Ubuntu 16.04 brms error

AFNI Message Board
1

Hi,
I have updated R ver 3.6.1 and the recent rPkgsInstall -pkgs ALL -check command issued the following status:
rPkgsInstall -pkgs ALL -check
This package has been verified on the computer: afex
This package has been verified on the computer: phia
This package has been verified on the computer: snow
This package has been verified on the computer: nlme
This package has been verified on the computer: lme4
This package has been verified on the computer: paran
This package has been verified on the computer: psych
This package has been verified on the computer: brms
This package has been verified on the computer: corrplot
This package has been verified on the computer: metafor

Despite this, when I run BayesianGroupAna.py using the following syntax:
BayesianGroupAna.py -dataTable datatable_FA.txt -y FA_mean -prefix bayesian_N1_FA.txt

I get the following error:

Variables in the table are:

Subj
ROI
FA_mean

Loading required package: brms
Failed with error: ‘cannot read workspace version 3 written by R 3.6.1; need R 3.5.0 or newer’
[1] “missing brms library”

ERROR: Something failed in R!! There is no output file!

Any insight into what maybe going wrong?

Thanks,
Amritha

2

Amritha,

First, verify your R version by typing

R --version

What AFNI version do you have? Try using the program ‘RBA’, and see if you can get it working.

3

I’ve had this problem before. I eventually ended up manually deleting all my R folders and files (because there were old versions of R mixed with new versions of R). Then I re-installed the R-base-core and the AFNI packages to get it to work. But you should try this as your last resort.

4

HI,
I have updated AFNI and R and the versions are as follows:
Precompiled binary linux_ubuntu_16_64: Jul 25 2019 (Version AFNI_19.2.05 ‘Claudius’)

R version 3.6.1 (2019-07-05)

In addition, I just tried running RBA and it ran successfully.
Few of the beginning lines displayed in the terminal are as follows:

RBA -prefix RBA_datatable_FA_ordered.txt -dataTable datatable_FA_ordered.txt -Y FA
Loading required package: Rcpp
Registered S3 method overwritten by ‘xts’:
method from
as.zoo.xts zoo
Loading ‘brms’ package (version 2.9.0). Useful instructions
can be found by typing help(‘brms’). A more detailed introduction
to the package is available through vignette(‘brms_overview’).
Compiling the C++ model
Start sampling

SAMPLING FOR MODEL ‘58ebb7b1a8ff7daaba8b918ff8e8ccce’ NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000277 seconds
…

Following this I tried running BayesianGroupAna.py, adding an additional column ‘group’, to receive the same error as previously posted:
BayesianGroupAna.py -dataTable datatable_FA_ordered.txt -y FA -prefix bayesian_test.txt

Variables in the table are:

Subj
Group
ROI
FA

Loading required package: brms
Failed with error: ‘cannot read workspace version 3 written by R 3.6.1; need R 3.5.0 or newer’
[1] “missing brms library”

ERROR: Something failed in R!! There is no output file!

Amritha

5

Amritha,

How does the result from RBA look to you: making sense? Since RBA works fine, you don’t have to worry about BayesianGroupAna.py: the two programs share roughly the same functionality (and RBA is being constantly maintained and updated).

6

Hi Gang,
The RBA results look sensible and generates the results consistently without complaining. I will continue using this.
Thanks,
Amritha