Pear installation MI MBPro macOS Monterey

[Rob Weeks]

Hi,

I am trying to install PEAR on my new M1 MBPro running macOS Monterey (12.3.1).

I downloaded 'pear-src-0.9.11.tar.gz' from Github, decompressed file and cd into directory.

Now when I run './configure', everything seems ok, but 'make' generates errors:

Making all in src

 cd .. && /bin/sh /Users/weero44p/pear-src-0.9.11/missing automake-1.14 --gnu src/Makefile

/Users/weero44p/pear-src-0.9.11/missing: line 81: automake-1.14: command not found

WARNING: 'automake-1.14' 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

These errors suggest that I need to install gcc, but the ./compile output confirmed that gcc was good. To be clear, this is a new MBPro and I have not installed gcc onto it, but gcc is installed with Monterey:

gcc --version

Apple clang version 13.1.6 (clang-1316.0.21.2)

Target: arm64-apple-darwin21.4.0

Thread model: posix

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Also, I have installed 'perl'.

Does anyone have any insight into these issues?  

I have also tried to install pear through 'conda install pear' or 'conda install bioconda pear' to no avail. Can anyone help with installing pear on my new M1 MBPro?

Cheers

Rob

[Alexandros Stamatakis]

Hi Rob,

Below you can find how my current PhD student Julia and Mac expert in
our group did to solve the problem.

Julia, many thanks for looking into this :-)

I was able to reproduce that error on my M1 Pro as well and once I fixed
the automake issue, I ran into another problem since pear apparently
cannot be build yet on the M1 directly. But luckily Apple has the
Rosetta emulator with which you can build pear for x86 and then run it
on the M1 Pro anyways.

Here is how to do this:

1. First you need to install automake, it seems that the latest Xcode
build tools version does not include automake. I recommend installing it
with the package manager homebrew (https://brew.sh): `brew install
automake`

2. Second you need to install Rosetta. To do this run `softwareupdate
--install-rosetta` in the terminal.

3. Go to your applications folder and copy and paste your terminal app.
Select the copied app and press Cmd+I. This should open the information
window. In this window check the "Open using Rosetta“ box, then close
the information window.
Open the copied terminal application version. This version now runs
using the Rosetta x86 emulation. Run all of the following steps in this
terminal.

4. Download and unzip the pear source files. I recommend using a fresh
copy (meaning do not re-use a directory where you tried to build pear
before).

5. Since the installed automake version does not match the configured
version, run `autoreconf -f -i`.

6. Finally, run `./configure && make`. There should not be any errors
anymore.

You now should be able to run ./src/pear from this terminal, as well as
the unmodified one (so the one NOT opening with Rosetta).

I hope this works!

Greetings
Julia

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Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas

www.exelixis-lab.org

[Rob Weeks]

Hi Alexandros and Julia

I can't thank you enough for the instructions (and for the PEAR program!). 

The instructions worked perfectly and I now have PEAR working on my new M1 MacBook.

Cheers

Rob

[David Cheishvili]

Hello, 

Thank you for this guidelines. 

I am trying to install rosetta on macOS Monterey (version 12.4) without success. Getting error message:  

Installing Rosetta 2 on this system is not supported

I then tried: sudo /usr/sbin/softwareupdate --install-rosetta --agree-to-license

getting the same errror message.

Please advice

David

[Julia Haag]

Hello David,

I have never encountered this issue, but here are a few ideas:

- If you Mac is does not have an M1 chip you don’t need Rosetta (and won’t be able to install it), but since you are replying to this post I am assuming that you are using an M1 Mac :-) if you are not sure, you can run the `arch` command in a terminal and if it says `arm64` than you have an M1 chip and can try the other suggestions

- Make sure that the terminal you are using is not running in emulation mode. To verify this go to your applications folder, select the terminal app, press Cmd+I and verify that the checkbox "Open using Rosetta" is unchecked. If it was checked, terminate the terminal app, uncheck the box, restart the terminal, and try to run the install command again. 

- Another way to install Rosetta is trying to open an app that is not (yet) ported to M1, for example Skype. When you try to open Skype, your Mac should prompt you to install Rosetta.

- Finally, in some cases I read about in an apple forum a simple reboot of the system helped :-) 

I hope any of this solves your issue.

Greetings,

Julia

[Stephan Bitterwolf]

Hi All,

I just wanted to add to this thread since I had the same issue on the new M2 mac and could not duplicate the terminal app (this has been blocked by apple in the new OS). The solution I found that works for pear 0.9.6 is to do the following:
1. Follow the instructions here to create an "intel" environment in your terminal.

2. Install homebrew inside of the intel environment (instructions in the link above)

3. Install miniconda with homebrew "brew install miniconda" (just be sure that you are using the intel version - you can check by typing "arch" and it should say something like "i386")

4. Once conda is installed follow the instructions for adding the bioconda libraries: link here

5. Then update conda with the command "conda update conda" say yes to the updates

6. Install the PEAR package on bioconda by typing "conda install pear"

7. After the install is complete you should see a message appear after typing "pear".

8. You are done. 

9. When you are done with using PEAR you can return to the arm terminal by typing arm (this assumes that you set up the aliases as instructed in step 1). Alternatively, close the terminal and reopen it. This should automatically be an ARM based terminal and you can check by typing "arch" and confirming a message like "arm64"

Note: if you get an error saying that pear doesn't exist but conda says it does (you can check conda packages with this command "conda list"), then you need to add some paths to your .zshrc file. To do this:

1. Navigate to your home folder using finder.

2. Show hidden files: press shift + command + period

3. Open the now visible .zshrc file using BBEdit or some other text editor and add: the below lines

               export PATH="/usr/local/bin:$PATH"
               export PATH="/opt/homebrew/bin:$PATH"

4. The lines above just tell your computer where to find the programs you installed. After doing that PEAR showed up for me.

I hope this helped!

Stephan