I am trying to install biogrinder on my macOS Monterey, which needs some perl modules.
All necessary modules are installed except Math::Random::MT
When trying to install this module using the following command:
sudo cpan install Math::Random::MT
I get the following error
Loading internal null logger. Install Log::Log4perl for logging messages
CPAN: Storable loaded ok (v2.62)
Reading '/Users/imac/.cpan/Metadata'
Database was generated on Mon, 17 Oct 2022 13:29:01 GMT
Running install for module 'Math::Random::MT'
CPAN: Digest::SHA loaded ok (v5.96)
CPAN: Compress::Zlib loaded ok (v2.074)
Checksum for /Users/imac/.cpan/sources/authors/id/F/FA/FANGLY/Math-Random-MT-1.17.tar.gz ok
CPAN: YAML loaded ok (v1.30)
CPAN: CPAN::Meta::Requirements loaded ok (v2.140)
CPAN: Parse::CPAN::Meta loaded ok (v2.150010)
CPAN: CPAN::Meta loaded ok (v2.150010)
CPAN: Module::CoreList loaded ok (v5.20180414_26)
Configuring F/FA/FANGLY/Math-Random-MT-1.17.tar.gz with Makefile.PL
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Math::Random::MT
Writing MYMETA.yml and MYMETA.json
FANGLY/Math-Random-MT-1.17.tar.gz
/Users/imac/opt/anaconda3/bin/perl Makefile.PL -- OK
Running make for F/FA/FANGLY/Math-Random-MT-1.17.tar.gz
cp MT.pm blib/lib/Math/Random/MT.pm
Running Mkbootstrap for MT ()
chmod 644 "MT.bs"
"/Users/imac/opt/anaconda3/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- MT.bs blib/arch/auto/Math/Random/MT/MT.bs 644
"/Users/imac/opt/anaconda3/bin/perl" "/Users/imac/opt/anaconda3/lib/5.26.2/ExtUtils/xsubpp" -typemap '/Users/imac/opt/anaconda3/lib/5.26.2/ExtUtils/typemap' -typemap '/Users/imac/.cpan/build/Math-Random-MT-1.17-48/typemap' MT.xs > MT.xsc
mv MT.xsc MT.c
x86_64-apple-darwin13.4.0-clang -c -fno-common -DPERL_DARWIN -no-cpp-precomp -mmacosx-version-min=10.9 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -O3 -DVERSION=\"1.17\" -DXS_VERSION=\"1.17\" -fPIC --sysroot=/Applications/Xcode_12.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk "-I/Users/imac/opt/anaconda3/lib/5.26.2/darwin-thread-multi-2level/CORE" MT.c
In file included from MT.xs:2:
/Users/imac/opt/anaconda3/lib/5.26.2/darwin-thread-multi-2level/CORE/perl.h:694:10: fatal error: 'sys/types.h' file not found
#include <sys/types.h>
^~~~~~~~~~~~~
1 error generated.
make: *** [MT.o] Error 1
FANGLY/Math-Random-MT-1.17.tar.gz
/usr/bin/make -- NOT OK
My perl version is:
perl --version
This is perl 5, version 26, subversion 2 (v5.26.2) built for darwin-thread-multi-2level
Copyright 1987-2018, Larry Wall
Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.
Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl". If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.
What doesn't look Okay, is that I don't have /usr/include folder on my machine, instead the types.h file is located in /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/sys/types.h
PS: I already installed Bio:SeqIO module using the exact same command and it worked.
Any idea on how to get over this issue ?
Many thanks
Related
I've been successfully using XML::LibXML module for a while on macOS.
Now I am trying to install it on a new machine with macOS BigSur:
perl Makefile.PL
make
make test
make install
However, in "make test" I get multiple errors of the kind:
t/00-report-prereqs.t .............................. ok
t/01basic.t ........................................
Can't load '/Users/lockit/Desktop/TESTS_Irina/XML-LibXML-2.0204/blib/arch/auto/XML/LibXML/LibXML.bundle'
for module XML::LibXML: dlopen(/Users/lockit/Desktop/TESTS_Irina/XML-LibXML-2.0204/blib/arch/auto/XML/LibXML/LibXML.bundle, 0x0002):
symbol '_xmlFree' not found, expected in flat namespace by
'/Users/lockit/Desktop/TESTS_Irina/XML-LibXML-2.0204/blib/arch/auto/XML/LibXML/LibXML.bundle'
at /System/Library/Perl/5.28/darwin-thread-multi-2level/DynaLoader.pm line 197.
at /Users/lockit/Desktop/TESTS_Irina/XML-LibXML-2.0204/blib/lib/XML/LibXML.pm line 156.
BEGIN failed--compilation aborted
at /Users/lockit/Desktop/TESTS_Irina/XML-LibXML-2.0204/blib/lib/XML/LibXML.pm line 156.
Compilation failed in require at t/01basic.t line 6.
And the module cannot be installed.
Any hints what I am missing and how to fix?
Thanks,
Irina
Have you read the README for the module? It includes the following:
DEPENDENCIES
============
Prior to installation you MUST have installed the libxml2 library. You can get the
latest libxml2 version from
http://xmlsoft.org/
Without libxml2 installed this module will neither build nor run.
Also XML::LibXML requires the following packages:
o XML::SAX - base class for SAX parsers
o XML::NamespaceSupport - namespace support for SAX parsers
These packages are required. If one is missing some tests will fail.
Again, libxml2 is required to make XML::LibXML work. The library is not just required
to build XML::LibXML, it has to be accessible during run-time as well. Because of
this you need to make sure libxml2 is installed properly. To test this, run the
xmllint program on your system. xmllint is shipped with libxml2 and therefore should
be available. For building the module you will also need the header file for libxml2,
which in binary (.rpm,.deb) etc. distributions usually dwell in a package named
libxml2-devel or similar.
So you need to have libxml2 (and its development header files) installed on your system.
Looks like it's an issue with Apple's dynamic linker as described here:
https://github.com/Perl-Toolchain-Gang/ExtUtils-MakeMaker/issues/381.
I installed the suggested ExtUtils-MakeMaker-7.58 module and this solved the initial issue.
However, now there is a new error on make:
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- LibXML.bs blib/arch/auto/XML/LibXML/LibXML.bs 644
cc -c -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -g -pipe -fno-strict-aliasing -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -Wno-error=implicit-function-declaration -Os -DVERSION="2.0206" -DXS_VERSION="2.0206" "-I/System/Library/Perl/5.28/darwin-thread-multi-2level/CORE" -DHAVE_UTF8 Av_CharPtrPtr.c
Av_CharPtrPtr.c:6:10: fatal error: 'EXTERN.h' file not found
#include "EXTERN.h"
Any clue?
When trying to install Crypt::SSLeay on Mac OS X I get the following error:
$ sudo perl -MCPAN -e shell
cpan[1]> install Crypt::SSLeay
Reading '/Users/.cpan/Metadata'
Database was generated on Thu, 26 Oct 2017 01:53:54 GMT
Running install for module 'Crypt::SSLeay'
Running make for N/NA/NANIS/Crypt-SSLeay-0.72.tar.gz
Checksum for /Users/.cpan/sources/authors/id/N/NA/NANIS/Crypt-SSLeay-0.72.tar.gz ok
Scanning cache /Users/.cpan/build for sizes
............................................................................DONE
CPAN.pm: Building N/NA/NANIS/Crypt-SSLeay-0.72.tar.gz
Cannot link with any of the requested SSL libraries 'ssl, crypto, ssl32, ssleay32, eay32, libeay32, z'
No 'Makefile' created'YAML' not installed, will not store persistent state
NANIS/Crypt-SSLeay-0.72.tar.gz
/usr/bin/perl Makefile.PL -- NOT OK
Running make test
Make had some problems, won't test
Running make install
Make had some problems, won't install
Could not read metadata file. Falling back to other methods to determine prerequisites
Failed during this command:
NANIS/Crypt-SSLeay-0.72.tar.gz : writemakefile NO -- No 'Makefile' created
I have installed openssl as per the instructions found here and the output of openssl version -a is:
OpenSSL 1.1.0f 25 May 2017
built on: reproducible build, date unspecified
platform: darwin64-x86_64-cc
compiler: cc -DDSO_DLFCN -DHAVE_DLFCN_H -DNDEBUG -DOPENSSL_THREADS -DOPENSSL_NO_STATIC_ENGINE -DOPENSSL_PIC -DOPENSSL_IA32_SSE2 -DOPENSSL_BN_ASM_MONT -DOPENSSL_BN_ASM_MONT5 -DOPENSSL_BN_ASM_GF2m -DSHA1_ASM -DSHA256_ASM -DSHA512_ASM -DRC4_ASM -DMD5_ASM -DAES_ASM -DVPAES_ASM -DBSAES_ASM -DGHASH_ASM -DECP_NISTZ256_ASM -DPADLOCK_ASM -DPOLY1305_ASM -DOPENSSLDIR="\"/usr/local/mac-dev-env/openssl-1.1.0f/ssl\"" -DENGINESDIR="\"/usr/local/mac-dev-env/openssl-1.1.0f/lib/engines-1.1\""
OPENSSLDIR: "/usr/local/mac-dev-env/openssl-1.1.0f/ssl"
ENGINESDIR: "/usr/local/mac-dev-env/openssl-1.1.0f/lib/engines-1.1"
I'm not sure what else I can do, as I have the ssl library required but it doesn't seem to link it?
OPENSSLDIR: "/usr/local/mac-dev-env/openssl-1.1.0f/ssl"
This is not a standard location for openssl. Which explains why it cannot find the necessary files:
Cannot link with any of the requested SSL libraries 'ssl, crypto, ssl32, ssleay32, eay32, libeay32, z'
When looking at the README for Crypt::SSLeay you will find:
If you have OpenSSL headers and libraries in nonstandard locations, you can use
$ perl Makefile.PL --incpath=... --libpath=...
There are further instructions in the README how to set the path when using cpanm etc.
Apart from that, in most cases you don't want to install Crypt::SSLeay but instead Net::SSLeay. Crypt::SSLeay is only supported to keep older versions of LWP working, all newer things (including current versions of LWP) use Net::SSLeay and IO::Socket::SSL on top of Net::SSLeay.
If this is related to installing LWP::Protocol::https , because you wanted to use LWP::UserAgent ... you will be bettor off installing: IO::Socket::SSL instead off aforementioned Crypt::SSLeay
As stated above, in README it's mentioned "--incpath" and "--libpath" to use custom paths to your openssl instalation.
So it should be something like this (Note:check your openssl version, in this example it's 1.1.1d):
$ sudo perl Makefile.PL --incpath="/usr/local/Cellar/openssl#1.1/1.1.1d/include" --libpath="/usr/local/Cellar/openssl#1.1/1.1.1d/lib"
I struggled to understand what path should be used on those parameters. Those worked though.
I want to install perl Gtk2, and for this I need first to have Glib installed. I tried sudo cpanm Glib, but I get an error when compiling (I also tried downloading the .tar.gz source etc., with the same effect). I also tried with an older version of Glib. I’m on OS X 10.11 (El Capitan). Here’s the error :
error: '_GStaticAssertCompileTimeAssertion_0' declared as an array with a negative size
I don’t know how to fix it… Thanks a lot if anyone can do something for me !
(BTW, brew install glib works fine, but it seems the app that I’m trying to build and run — auto-multiple-choice, for instance — is looking for a Gtk2.pm somewhere. So, the ‘glib’ installed by Homebrew is of no help.)
Benjamin
p.-s. : below is the complete log, if it helps :
cpanm (App::cpanminus) 1.7042 on perl 5.018002 built for darwin-thread-multi-2level
Work directory is /Users/benjamin/.cpanm/work/1474765262.7331
You have make /usr/bin/make
You have LWP 6.05
You have /usr/bin/tar: bsdtar 2.8.3 - libarchive 2.8.3
You have /usr/bin/unzip
Searching Glib () on cpanmetadb ...
--> Working on Glib
Fetching http://www.cpan.org/authors/id/X/XA/XAOC/Glib-1.322.tar.gz
-> OK
Unpacking Glib-1.322.tar.gz
Entering Glib-1.322
Checking configure dependencies from META.json
Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (6.66)
Checking if you have ExtUtils::PkgConfig 1.000 ... Yes (1.15)
Checking if you have ExtUtils::Depends 0.300 ... Yes (0.306)
Configuring Glib-1.322
Running Makefile.PL
Including generated API documentation...
Checking if your kit is complete...
Looks good
Writing Makefile for Glib
Writing MYMETA.yml and MYMETA.json
-> OK
Checking dependencies from MYMETA.json ...
Checking if you have ExtUtils::Depends 0.300 ... Yes (0.306)
Checking if you have ExtUtils::PkgConfig 1.000 ... Yes (1.15)
Checking if you have ExtUtils::MakeMaker 0 ... Yes (6.66)
Building and testing Glib-1.322
cp lib/Glib/CodeGen.pm blib/lib/Glib/CodeGen.pm
cp /Users/benjamin/.cpanm/work/1474765262.7331/Glib-1.322/typemap blib/arch/Glib/Install/typemap
cp lib/Glib/ParseXSDoc.pm blib/lib/Glib/ParseXSDoc.pm
cp doctypes blib/arch/Glib/Install/doctypes
cp devel.pod blib/lib/Glib/devel.pod
cp gperl_marshal.h blib/arch/Glib/Install/gperl_marshal.h
cp lib/Glib/MakeHelper.pm blib/lib/Glib/MakeHelper.pm
cp gperl.h blib/arch/Glib/Install/gperl.h
cp lib/Glib.pm blib/lib/Glib.pm
cp lib/Glib/Object/Subclass.pm blib/lib/Glib/Object/Subclass.pm
cp build/IFiles.pm blib/arch/Glib/Install/Files.pm
cp lib/Glib/GenPod.pm blib/lib/Glib/GenPod.pm
[ XS Glib.xs ]
[ CC Glib.c ]
In file included from Glib.xs:22:
In file included from ./gperl.h:37:
In file included from /usr/local/Cellar/glib/2.48.2/include/glib-2.0/glib-object.h:23:
In file included from /usr/local/Cellar/glib/2.48.2/include/glib-2.0/gobject/gbinding.h:28:
In file included from /usr/local/Cellar/glib/2.48.2/include/glib-2.0/glib.h:30:
In file included from /usr/local/Cellar/glib/2.48.2/include/glib-2.0/glib/galloca.h:32:
/usr/local/Cellar/glib/2.48.2/include/glib-2.0/glib/gtypes.h:422:3: error: '_GStaticAssertCompileTimeAssertion_0' declared as an array with a negative size
G_STATIC_ASSERT(sizeof (unsigned long long) == sizeof (guint64));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/glib/2.48.2/include/glib-2.0/glib/gmacros.h:232:103: note: expanded from macro 'G_STATIC_ASSERT'
#define G_STATIC_ASSERT(expr) typedef char G_PASTE (_GStaticAssertCompileTimeAssertion_, __COUNTER__)[(expr) ? 1 : -1] G_GNUC_UNUSED
^~~~~~~~~~~~~~~
1 error generated.
make: *** [Glib.o] Error 1
-> FAIL Installing Glib failed. See
/Users/benjamin/.cpanm/work/1474765262.7331/build.log for details. Retry with --force to force install it.
This was posted to a GitHub issue.
I tracked down the problem by running:
cpanm --verbose --build-args=NOECHO=' ' Glib
so that I could see the specific compilation command that failed:
cc -c -I. -I/usr/local/Cellar/glib/2.50.0/include/glib-2.0 -I/usr/local/Cellar/glib/2.50.0/lib/glib-2.0/include -I/usr/local/opt/gettext/include -I/usr/local/Cellar/pcre/8.39/include -D_REENTRANT -arch x86_64 -arch i386 -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector -Os -DVERSION=\"1.323\" -DXS_VERSION=\"1.323\" -o Glib.o "-I/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE" Glib.c
Since the problem was something to do with mismatching sizeof's, I figured that the problem was that the architecture that Perl was building with does not the architecture that Homebrew's libglib-2.0 was built against.
The fix is to specify that you only want to build for x86_64 by setting the ARCHFLAGS environment variable:
ARCHFLAGS="-arch x86_64" cpanm --verbose Glib
This is all using the system Perl. If you want the install to work in the long run across system upgrades, you will want to install your own user Perl using either perlbrew or plenv.
I ran into the same issue.
Installing gtk+ as a prerequisite fixed it.
I am attempting to install the Perl package Math::GMP on OS X El Capitan.
I had one computer where this worked without issue - but a second computer is running into the following problem:
The Perl module Math::GMP requires the C library for GMP, so I have done a brew install gmp
This installed GMP including the following file:
/usr/local/include/gmp.h
But the package install still fails claiming I don't have gmp installed:
$ sudo perl -MCPAN -e shell
cpan[1]> install Math::GMP
Reading '/Users/chaosadmin/.cpan/Metadata'
Database was generated on Sat, 14 Nov 2015 09:17:02 GMT
Running install for module 'Math::GMP'
Checksum for /Users/me/.cpan/sources/authors/id/S/SH/SHLOMIF/Math-GMP-2.11.tar.gz ok
Scanning cache /Users/me/.cpan/build for sizes
............................................................................DONE
'YAML' not installed, will not store persistent state
Configuring S/SH/SHLOMIF/Math-GMP-2.11.tar.gz with Makefile.PL
Can't link/include C library 'gmp.h', 'gmp', aborting.
No 'Makefile' created SHLOMIF/Math-GMP-2.11.tar.gz
/usr/bin/perl Makefile.PL -- NOT OK
Failed during this command:
SHLOMIF/Math-GMP-2.11.tar.gz : writemakefile NO -- No 'Makefile' created
The obvious line is:
Can't link/include C library 'gmp.h', 'gmp', aborting.
But I definitely have "gmp.h" installed in /usr/local/include/gmp.h
I'm unsure why it's failing to install on this OS X El Capitan machine (it worked fine on my other one).
In the CPAN shell I used:
look Math::GMP
And updated the Makefile.PL to debug:
check_lib_or_exit(
header => 'gmp.h',
lib => 'gmp',
debug => 'true'
);
Which displayed the following error when running perl Makefile.PL
# /usr/bin/cc -arch i386 -arch x86_64 -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector -arch i386 -arch x86_64 -fstack-protector assertlibD4RJzZEa.c -o assertlibwGFzIVsM
assertlibD4RJzZEa.c:1:10: fatal error: 'gmp.h' file not found
include
On Centos :
Just install this : yum install gmp* -y
Good Luck :)
I've worked on this problem for a few days and couldn't find any solution even after reading several other blogs.
Whenever I try to install modules using CPAN, these installs fail since 'make' errors.
cpan[1]> install Clone
CPAN: Storable loaded ok (v2.18)
Reading '/Users/erikhanschen/.cpan/Metadata'
Database was generated on Wed, 11 Jun 2014 12:06:12 GMT
CPAN: YAML loaded ok (v0.92)
CPAN: Time::HiRes loaded ok (v1.9711)
Reading 49 yaml files from /Users/erikhanschen/.cpan/build/
DONE
Restored the state of none (in 1.7859 secs)
Running install for module 'Clone'
GARU/Clone-0.37.tar.gz
Has already been unwrapped into directory /Users/erikhanschen/.cpan/build/Clone-0.37-F3R5u0
GARU/Clone-0.37.tar.gz
Has already been prepared
GARU/Clone-0.37.tar.gz
Could not make: Unknown error
CPAN: CPAN::Meta loaded ok (v2.120351)
cpan[2]>
After I had to replaced my hard drive recently, I had to re-install Xcode but even after that, the make command didn't work. Uninstalling Xcode and installing GCC compiler instead didn't help. make is in /usr/bin/ and that directory is in my PATH, and make and GCC run when run without arguments, but the CPAN installer still can't find it when I'm trying to install a module.
After removing the contents of the CPAN build directory, trying to install a module still crashes at "make".
cpan[2]> install Clone
Running install for module 'Clone'
CPAN: Digest::SHA loaded ok (v5.45)
CPAN: Compress::Zlib loaded ok (v2.008)
Checksum for /Users/erikhanschen/.cpan/sources/authors/id/G/GA/GARU/Clone- 0.37.tar.gz ok
Scanning cache /Users/erikhanschen/.cpan/build for sizes
DONE
CPAN: Archive::Tar loaded ok (v1.96)
x Clone-0.37/
x Clone-0.37/Changes
x Clone-0.37/Clone.pm
x Clone-0.37/Clone.xs
x Clone-0.37/Makefile.PL
x Clone-0.37/MANIFEST
x Clone-0.37/META.json
x Clone-0.37/META.yml
x Clone-0.37/README
x Clone-0.37/t/
x Clone-0.37/t/01array.t
x Clone-0.37/t/02hash.t
x Clone-0.37/t/03scalar.t
x Clone-0.37/t/04tie.t
x Clone-0.37/t/05dtype.t
x Clone-0.37/t/06refcnt.t
x Clone-0.37/t/07magic.t
x Clone-0.37/t/08fieldhash.t
x Clone-0.37/t/dclone.t
x Clone-0.37/t/dump.pl
x Clone-0.37/t/tied.pl
CPAN: File::Temp loaded ok (v0.2304)
CPAN: Module::CoreList loaded ok (v2.13)
Configuring G/GA/GARU/Clone-0.37.tar.gz with Makefile.PL
Checking if your kit is complete...
Looks good
'EXPATINCPATH' is not a known MakeMaker parameter name.
'EXPATLIBPATH' is not a known MakeMaker parameter name.
Generating a Unix-style Makefile
Writing Makefile for Clone
Writing MYMETA.yml and MYMETA.json
GARU/Clone-0.37.tar.gz
/usr/bin/perl Makefile.PL EXPATLIBPATH=/non-standard/lib EXPATINCPATH=/non-standard/include -- OK
Running make for G/GA/GARU/Clone-0.37.tar.gz
cp Clone.pm blib/lib/Clone.pm
AutoSplitting blib/lib/Clone.pm (blib/lib/auto/Clone)
Running Mkbootstrap for Clone ()
chmod 644 Clone.bs
/usr/bin/perl /Library/Perl/Updates/5.10.0/ExtUtils/xsubpp -typemap /System/Library/Perl/5.10.0/ExtUtils/typemap Clone.xs > Clone.xsc && mv Clone.xsc Clone.c
gcc-4.2 -c -arch x86_64 -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -O3 -DVERSION=\"0.37\" -DXS_VERSION=\"0.37\" "- I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE" Clone.c
/usr/libexec/gcc/powerpc-apple-darwin10/4.2.1/as: assembler (/usr/bin/../libexec/gcc/darwin/ppc/as or /usr/bin/../local/libexec/gcc/darwin/ppc/as) for architecture ppc not installed
Installed assemblers are:
/usr/bin/../libexec/gcc/darwin/x86_64/as for architecture x86_64
/usr/bin/../libexec/gcc/darwin/i386/as for architecture i386
lipo: can't open input file: /var/tmp//cc23LjqR.out (No such file or directory)
make: *** [Clone.o] Error 2
GARU/Clone-0.37.tar.gz
/usr/bin/make -- NOT OK
Failed during this command:
GARU/Clone-0.37.tar.gz : make NO
I've already updated perl, CPAN, and Module::Build. I'm thinking the next step is to upgrade to 10.7, 10.8, or 10.9 and try to reinstall Command Line Tools straight from Apple.
Thoughts?
I had to re-install Xcode but even after that, the make command didn't work...
Install Command Line tools. Open Xcode, and then go to Xcode → Preferences → Downloads.