at /opt/local/bin/gcc-mp-4.8. I remember having this problem earlier with installing some other python packages (or maybe it was this one, I don't remember), so I forced macports to use the newer compiler by changing the makefile and it worked temporarily. Until I started upgrading my outdated ports. Obviously now macports encountered linking errors and just reinstalled the all those packages (this is where I am now). So why does macports not just use the newer compiler? Or how can I make him do this? (maybe I shouldn't?)
Any help is appreciated. Thanks.
On 10.5.8 with Xcode 3.1.4 MacPorts uses the following compilers (in-order, unless blacklisted by ports because known to break):
GCC 4.2 from /usr/bin
A MacPorts build of the same compiler (with a few minor bugfixes)
GCC 4.0 from /usr/bin
Clang 3.3 from MacPorts
It seems this port should be blacklisting GCC 4.2 (and probably 2. and 3., too). You could file that as a bug, but to be honest, support for 10.5 is only given on a best-effort basis because most maintainers can't test on this platform anymore, so that's probably not getting you anywhere unless you provide a patch with your report.
You could override the compiler from command line like you did before. To stop rev-upgrade from immediately starting rebuilds, you can set revupgrade_mode report in your macports.conf. I'd have to see the output of port -dy rev-upgrade when it encounters broken ports to know why it produces broken binaries.
It has already been mentioned that the select mechanism doesn't affect which compilers MacPorts chooses for its ports (because depending on what's selected by the user would add another variable that might make builds unreproducible, which is something we're trying to avoid). MacPorts' default compilers can be changed, but doing so is completely unsupported and deliberately undocumented. That being said, if you still want to attempt this, https://apple.stackexchange.com/questions/118550/define-local-keyword-globally-in-a-macports-config/122997#122997 has some info on how to do that.
I am trying to install the R library BRugs on my Ubuntu 12.04 desktop.
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
But I get the following error:
* installing *source* package ‘BRugs’ ...
** package ‘BRugs’ successfully unpacked and MD5 sums checked
checking for prefix by checking for OpenBUGS... /usr/bin/OpenBUGS
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/tmp/RtmpnNLTG1/R.INSTALL488b7635d4c0/BRugs':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘BRugs’
* removing ‘/home/myuser/lib/R/BRugs’
Warning in install.packages("BRugs") :
installation of package ‘BRugs’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp2ytOWn/downloaded_packages’
Here is a link to config.log. It is difficult to tell what the error is, except that the errors starts with gcc: error: unrecognized option '-V'.
How can I get around this error (and install BRugs)?
According to the package description:
Versions running on Linux and on 64-bit R under Windows are in "beta"
status and less efficient.
And it looks like configure is trying to build the package using 32-bit executables (note the -m32 flags). It's probably best if you contact the package maintainer(s) and ask them how to build the 32-bit executable under 64-bit Ubuntu.