R_io.so error message: Library not loaded: /sw/lib/libXm.4.dylib

uppsalaman · December 7, 2017, 9:39am

Hi-

I recently installed AFNI on a Mac:


$ afni -ver
Precompiled binary macos_10.12_local: Nov 27 2017 (Version AFNI_17.3.05)

and most things look fine, but when I try to run the following AFNI Bootcamp script that calls 3dANOVA, I get the following error:


$ tcsh MVM.txt 

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

Error in dyn.load(ll) : 
  unable to load shared object '/Users/xyz/abin/R_io.so':
  dlopen(/Users/xyz/abin/R_io.so, 6): Library not loaded: /sw/lib/libXm.4.dylib
  Referenced from: /Users/xyz/abin/R_io.so
  Reason: image not found
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

I get the same error even trying to run “rPkgsInstall -pkgs ALL”.

Any suggestions would be great, thanks.

Gang · December 7, 2017, 8:06pm

Could you paste the output of the following command?

afni_system_check.py -check_all

uppsalaman · December 8, 2017, 4:06am

Hi-


-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              17.2.0
version:              Darwin Kernel Version 17.2.0: Fri Sep 29 18:27:05 PDT 2017; root:xnu-4570.20.62~3/RELEASE_X86_64
distribution:         10.13.1 x86_64
number of CPUs:       4
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/xyz/abin/afni
afni version         : Precompiled binary macos_10.12_local: Nov 27 2017 
                     : AFNI_17.3.05
AFNI_version.txt     : AFNI_17.3.05, macos_10.12_local, Nov 27 2017
which python         : /usr/bin/python
python version       : 2.7.10
which R              : /usr/local/bin/R
R version            : R version 3.4.2 (2017-09-28) -- "Short Summer"
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/Users/xyz/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
    python  : 1   (/usr/bin/python)
    python2 : 1   (/usr/local/Cellar/python/2.7.14/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
    python3 : 1   (/usr/local/Cellar/python3/3.6.3/Frameworks/Python.framework/Versions/3.6/bin/python3.6)


testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    uber_subject.py      : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success

checking for R packages...
    rPkgsInstall -pkgs ALL -check : FAILURE
        Error in dyn.load(ll) : 
          unable to load shared object '/Users/xyz/abin/R_io.so':
          dlopen(/Users/xyz/abin/R_io.so, 6): Library not loaded: /sw/lib/libXm.4.dylib
          Referenced from: /Users/xyz/abin/R_io.so
          Reason: image not found
        Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
        Execution halted

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

------------------------------ python libs -------------------------------
** python module not found: PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/xyz/abin

PYTHONPATH = /usr/local/lib/python2.7/site-packages

R_LIBS = 
LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = /Users/xyz/abin

------------------------------ data checks -------------------------------
data dir : found AFNI_data6   under $HOME/CD
           top history: ...PPI scripts are now based on FT_analysis/s05.ap.uber
data dir : found AFNI_demos   under $HOME/CD
           top history: ... [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo    under $HOME/CD
           top history: .../SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME/Documents/AFNI
atlas    : found TT_N27+tlrc  under /Users/xyz/abin

------------------------------ OS specific -------------------------------
which brew           : /usr/local/bin/brew
brew version         : Homebrew 1.3.9

-- for PyQt4 under brew, consider running:
   brew install cartr/qt4/pyqt
++ found valid link /usr/local/lib/libgomp.1.dylib
   to /usr/local/Cellar/gcc/7.2.0/lib/gcc/7/libgomp.1.dylib
++ found valid link /usr/local/lib/libglib-2.0.dylib
   to ../Cellar/glib/2.54.2/lib/libglib-2.0.dylib
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
   -- found 'libXt' dylib files:
      /opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'bash'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

=========================  summary, please fix:  =========================
*  login shell 'bash', trusting user to translate from 'tcsh'
*  shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
*  missing R packages (see rPkgsInstall)

Thanks.

rickr · December 8, 2017, 3:18pm

R does not like the method we use for loading
libraries that are local to the distribution. I will
look into this.

If you want to try a different package, go with
the 10.7 version:

@update.afni.binaries -package macosx_10.7_local

rick

Gang · December 8, 2017, 7:36pm

Rick, I wonder if the issue might have something to do with the following line in abin/rPkgsInstall.R:

lop$site ← ‘http://cran.mtu.edu/’

If so, would replacing the above line with the following fix the issue?

lop$site ← ‘http://cran.us.r-project.org’

rickr · December 8, 2017, 8:25pm

Hi Gang,

This seems to be about loading our R_io.so library, which
has its own dependencies, for which we want it to search
in the same directory (abin). Daniel and I have been doing
some searching, but have not found a solution.

So without installing the libraries we are trying to let people
avoid, it seems that no one using the local packages should
be able run the R programs.

The library mechanism for R does not seem to allow for
@executable_dir.

rick

uppsalaman · December 9, 2017, 1:59pm

Hi Rick,

Thank you very much!

-upps

EXP.2086 · August 24, 2019, 1:17pm

Hi Gang,

AFNI version 22 Aug 2019 has similar issue.

2086

rickr · August 26, 2019, 1:40pm

Hi 2086

To be sure, what is the actual error? That is with the 10.12_local package?

Thanks,

rick

EXP.2086 · August 27, 2019, 12:59am

Hi Rick,

Thanks for your reply. I have re-installed AFNI to previous version(Jul 25 2019), I remember the error message was:

R_io.so error message: Library not loaded: /sw/lib/libXm.6.dylib

The afni_check of current installation:

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Thu Jun 20 18:42:21 PDT 2019; root:xnu-4903.270.47~4/RELEASE_X86_64
distribution: 10.14.6 x86_64
number of CPUs: 12
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/afni
afni version : Precompiled binary macos_10.12_local: Jul 25 2019
: AFNI_19.2.05 ‘Claudius’
AFNI_version.txt : AFNI_19.2.05, macos_10.12_local, Jul 25 2019
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.5.2 (2018-12-20) – “Eggshell Igloo”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/afni/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 1 (/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

** have python3 but not python2

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

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

------------------------------ python libs -------------------------------
** python module not found: PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

-------------------------------- env vars --------------------------------
PATH = /usr/local/ants/bin/:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/afni:/Applications/MATLAB_R2019a.app/bin:/Users/z/Documents/OneDrive/Sync/Scripts

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /usr/local/afni

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.10

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
– consider installing gcc under homebrew
++ found valid link /usr/local/lib/libglib-2.0.dylib
to …/Cellar/glib/2.60.6/lib/libglib-2.0.dylib
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
– recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell ‘bash’…
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
– recent OS X, cheating to check DYLD_LIBRARY_PATH in shell ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
insufficient data for AFNI bootcamp

Thanks,
2086

EXP.2086 · September 2, 2019, 2:13pm

Hi Rick,

The latest AFNI (version Aug 29 2019) still has this issue:

Error message when source AFNIio.R in R:

source(“/usr/local/afni/AFNIio.R”)

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

Error in dyn.load(ll) :
unable to load shared object ‘/usr/local/afni/R_io.so’:
dlopen(/usr/local/afni/R_io.so, 6): Library not loaded: /sw/lib/libXt.6.dylib
Referenced from: /usr/local/afni/R_io.so
Reason: image not found

afni_check info:

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64
distribution: 10.14.6 x86_64
number of CPUs: 12
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/afni
afni version : Precompiled binary macos_10.12_local: Aug 29 2019
: AFNI_19.2.21 ‘Claudius’
AFNI_version.txt : AFNI_19.2.21, macos_10.12_local, Aug 29 2019
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.5.2 (2018-12-20) – “Eggshell Igloo”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/afni/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 1 (/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

** have python3 but not python2

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

R RHOME : /Library/Frameworks/R.framework/Resources

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

------------------------------ python libs -------------------------------
** failed to load module PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

-------------------------------- env vars --------------------------------
PATH = /usr/local/ants/bin/:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/afni:/Applications/MATLAB_R2019a.app/bin:/Users/z/Documents/OneDrive/Sync/Scripts

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /usr/local/afni

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.11

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
– consider installing gcc under homebrew
++ found valid link /usr/local/lib/libglib-2.0.dylib
to …/Cellar/glib/2.60.6/lib/libglib-2.0.dylib
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
– recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell ‘bash’…
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
– recent OS X, cheating to check DYLD_LIBRARY_PATH in shell ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
insufficient data for AFNI bootcamp

Thank you,
2086

rickr · September 2, 2019, 9:48pm

What are you doing to get that error, sourcing from R? The system check shows success with 3dMVM.

Thanks,

rick

EXP.2086 · September 3, 2019, 1:02am

Hi Rick,

Thanks for your reply. Yes, when sourcing from R. I use read.AFNI in R to do some data extraction, then do some calculation with R, and read.AFNI in R works more quickly than in Matlab. AFNI version before Jul 25 2019 works well, I did not test all versions after that, but version 22 Aug 2019 and version Aug 29 2019 showed the same error message.

Thank you,
2086

rickr · September 3, 2019, 1:23am

Hi 2086,

Okay, that is helpful to know. Due to the way macs now restrict dynamic loading, R_io.so will probably not change its style of handling that any time soon. So when loading it directly in R, you should use the method applied in the similar R programs, such as 3dMVM (a very short shell script). See how it sets R_LD_LIBRARY_PATH, and apply that in your own shell.

Hopefully that will work better.

rick

EXP.2086 · September 3, 2019, 7:25am

It works now, thank you Rick!

EXP.2086 · May 11, 2021, 3:36am

Hi Rick,
Is there a way to make source("/usr/local/afni/AFNIio.R") works in RStudio? It did work for R in terminal after add “R_LD_LIBRARY_PATH” in bashrc; but I could not make it work in RStudio. I tried to add lines below into ~/.Renviron file:


PATH=${PATH}:/usr/local/afni
DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH=${R_HOME}/lib:/usr/local/afni:/opt/X11/lib/flat_namespace:/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server
R_LD_LIBRARY_PATH=${R_HOME}/lib:/usr/local/afni:/opt/X11/lib/flat_namespace

But it show this error when source("/usr/local/afni/AFNIio.R") :


Error in dyn.load(ll) : 
  unable to load shared object '/usr/local/afni/R_io.so':
  dlopen(/usr/local/afni/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
  Referenced from: /usr/local/afni/R_io.so
  Reason: image not found

Thanks,
2086