installation error when downloading R packages (LinuxMint 17.1)

Galit · October 10, 2018, 1:40pm

Hello,

I am trying to install afni on Linux. I am new to Linux, so I have very little knowledge on how things work with it.

When I download the R packaes (using rPkgsInstall -pkgs ALL) I get the following error:


oo Warning: 
   Failed to load R_io.so with this error message:

Error in dyn.load(ll) : 
  unable to load shared object '/home/galit/abin/R_io.so':
  /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.23' not found (required by /home/galit/abin/R_io.so)
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

I tried to update and install GLIBC, but nothing seemed to work.
I used this setup for installation.
What do you advice me to do?

Thanks you!

rickr · October 11, 2018, 1:44pm

That version might not be appropriate for your OS.
What is the output from:

ldd --version

rick

Galit · October 14, 2018, 7:22am

Hi Rick,
It says:
ldd (Ubuntu EGLIBC 2.19-0ubuntu6.5) 2.19
It’s from 2014… Is that too old?
Thanks,
Galit

rickr · October 14, 2018, 1:08pm

Try the openmp_64 package, instead:

@update.afni.binaries -package linux_openmp_64

Then test it with:

afni_system_check.py -check_all

Then you can show us the output from this.

rick

Galit · October 15, 2018, 10:31am

Hi Rick,
Here is the whole output:


-------------------------------- general ---------------------------------
architecture:         64bit ELF
system:               Linux
release:              3.13.0-37-generic
version:              #64-Ubuntu SMP Mon Sep 22 21:28:38 UTC 2014
distribution:         LinuxMint 17.1 rebecca
number of CPUs:       8
apparent login shell: tcsh
shell RC file:        .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /home/galit/abin/afni
afni version         : Precompiled binary linux_openmp_64: Oct 12 2018 
                     : AFNI_18.3.01
AFNI_version.txt     : AFNI_18.3.01, linux_openmp_64, Oct 12 2018
which python         : /usr/bin/python
python version       : 2.7.6
which R              : /usr/bin/R
R version            : R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
which tcsh           : /usr/bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/home/galit/abin/afni)
    R       : 1   (/usr/bin/R)
    python  : 1   (/usr/bin/python2.7)
    python2 : 1   (/usr/bin/python2.7)
    python3 : 1   (/usr/bin/python3.4)


testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : FAILURE
        3dSkullStrip: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
    uber_subject.py      : success
    3dAllineate          : success
    3dRSFC               : FAILURE
        3dRSFC: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
    SurfMesh             : success
    3dClustSim           : success

checking for R packages...
    rPkgsInstall -pkgs ALL -check : FAILURE
        
        oo Warning: 
           These packages are not installed on the computer: afex!
        These packages are not installed on the computer: phia!
        These packages are not installed on the computer: snow!
        These packages are not installed on the computer: nlme!
        These packages are not installed on the computer: lme4!
        These packages are not installed on the computer: paran!
        These packages are not installed on the computer: psych!
        These packages are not installed on the computer: brms!
        

checking for $HOME files...
    .afnirc                   : found
    .sumarc                   : missing
    .afni/help/all_progs.COMP : missing

------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /usr/lib/python2.7/dist-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/galit/abin

PYTHONPATH = 
R_LIBS = /home/galit/R

LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH = 
DYLD_FALLBACK_LIBRARY_PATH = 

------------------------------ data checks -------------------------------
data dir : found AFNI_data6   under $HOME
           top history: ... Jun 2018 [gangc]: added 0.BGA and updated 2.3groups
data dir : found AFNI_demos   under $HOME
           top history: ... [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo    under $HOME
           top history: .../SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas    : found TT_N27+tlrc  under /home/galit/abin

------------------------------ OS specific -------------------------------
which apt-get        : /usr/bin/apt-get
apt-get version      : apt 1.0.1ubuntu2 for amd64 compiled on Oct 28 2014 20:55:14


=========================  summary, please fix:  =========================
*  AFNI programs show FAILURE
*  missing R packages (see rPkgsInstall)
*  consider running "suma -update_env" for .sumarc
*  consider running: apsearch -update_all_afni_help

rickr · October 15, 2018, 1:14pm

Linux Mint 17.1 seems to be based on Ubuntu 14, and the
Ubuntu notes include this setup:

sudo apt-get install libxp6 python-qt4 r-base libpng16 libgsl0-dev tcsh
sudo apt-get update

sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/libgsl.so.0

The last line is probably what you now need.

rick

Galit · October 16, 2018, 6:19am

OK, great. The R package installation seemed to work now. However, when I evaluate the setup, I still get an error that R packages are not installed. That is weird, because the installation seemed to work smoothly. I tried to install each package separately (phia, afex and brms) and got a note for each package that it was successfully installed on the computer (and a few warning messages that seemed irrelevant). But the evaluation still insisted the R programs are not installed! Maybe there is a different way to evaluate the setup?
Thanks a lot.

rickr · October 24, 2018, 12:52pm

We are indeed running into some difficulties with the R packages.
It is possible that the R version that comes with your system is not
compatible with the current packages. But just to back up a little,
are you having any trouble running any of the group analysis R
programs? It is possible that you don’t need to worry about it.

rick

Galit · October 29, 2018, 7:44am

Hi Rick,
I didn’t get there yet, at the moment I have problems with running 3dSkullStrip. I get an error that libgsl.so.0 does not exist. But when I run again sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/x86-linux-gnu/libgsl.so.0 (the command that you suggested to solve the R problem) I get the message:
ln: failed to create symbolic link ‘/usr/lib/x86_64-linux-gnu/libgsl.so.0’: File exists
I’m not sure what it means or how to proceed from here. What should I do now?
Many thanks again,
Galit

rickr · October 29, 2018, 12:51pm

Hi Galit,

Your ‘ln’ command should not have the x86 directory in
the destination name, it is just under /usr/lib:

sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/libgsl.so.0

rick

Galit · November 1, 2018, 11:49am

Hi Rick,
Sorry, my misake in typing here the library name.
Anyway, I get the same error message using 3dSkullStrip - that libgsl.so.0 does not exist. I manually tried to open libgsl.so.0 (in both /usr/lib/ and /usr/lib/x86_64-linux/gnu/), and got a message that the link was broken. I removed the file and re-installed it (using the command lines you suggested on October 15 in this thread). And still the link is broken.
If it helps, running again sudo apt-get install libxp6 python-qt4 r-base libpng16 libgsl0-dev tcsh, I noticed the message “unable to locate package libpng16”. Perhaps that’s where the crux is?
Thanks,
Galit

rickr · November 1, 2018, 12:54pm

Hi Galit,

That certainly might be the problem. Try to look that
package up on the LinuxMint documentation website.
To verify, what is the output of:

ls -l /usr/lib/x86_64-linux-gnu/libgsl.*

It is possible the package is libgsl-dev, try also:

sudo apt-get install libgsl-dev

Regarding libpng16, I guess you need to see what
is available for libpng, too.

Another option is backing up to the linux_xorg7_64.tgz
package, just to see if that is better.

rick

Galit · November 5, 2018, 1:17pm

Hi Rick,

This is what I get with ls -l /usr/lib/x86_64-linux-gnu/libgsl.* :

lrwxrwxrwx 1 root root 35 Oct 29 09:34 /usr/lib/x86_64-linux-gnu/libgsl.so.0 → /usr/lib/x86_64-linux-gnu/libgsl.so
lrwxrwxrwx 1 root root 16 May 6 2017 /usr/lib/x86_64-linux-gnu/libgsl.so.19 → libgsl.so.19.3.0
-rw-r–r-- 1 root root 2455464 May 6 2017 /usr/lib/x86_64-linux-gnu/libgsl.so.19.3.0

The first line, I suppose is the broken link that I installed.

Still looking for a libpng16 compatible with Mint.

Galit

dglen · November 5, 2018, 5:27pm

The libpng library should be available three ways. I would try the first way, then work down to the others. libpng16 is the latest version at the moment.

sudo apt-get install libpng16-16
sudo dpkg -i libpng16-16_1.6.26-6_amd64.deb
or from source at https://sourceforge.net/projects/libpng/?source=directory , then build with

./configure
make check
make install
ldconfig

Galit · November 6, 2018, 11:28am

Thanks, Daniel. The two first ways yielded error messages, but downloading and installing the source seemed to do the job! 3dSkullStrip is now finally running!
Thank you also Rick. I will let you know, when I reach the stage of group analysis, if the R packages properly work (the original motivation of this thread).
Best,
galit