Linux Error : Undefined reference to BAMTools while compiling makefile

Question

[Bioinfo_learner]

Hi, Iam currently trying to install EUPAN toolkit (EUkaryotic pangenome analysis toolkit) for pangenome analysis using this installation guide: http://cgm.sjtu.edu.cn/eupan/installation.html I have downloaded the toolkit but the make command doesn't run and gives error as shown in the screenshot. Kindly guide me step by step commands as to how the issue can be resolved. (This is my first time working in linux)

[lieven.sterck]

your screenshot is not showing.

have a look here, How to add images: How to add images to a Biostars post

[Ram]

Did you run Rscript installRPac first? It seems to me that your error is caused by a missing package.

[Bioinfo_learner]

I had run the Rscript which was just for installing R packages. My problem is resolved though. I shall be grateful if you could answer this question for me? How to download proteins in my scenario?

Answer 1

[Kevin Blighe]

I fixed your post.

You are using a version of gcc that is too advanced. You have to compile it with a version pre gcc v5.0 (I think) - try gcc v4.1 if possible. I am not sure if you can even install that easily on your Ubuntu 18.04 OS. As you say that this is your first time working in linux, please ask your System Administrator, or a friend / colleague who has experience in this area.

Kevin

[Bioinfo_learner]

@kevin Thankyou for fixing my post and also resolving my error. This certainly worked for me. Could you answer another query for me? How to download proteins in my scenario?

Answer 2

[Harshit]

This issue can be fixed by compiling using gcc and g++ version <5. So gcc-4.8 and g++-4.8 will do the trick.
To downgrade GCC and G++:

1. [Dangerous] Add deb http://archive.ubuntu.com/ubuntu/ bionic main universe to /etc/apt/sources.list.
   To edit the file using nano :

   1. sudo nano /etc/apt/sources.list
   2. Add deb http://archive.ubuntu.com/ubuntu/ bionic main universe
   3. Ctrl+X, Y, Enter

2. Run sudo apt update

3. Run sudo apt install g++-4.8

4. Run sudo apt install gcc-4.8

5. [Optional] You can remove the added deb repository in step 1. This will safeguard you from downloading old and outdated softwares and packages.

6. Run sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 4

7. Run sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 4

8. Run sudo update-alternatives --config gcc. Choose the Selection number corresponding to version 4.8

9. Run sudo update-alternatives --config g++. Choose the Selection number corresponding to version 4.8

Verify the versions using gcc --version and g++ --version.

Now compiling with make should work.

[Optional] To revert the versions back to a higher version, do steps 8 and 9, and choose the selection number corresponding to the higher version.