Install ProbABEL on Mac

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mmold
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Joined: Fri Oct 17, 2014 12:50 am

Install ProbABEL on Mac

Postby mmold » Fri Oct 17, 2014 12:57 am

Dear colleagues,

I am trying to install and run ProbAbel on my MAC Pro machine (Processor: 2.7 GHz 12-Core Intel Xeon E5, Memory 64 GB 1867 MHz DDR3 ECC; Software: OS X 10.9.5 (13F34)), without success. From the Terminal, I run the following command (being located in the unpacked "probabel-0.4.3") derictory:

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./configure make install --prefix=/Users/max/Desktop/SAHMRI/Analysis_software/probabel_installed/ --with-eigen-include-path=/Users/max/Desktop/SAHMRI/Analysis_software/eigen-eigen-1306d75b4a21

The installation seems to run smooth and without any warnings (see the "config.log" and "config.status" attached), However:

1. All the files are put in the current "probabel-0.4.3" directory, despite I selected a different location with --prefix.
2. I simply can't locate "palinear" I need to run to pass the path to "run_Probabel.pl"

I spent quite a lot of time online trying to find relevant information and also attempting to follow the instructions in the manual (Manual for ProbABEL v0.4.3, April 1, 2014, pp. 3-6), but no success so far. Could you please advice how to instal the program properly and make it run?

Best wishes

Max
Attachments
config_logs.zip
Logs generated by ./configure make install...
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Last edited by lckarssen on Fri Oct 17, 2014 2:05 pm, edited 1 time in total.
Reason: Reformatted input with the code tag.

lckarssen
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Re: Install ProbABEL on Mac

Postby lckarssen » Fri Oct 17, 2014 2:25 pm

Sorry to hear you're having installation problems. Let's see if I can help you out...
mmold wrote:I am trying to install and run ProbAbel on my MAC Pro machine

That's an interesting case! I don't have a MacOS X machine myself, so I can't test the releases on that platform.

Code: Select all

./configure make install --prefix=/Users/max/Desktop/SAHMRI/Analysis_software/probabel_installed/ --with-eigen-include-path=/Users/max/Desktop/SAHMRI/Analysis_software/eigen-eigen-1306d75b4a21


This may be the point where the problem is. The way I read the above is that you put all commands on a single line, is that correct?

The actual order of the commands should be like this (where $ is the terminal prompt, which you don't have to type yourself):

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$ ./configure --prefix=/Users/max/Desktop/SAHMRI/Analysis_software/probabel_installed/ --with-eigen-include-path=/Users/max/Desktop/SAHMRI/Analysis_software/eigen-eigen-1306d75b4a21
$ make
$ make install

The --prefix argument should be given to the ./configure command, and the make command should be given after configure has finished. In total you run three commands (each followed by hitting the Enter key): ./configure, make, make install.

As for your second point about locating palinear: only if you install the executable programs (like palinear) into the default directories will you be able to run them without specifying the path. To see what the default directories are on your system check out the value of the $PATH environment variable. You can do that like this in a terminal:

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echo $PATH

On my system I get the following output:

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/home/lennart/bin:/usr/local/bin:/home/lennart/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games

Notice how the various directories are separated by colons. If you'd like to add for example the path /Users/max/Desktop/SAHMRI/Analysis_software/probabel_installed/bin to the $PATH environment variable you can type the following:

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PATH=/Users/max/Desktop/SAHMRI/Analysis_software/probabel_installed/bin/:$PATH

Notice that I appended bin/ to the path you specified in the --prefix argument to ./configure. This is because if you specify --prefix=/some/path/, the executables will be in /some/path/bin, configuration files will be in /some/path/etc/, etc.

If you want to make this a permanent change (so you won't have to type it in each terminal you open) you can add this line at the bottom of your Bash configuration file ~/.bashrc (assuming you use the Bash shell). After that each new terminal window you open will have the change enabled.
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mmold
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Joined: Fri Oct 17, 2014 12:50 am

Re: Install ProbABEL on Mac

Postby mmold » Wed Oct 22, 2014 5:47 am

Some success with

Code: Select all

./configure \
--prefix=/home/yourusername/ProbABEL/ \
--with-eigen-include-path=/home/yourusername/EIGEN

and

Code: Select all

make

but NOT with

Code: Select all

make install

Are there ways to get an assistance and have the program installed and running?

Best wishes

Max

lckarssen
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Re: Install ProbABEL on Mac

Postby lckarssen » Sun Oct 26, 2014 7:57 pm

mmold wrote:Some success with

Code: Select all

./configure \
--prefix=/home/yourusername/ProbABEL/ \
--with-eigen-include-path=/home/yourusername/EIGEN


Great!

In light of your 'make install' troubles: I assume you did change the prefix path /home/yourusername/ProbABEL/ to something specific to your situation
but NOT with

Code: Select all

make install


Can you be a bit more specific? What error message(s) did you get?

Are there ways to get an assistance and have the program installed and running?

That's what we are here for!
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mmold
Posts: 4
Joined: Fri Oct 17, 2014 12:50 am

Re: Install ProbABEL on Mac

Postby mmold » Sun Oct 26, 2014 11:55 pm

Dear Lennart,

Thanks a lot for having a look at it. I have run the following commands (the location of under prefix has been slightly changed indeed, which should not affect any relevant matters with installation):

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cd probabel-0.4.3

./configure --prefix=/Users/max/Desktop/Software_new/probabel_installed/ --with-eigen-include-path=/Users/max/Desktop/SAHMRI/Analysis_software/eigen-eigen-1306d75b4a21

make

make check

make install


The parts from
make check
and
make install
of the output that I would guess contain information on compilation problems are as follows:

Code: Select all

make check
...
Making check in checks/R-tests
/Applications/Xcode.app/Contents/Developer/usr/bin/make  run_R_test_palinear.sh run_R_test_palogist.sh run_R_test_pacox.sh
make[2]: Nothing to be done for `run_R_test_palinear.sh'.
make[2]: Nothing to be done for `run_R_test_palogist.sh'.
make[2]: Nothing to be done for `run_R_test_pacox.sh'.
/Applications/Xcode.app/Contents/Developer/usr/bin/make  check-TESTS
PASS: run_R_test_palinear.sh
XFAIL: run_R_test_palogist.sh
PASS: run_R_test_pacox.sh
make[4]: Nothing to be done for `all'.
============================================================================
Testsuite summary for ProbABEL 0.4.3
============================================================================
# TOTAL: 3
# PASS:  2
# SKIP:  0
# XFAIL: 1
# FAIL:  0
# XPASS: 0
# ERROR: 0
============================================================================
make[1]: Nothing to be done for `check-am'.


Code: Select all

make install
Making install in src
 .././install-sh -c -d '/Users/max/Desktop/Software_new/probabel_installed/bin'
  /usr/bin/install -c palinear palogist pacoxph '/Users/max/Desktop/Software_new/probabel_installed/bin'
 .././install-sh -c -d '/Users/max/Desktop/Software_new/probabel_installed/bin'
 /usr/bin/install -c probabel '/Users/max/Desktop/Software_new/probabel_installed/bin'
 .././install-sh -c -d '/Users/max/Desktop/Software_new/probabel_installed/etc'
 /usr/bin/install -c -m 644 probabel_config.cfg.example '/Users/max/Desktop/Software_new/probabel_installed/etc'
/Applications/Xcode.app/Contents/Developer/usr/bin/make  install-exec-hook
/usr/bin/sed -i "s;probabel_config.cfg;/Users/max/Desktop/Software_new/probabel_installed/etc/probabel_config.cfg;" \
      /Users/max/Desktop/Software_new/probabel_installed/bin/probabel
sed: 1: "/Users/max/Desktop/Soft ...": invalid command code m
make[3]: *** [install-exec-hook] Error 1
make[2]: *** [install-exec-am] Error 2
make[1]: *** [install-am] Error 2
make: *** [install-recursive] Error 1

lckarssen
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Re: Install ProbABEL on Mac

Postby lckarssen » Mon Oct 27, 2014 9:39 am

mmold wrote:OK, so 'make check' runs as expected (don't mind the XFAIL line, it stands for 'eXpected to fail').

Code: Select all

make install
Making install in src
 .././install-sh -c -d '/Users/max/Desktop/Software_new/probabel_installed/bin'
  /usr/bin/install -c palinear palogist pacoxph '/Users/max/Desktop/Software_new/probabel_installed/bin'
 .././install-sh -c -d '/Users/max/Desktop/Software_new/probabel_installed/bin'
 /usr/bin/install -c probabel '/Users/max/Desktop/Software_new/probabel_installed/bin'
 .././install-sh -c -d '/Users/max/Desktop/Software_new/probabel_installed/etc'
 /usr/bin/install -c -m 644 probabel_config.cfg.example '/Users/max/Desktop/Software_new/probabel_installed/etc'
/Applications/Xcode.app/Contents/Developer/usr/bin/make  install-exec-hook
/usr/bin/sed -i "s;probabel_config.cfg;/Users/max/Desktop/Software_new/probabel_installed/etc/probabel_config.cfg;" \
      /Users/max/Desktop/Software_new/probabel_installed/bin/probabel
sed: 1: "/Users/max/Desktop/Soft ...": invalid command code m
make[3]: *** [install-exec-hook] Error 1
make[2]: *** [install-exec-am] Error 2
make[1]: *** [install-am] Error 2
make: *** [install-recursive] Error 1

Ah, that provides an important clue. It looks like the 'sed' command on MacOS X is slightly different from the one found on Linux. Could you try the following:
  1. open the file 'src/Makefile' in a text editor (for example 'nano')
  2. go to the bottom of the file. There should be a section called install-exec-hook:, which should look like this:

    Code: Select all

    install-exec-hook:
       $(SED) -i "s;probabel_config.cfg;${prefix}/etc/probabel_config.cfg;" \
          $(DESTDIR)$(bindir)/probabel
       $(SED) -i "s;\./;${exec_prefix}/bin/;" $(DESTDIR)$(bindir)/probabel
       $(SED) -i "s;PROBABEL_VERSION;0.4.3;" $(DESTDIR)$(bindir)/probabel
       ln -s $(DESTDIR)$(bindir)/probabel $(DESTDIR)$(bindir)/probabel.pl
  3. In each of the $(SED) lines add -e after each -i, like this:

    Code: Select all

    install-exec-hook:
       $(SED) -i -e "s;probabel_config.cfg;${prefix}/etc/probabel_config.cfg;" \
          $(DESTDIR)$(bindir)/probabel
       $(SED) -i -e "s;\./;${exec_prefix}/bin/;" $(DESTDIR)$(bindir)/probabel
       $(SED) -i -e "s;PROBABEL_VERSION;0.4.3;" $(DESTDIR)$(bindir)/probabel
       ln -s $(DESTDIR)$(bindir)/probabel $(DESTDIR)$(bindir)/probabel.pl
  4. and try to run 'make install' again.
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mmold
Posts: 4
Joined: Fri Oct 17, 2014 12:50 am

Re: Install ProbABEL on Mac

Postby mmold » Tue Oct 28, 2014 8:07 am

Dear Lennart,

Thanks a lot for looking at it. This is probably not the question for this probABEL forum, but following your suggestions I've got the following issue.

Firstly, I've altered the 'src/Makefile' file as you suggested, and re-run .\configure, followed by make. Here is the error message I've got:

Code: Select all

sph262364:probabel-0.4.3 max$ make
Making all in src
 cd .. && /bin/sh /Users/max/Desktop/Software_new/probabel-0.4.3/missing automake-1.13 --gnu src/Makefile
/Users/max/Desktop/Software_new/probabel-0.4.3/missing: line 81: automake-1.13: command not found
WARNING: 'automake-1.13' is missing on your system.
         You should only need it if you modified 'Makefile.am' or
         'configure.ac' or m4 files included by 'configure.ac'.
         The 'automake' program is part of the GNU Automake package:
         <http://www.gnu.org/software/automake>
         It also requires GNU Autoconf, GNU m4 and Perl in order to run:
         <http://www.gnu.org/software/autoconf>
         <http://www.gnu.org/software/m4/>
         <http://www.perl.org/>
make[1]: *** [Makefile.in] Error 127
make: *** [all-recursive] Error 1




Further, I've installed the latest automake-1.14:

Code: Select all

./configure --prefix=/Users/max/Desktop/Software_new/automake_installed

make

make install

sudo nano /Users/max/Desktop/Software_new/automake_installed/bin


The latter command was to put "automake" in the path. Checking if it is so, I ran

Code: Select all

echo $PATH


which brought

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/Users/max/Desktop/Software_new/automake_installed/bin/:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin


And still I am getting the same "WARNING: 'automake-1.13' is missing on your system." massage a above.

Any advice on that?

lckarssen
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Re: Install ProbABEL on Mac

Postby lckarssen » Tue Oct 28, 2014 8:43 am

mmold wrote:Thanks a lot for looking at it.

You're welcome!
Firstly, I've altered the 'src/Makefile' file as you suggested, and re-run .\configure, followed by make.

Aha. Running './configure' wasn't necessary and resulted in the Automake requirement.

Here is the error message I've got:

Code: Select all

sph262364:probabel-0.4.3 max$ make
Making all in src
 cd .. && /bin/sh /Users/max/Desktop/Software_new/probabel-0.4.3/missing automake-1.13 --gnu src/Makefile
/Users/max/Desktop/Software_new/probabel-0.4.3/missing: line 81: automake-1.13: command not found
WARNING: 'automake-1.13' is missing on your system.
         You should only need it if you modified 'Makefile.am' or
         'configure.ac' or m4 files included by 'configure.ac'.
         The 'automake' program is part of the GNU Automake package:
         <http://www.gnu.org/software/automake>
         It also requires GNU Autoconf, GNU m4 and Perl in order to run:
         <http://www.gnu.org/software/autoconf>
         <http://www.gnu.org/software/m4/>
         <http://www.perl.org/>
make[1]: *** [Makefile.in] Error 127
make: *** [all-recursive] Error 1


Further, I've installed the latest automake-1.14:

Thanks for going to such lengths as installing automake! Not the kind of effort I see every day :-).

Code: Select all

echo $PATH


which brought

Code: Select all

/Users/max/Desktop/Software_new/automake_installed/bin/:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin


Hmm, that should be enough, I'd say.

I think this is a nice trigger for me to finally wrap up the release of ProbABEL 0.4.4 and include the proposed change to the sed lines. That should make your life easier.
I'll try to do so today. Please keep an eye on http://www.genabel.org for a release announcement.
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lckarssen
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Re: Install ProbABEL on Mac

Postby lckarssen » Fri Oct 31, 2014 7:58 pm

As you may have noticed, I didn't manage to do the release this week. I've put it on my todo list for next week.
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lckarssen
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Re: Install ProbABEL on Mac

Postby lckarssen » Fri Nov 07, 2014 12:00 pm

I've added this installation bug to our bug tracker: https://r-forge.r-project.org/tracker/i ... &atid=2058
It turns out the bug also occurs when trying to install ProbABEL on FreeBSD 10.0.
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