While trying to install Perl modules like JSON::XS or YAML::XS, i receive the same error:
XS.xs:1:10: fatal error: 'EXTERN.h' file not found
I use MacBook, xCode is up to date, everything else that could help is up to date too.
Since OS X El Capitan, Apple introduced System Integrity Protection which restricts writing to /usr/lib /usr/bin and other sensitive directories (even to root or sudo user) that are used by the installation of Perl bundled with the Operating System. This can cause issues when it comes to installing new modules and also if trying to install XS modules ( those linked to external C libraries ).
For this reason you should not consider the default Perl installation as a working development environment, especially if you are installing custom modules.
Check out this thread on PM and others. I had since El-Capitan managed to solve this before by manually building from tarball and adding a few params or environment variables to set the paths believing that it would be best to retain use of the system Perl but this is not the way to go. This makes your environment difficult to build but also brittle and sensitive to OS updates that may either break things in many different ways.
The best practice seems to be starting with a Perl using brew install perl and work in this environment, remembering to setup your bash_profile as directed by the installer.
Also worth remembering to do a brew link perl. If you receive warnings about this clobbering what looks like system Perl libraries don't worry - these are likely modules that were installed by you over the top and it will cause you less trouble to link over these. If you have concerns, make a note of which module installs will be cleared and re-install them once your environment is configured ( ie your module installer approach is configured using cpanm or sticking with the old perl -MCPAN -e shell etc)
This new Perl setup from brew eliminates the need to continuing running sudo which adds another layer of things that can go wrong as environment variables don't follow through and permission conflicts arise etc.
Finally to simplify package/module installation I suggest doing a brew install cpanminus. If you had previously already installed this, you can ensure the paths etc are configured by doing a brew reinstall cpanminus
If you want to take it another step further then you can install perlbrew as well which will give you the ability to run multiple versions of Perl as your user and configure these with their own libs and modules which can be very useful particularly if aligning with your production environment for testing etc.
One problem you may face if moving from system Perl to this kind of approach is needing to deal with any hangovers from installing things with sudo. It wis worth taking a little time to get all this set up right though and your issues going forward will be greatly reduced and you won't be left with that nagging feeling that you don't want to change anything for fear of it all breaking.
I have also come across a Perl Blog Article that suggests a fix for XS issues with perlbrew on Mojave
This Gist described updating your cpan shell install root though this shouldn't be necessary unless your cpan is stuck in an old config after taking steps above.
I've also raised this as a new issue on PerlMonks
After reading https://developer.apple.com/documentation/xcode_release_notes/xcode_10_release_notes#3035624 and installing the Additional headers via
sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /
I successfully compiled without the missing 'EXTERN.h' error
In order to follow the common advice I also tried with Perlbrew to install a dedicated development version of Perl. Especially with the advice in mind First, do not use the system Perl on MacOS. The installed version is for Apple, not for you (see the discussion here: https://www.perlmonks.org/?node_id=1224727).
Unfortunately, the following error occurred:
Test Summary Report
-------------------
porting/libperl.t (Wstat: 65280 Tests: 35 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
Files=2653, Tests=1217766, 708 wallclock secs (52.74 usr 9.40 sys + 395.38 cusr 49.90 csys = 507.42 CPU)
Result: FAIL
make: *** [test_harness] Error 1
##### Brew Failed #####
Therefore, I decided to install it the following way (and not following the advice due to the error).
Even after having the above mentioned macOS SDK headers already installed on Catalina (macOS 10.15.2) it didn't work for me. I faced the issue during the installation of the Perl module Mac-SystemDirectory-0.13. The following steps (by identifying the missing file in hope of having a more generic approach for more or less equivalent issues) did the trick:
Locate the header file (in this case EXTERN.h)
sudo find /Library -type f -name EXTERN.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/EXTERN.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Perl/5.28/darwin-thread-multi-2level/CORE/EXTERN.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/EXTERN.h
Ensure the installed Perl version (here 5.18) match the header file:
perl -v | grep version
This is perl 5, version 18, subversion 4 (v5.18.4) built for darwin-thread-multi-2level
Export the path for the C-Compiler (note MacOSX10.15.sdk for Catalina and Perl Version 5.18)
export CPATH=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE
Invoke the Makefile.PL with perl
perl Makefile.PL
BTW — For anybody who's still struggling with this, my workaround was:
bash% module="Sub::Util" # For example
bash% cpanm --configure-args="INC=-I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE" "$module"
Please try this
CPATH=$(dirname $(find /usr/local/Cellar/ -name EXTERN.h)) cpan JSON::XS
For Big Sur and perl 5.30, EXTERN.h is at /Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/System/Library/Perl/5.30/darwin-thread-multi-2level/CORE
I'm trying to upgrade CPAN itself and got that error. But I have /usr/bin/cpan and I can't write there so I have to tweak it to write the updated version to /usr/local/bin/cpan.
No promises, but yum install perl-devel worked for me.
As #huyz has helpfully pointed out, if you hit this error on a Mac, you don't have this option, even though this is probably your issue, and you need to follow one of the above methods of getting a version of Perl that isn't missing important chunks, as per other answers.
But if, dear reader, you hit this error on a linux host, as I did, then this might be an option for you.
Building on what E Lisse suggested, you might also have luck looking in
/System/Volumes/Data/Library/Developer/CommandLineTools/SDKs/
For example:
CPATH=$(dirname $(find /System/Volumes/Data/Library/Developer/CommandLineTools/SDKs/ -name EXTERN.h)) cpan JSON::XS
You could also find where EXTERN.h is located and add that to your shell by default, e.g. in your .bashrc or .zshrc file:
export CPATH=/System/Volumes/Data/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE/
Related
I have a process that works in the production environment, that I need to get working on my local Windows 10 environment. It is a Perl script that calls mySql stored procedures.
I have installed ActivePerl 5.26.3 (64-Bit) from Active State. When I attempt to execute the script I get an error:
Can't locate DBD/mysql.pm (you may need to install the DBD::mysql module)...
So, I went to https://metacpan.org/release/DBD-mysql and found instructions that indicated I needed to do the following:
perl -MCPAN -e shell
install DBD::mysql
But, when I type the first command I get a message stating:
It looks like you don't have a C compiler and make utility installed. Trying to install dmake and the MinGW gcc compiler using the Perl Package Manager. This may take several minutes....
Then it goes thru what appears to be a successful installation. So I type in the second command. It scrolls by for a while, but ends with:
Failed during this command
DVEEDEN/DBD-mysql-4.050.tar.gz: writemakefile NO 'C:\Perl64\bin\perl.exe MakeFile.PL INSTALLDIRS=site' returned status 512
Not sure how to proceed.
For ActivePerl, use their package manager PPM.
Or, use Strawberry Perl for a more unixy experience. It comes with all the stuff to compile and install modules.
No matter which Perl you use, on Windows or elsewhere, modules typically need to be compiled the same. Mixing compilers (such as Visual Studio and gcc) or options can lead to incompatible binaries. The same might happen across Perl versions too. That means to use the same Perl (and compilation method) for everything in your project).
The cpan utility doesn't figure out those things for you. It does whatever it's configured to do.
For what it's worth, the cpan method to install modules can be simpler:
$ cpan DBD::mysql
I am trying to setup a MySQL server using CentOS (No GUI) and I need to switch to OpenSSL instead of YaSSL in order to have access to the encryption tools.
The issues happen when runing the cmake. At first I got the error that cmake was not able to find boost, I fixed this adding the parameter -DWITH_BOOST.
The cmake line is as follows.
cmake . -DWITH_READLINE=ON -DWITH_SSL=system -DWITH_BOOST=/usr/local/src/mysql-5.7.20/boost/
After the adjustment I ran again the CMAKE the I got several errors.
SSL Error, cmake can not find the OpenSSL files. I checked if the library was installed, I also downloaded the tar.gz file and decompress it and pointed the cmake to the folder, none of this worked.
Can not find NUMA libraries, again I checked and it is installed, at this point I ran the system update to check for everything but this did not solve the issue.
Can not find the ncurses, the same thing, is on the system but for some reason cmake is not able to find those.
Can not fin libaio, I didn't have this one installed, I installed, ran cmake again, and again cmake was not able to find it.
I been looking around, trying to figure out all this issues, I've been joining information from different websites but still not able to figure out this.
Thanks ahead to everyone for the help.
You're facing the dependencies hell with MySQL. If you don't really need to compile from the sources, you still can install with the RPM which is much easier. The RPM method is described here : https://dev.mysql.com/doc/mysql-yum-repo-quick-guide/en/
As you're asking a ready-to-go install from the sources, this is what I just did and it worked, on a fresh CentOS 7.4 minimal, 2 vcpus 3Gb :
yum group install -y 'Development Tools'
yum install -y cmake ncurses-devel curl
curl -Ovk https://cdn.mysql.com/Downloads/MySQL-5.7/mysql-5.7.20.tar.gz
tar zxf mysql-5.7.20.tar.gz
cd mysql-5.7.20
cmake . -DDOWNLOAD_BOOST=1 -DWITH_BOOST=$HOME/boost -DENABLE_DOWNLOADS=1
make -j2
make install
After that you need to configure it, add the startup scripts, and of course secure it. Here are some additional docs :
http://howtolamp.com/lamp/mysql/5.6/installing/
https://dev.mysql.com/doc/refman/5.7/en/mysql-secure-installation.html
Perhaps try make clean; cmake clean; ldconfig then run your cmake command. Sometimes the system can't find the shared libraries, and ldconfig refreshes the library search path. This helped once when I was compiling something (emscripten?) which required a lot of libraries which I was installing as compilation errors arose.
The make clean; cmake clean will ensure that the compiler isn't looking at the old library search path when you recompile.
I looked everywhere and I can't find any help on how to get JRuby to work on AIX. I tried unpacking the binary package, tried using the jruby-complete.jar but I stumble on the same problems.
All errors seem to occur because JRuby is looking in the wrong directories for lib files.
For instance, I set my GEM_PATH=/home/dev999/install_tmp/gem and then I try to require activerecord-jdbc-adapter, which is installed under ./gem/gems/activerecord-jdbc-adapter-1.3.12, but for some reason JRuby keeps looking for the gem under ./gem/gems/activemodel-4.1.8/lib as shown below.
dev-host:/home/dev999/install_tmp$ jruby -e "require 'activerecord-jdbc-adapter'"
Errno::ENOENT: ENOENT - /home/dev999/install_tmp/gem/gems/activemodel-4.1.8/lib/activerecord-jdbc-adapter
file? at org/jruby/RubyFileTest.java:131
contains_requirable_file? at /usr/local/jruby-1.7.16.1/lib/ruby/shared/rubygems/basic_specification.rb:46
any? at org/jruby/RubyEnumerable.java:1473
contains_requirable_file? at /usr/local/jruby-1.7.16.1/lib/ruby/shared/rubygems/basic_specification.rb:46
any? at org/jruby/RubyEnumerable.java:1473
contains_requirable_file? at /usr/local/jruby-1.7.16.1/lib/ruby/shared/rubygems/basic_specification.rb:44
find_inactive_by_path at /usr/local/jruby-1.7.16.1/lib/ruby/shared/rubygems/specification.rb:898
find at org/jruby/RubyEnumerable.java:592
find_inactive_by_path at /usr/local/jruby-1.7.16.1/lib/ruby/shared/rubygems/specification.rb:897
try_activate at /usr/local/jruby-1.7.16.1/lib/ruby/shared/rubygems.rb:183
require at /usr/local/jruby-1.7.16.1/lib/ruby/shared/rubygems/core_ext/kernel_require.rb:132
(root) at -e:1
Any insights on what may be causing this are greatly appreciated.
EDIT: The server is an AIX 64 bits; we tried Java 1.6 and 1.7 both 64 and 32 bits (IBM custom build for AIX) but we ended up sticking with 1.7 64 bits in the final solution, although the version doesn't seem to affect the issues found in the Ruby 1.7.9 installation, but since we couldn't get JRuby 1.7.16 to work, I can't be sure if the Java builds we used could have played part in the problem.
OK, so the server admin and I spent two days trying to figure these things out and I can finally summarize the solution we ended up with to get JRuby working on AIX_64.
1 . First and most important of all, I had to install JRuby 1.7.9 since the 1.7.16 stable version from the main download page in jruby.org has many (seemingly AIX specific) bugs that we could not figure out; for instance, the wrong gem path resolution shown in my original question. Version 1.7.9 sorts out most of the issues automatically;
2) For some weird reason that I'm still unable to figure out, jirb won't work with the jline-2.11.jar lib that comes with the downloaded JRuby package. At some point I got it to work but then I could not retrace my steps so I gave up. To sort this issue out I downloaded jline-1.0.jar and replaced the jline jar located under <jruby_path>/lib/ruby/shared/readline/jline-2.11.jar; please note that even if we are replacing this with jline-1.0, the jar file name must still be the same i.e. jline-2.11.jar otherwise jirb will complain about a missing lib;
3) Some common steps: add jruby/bin to $PATH; make sure which java shows the correct Java version you want to use; set $JAVA_HOME;
4) (Optional, but very useful) in order to avoid having to grant my user write access to the /usr/<jruby>/<gem_paths> directories but still allow me to install gems without having to ask the admin I added export GEM_PATH=~/.gem to my .profile, then mkdir ~/.gem. To install gems to my home directory I do jgem install <gem_name> -i $GEM_PATH.
Hopefully this helps other users struggling with the same problems.
My main suggestion is to join the jruby mailing list and ask there. I've used jruby just once and managed to get it working. Here is a bit of magic that I don't really understand that I have at the top of one of the first files I require:
# We need the db2j.jar loaded
require 'db2j.jar'
# Some feaking magic Java needs
Java::JavaClass.for_name 'com.ibm.db2j.jdbc.DB2jDriver'
# The connection string is jdbc:db2j:the/path/to/the/file where the
# file is actually a directory.
CloudscapeDriver = 'jdbc:db2j'
You can see the email thread here: http://comments.gmane.org/gmane.comp.lang.jruby.user/17856
good luck
I have a solaris machine configuration: SunOS indevel07 5.10 Generic_147440-15 sun4v sparc sun4v. I am trying to install expect utility on this. expect utility requires tcl to be installed. I have tried to install that too, but i am getting errors. I have downloaded the tcl-8.5.12-sol10-sparc-local.gz and expect-5.45-sol10-sparc-local.gz from sunfreeware. I have unzipped them and tried to install them like pkgadd -d pkgname. I am getting errors like:
ERROR: attribute verification of </usr/local/man/man3/Tcl_Seek.3> failed
pathname does not exist
There are lots of errors like this. I tried to troubleshoot it by googling but could not find anything about it. I am stuck with my development because of this.
Try building Tcl/Tk and Expect from the source. Here is the instruction - How to Compile Tcl. Expect download - Obtaining Expect for UNIX. That worked for me on Solaris 10 and I did not hit any serious bumps.
For those who want to install tcl please refer this URL. it has got steps to do that. URL: http://www.wellho.net/mouth/1174_Installing-Tcl-and-Expect-on-Solaris-10-a-checklist.html
This is driving me crazy- if you can be of assistance, I'd be much obliged. I am running Cygwin on Windows 7.
I have been attempting to write a Perl script to obtain and work with some JSON information. However, my cpan will not install some packages properly. If I try to execute
install CPAN
or
install JSON
It seems to be going well for a while, but then I get an error message over and over again:
0 [main] perl 3288 child_copy: loaded dll data write copy failed, 0x740D1000..0x740D27F0, done 0, windows pid 6600, Win32 error 487
Some people suggested executing ash from the DOS command prompt, and using rebaseall. I tried this, and dash, to no avail. The install still hangs, and when I start up cpan it displays
There seems to be running another CPAN process (pid 3764). Contacting...
Other job not responding. Shall I overwrite the lockfile '/home/me/.cpan/.lock'? (Y/n) [y] y
I have gcc and as many other possible dependencies installed as many online have suggested in my search for help. If you have any leads, I'd be most obliged. Thank you.
i had issues installing pretty much any cpan module - same 'cant move' error!!
just disabled McAfee and all resolved.
Check and disable your AV.
Re-run the cygwin installer to add the needed packages.