error installing minpath and glpk

[Mrinmoy Das]

Hi,

I recently installed humann2 on a linux server (Debian OS) but it seems Minpath is not properly installed. Test running humann2 gives me this error:

Computing gene families ...

Computing pathways abundance and coverage ...
/usr/local/bin/glpsol: error while loading shared libraries: libglpk.so.36: cannot open shared object file: No such file or directory
/usr/local/bin/glpsol: error while loading shared libraries: libglpk.so.36: cannot open shared object file: No such file or directory
/usr/local/bin/glpsol: error while loading shared libraries: libglpk.so.36: cannot open shared object file: No such file or directory

I tried to separately install Minpath and glpk but I got the following error while installing glpk.

make
Making all in include
make[1]: Entering directory `/home/mrinmoy/Programs/MinPath/glpk-4.6/include'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/mrinmoy/Programs/MinPath/glpk-4.6/include'
Making all in src
make[1]: Entering directory `/home/mrinmoy/Programs/MinPath/glpk-4.6/src'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/mrinmoy/Programs/MinPath/glpk-4.6/src'
Making all in examples
make[1]: Entering directory `/home/mrinmoy/Programs/MinPath/glpk-4.6/examples'
gcc  -g -O2  -o glpsol  glpsol.o ../src/libglpk.a -lm
/usr/bin/ld: i386 architecture of input file `../src/libglpk.a(glplpx6d.o)' is incompatible with i386:x86-64 output
/usr/bin/ld: i386 architecture of input file `../src/libglpk.a(glprng.o)' is incompatible with i386:x86-64 output
/usr/bin/ld: i386 architecture of input file `../src/libglpk.a(glpqmd.o)' is incompatible with i386:x86-64 output
collect2: error: ld returned 1 exit status
make[1]: *** [glpsol] Error 1
make[1]: Leaving directory `/home/mrinmoy/Programs/MinPath/glpk-4.6/examples'
make: *** [all-recursive] Error 1

I tried following the instructions given in the Minpath readme and this post:

https://groups.google.com/forum/#!topic/humann-users/MSVmXC7DSW0


Please suggest how to proceed?

Regards
Mrinmoy

[Lauren McIver]

Hi Mrinmoy,

If you install a newer version of glpk, it should resolve your error messages.

Here are the steps:

1. Download glpk

$ wget http://ftp.gnu.org/gnu/glpk/glpk-4.55.tar.gz

2. Install glpk

$ tar zxvf glpk-4.55.tar.gz

$ cd glpk-4.55

$ ./configure

$ make

$ make install

3. Test the install

$ glpsol --help

Another option (if you have internet access on your server), would be to remove the current glpk install and then reinstall humann2. This will install glpk-4.55. Alternatively, if you add the option "--replace-dependencies-install" when re-installing humann2, it will overwrite the existing glpk install.

Thank you,

Lauren

[p.pana...@gmail.com]

Had a similar issue using the newest version of glpk
$ sudo ldconfig
Solved the issue

[wend...@gmail.com]

Hello,

I am Wendi Ren who has the same error. I have tried to download a new version but still have the error. However, I do not have the sudo authority, so do you know how to solve this issue?

Thanks a lot.

Sincerely,

Wendi

在 2017年12月10日星期日 UTC+8上午12:31:50，p.pana...@gmail.com写道：

[Lauren McIver]

Hi Wendi - You should be able to install glpk without sudo permissions (if installing into the user space). When you installed humann2 did you see errors when it was trying to install glpk? If so, can you send those errors (either to the list serve or to me directly)? Then I can help you debug your install.

Thanks,

Lauren

[任文頔]

Dear Lauren,

I have reinstalled humann2, and it solved the problem.

Thanks.

Wendi

[upendrakuma...@googlemail.com]

Thank you so much for the fix..