afni.nimh.nih.gov

Hi All,

I am running AFNI 22.2.03 under a linux virtual machine (Mint v.20.3). When running 3dMVM using a script that runs successfully under afni 20.3.03, I get the following error on the virtual machine running AFNI 22.2.03 after which the output halts:

Error in ans[ypos] <- rep(yes, length.out = len)[ypos] :
replacement has length zero
Calls: process.MVM.opts -> gl_Constr -> ifelse

In the outputs (saved to files) the first line of the successful execution that does not appear in the output of the failed execution is:

Will read ave_mask_social70+tlrc
-- read.AFNI via clib BRIK

Any suggestions how I might troubleshoot this error would be much appreciated.

The 3dMVM script text and output of afni_system_check.py are below.

Thank you,
Jay

3dMVM -prefix money_masked -jobs 8 \
-bsVars Group \
-wsVars Condit \
-mask ave_mask_social70+tlrc \
-verb 4 \
-num_glt 9 \
-gltLabel 1 pic_outcome_controls -gltCode 1 'Group : 1*con Condit : 1*pic -1*outcome' \
-gltLabel 2 pic_outcome_patientss -gltCode 2 'Group : 1*sz Condit : 1*pic -1*outcome' \
-gltLabel 3 pic_controls -gltCode 3 'Group : 1*con Condit : 1*pic' \
-gltLabel 4 pic_patients -gltCode 4 'Group : 1*sz Condit : 1*pic' \
-gltLabel 5 outcome_controls -gltCode 5 'Group : 1*con Condit : 1*outcome' \
-gltLabel 6 outcome_patients -gltCode 6 'Group : 1*sz Condit : 1*outcome' \
-gltLabel 7 group_by_pic -gltCode 7 'Group : 1*con -1*sz Condit : 1*pic' \
-gltLabel 8 group_by_outcome -gltCode 8 'Group : 1*con -1*sz Condit : 1*outcome' \
-gltLabel 9 pic_outcome_int_con_pat -gltCode 9 'Group : 1*con -1*sz Condit : 1*pic -1*outcome' \
-dataTable \
Subj Group Condit InputFile \
3002 sz pic 3002_money_pic+tlrc \
3004 sz pic 3004_money_pic+tlrc \
3005 sz pic 3005_money_pic+tlrc \
3006 sz pic 3006_money_pic+tlrc \
3010 sz pic 3010_money_pic+tlrc \
3011 sz pic 3011_money_pic+tlrc \
3014 sz pic 3014_money_pic+tlrc \
3015 sz pic 3015_money_pic+tlrc \
3016 sz pic 3016_money_pic+tlrc \
3017 sz pic 3017_money_pic+tlrc \
3018 sz pic 3018_money_pic+tlrc \
3020 sz pic 3020_money_pic+tlrc \
3021 sz pic 3021_money_pic+tlrc \
3023 sz pic 3023_money_pic+tlrc \
3026 sz pic 3026_money_pic+tlrc \
3029 sz pic 3029_money_pic+tlrc \
3030 sz pic 3030_money_pic+tlrc \
3033 sz pic 3033_money_pic+tlrc \
3034 sz pic 3034_money_pic+tlrc \
3036 sz pic 3036_money_pic+tlrc \
3037 sz pic 3037_money_pic+tlrc \
3039 sz pic 3039_money_pic+tlrc \
3040 sz pic 3040_money_pic+tlrc \
3041 sz pic 3041_money_pic+tlrc \
3043 sz pic 3043_money_pic+tlrc \
3044 sz pic 3044_money_pic+tlrc \
3046 sz pic 3046_money_pic+tlrc \
3052 sz pic 3052_money_pic+tlrc \
3053 sz pic 3053_money_pic+tlrc \
3054 sz pic 3054_money_pic+tlrc \
4002 con pic 4002_money_pic+tlrc \
4003 con pic 4003_money_pic+tlrc \
4004 con pic 4004_money_pic+tlrc \
4005 con pic 4005_money_pic+tlrc \
4006 con pic 4006_money_pic+tlrc \
4007 con pic 4007_money_pic+tlrc \
4008 con pic 4008_money_pic+tlrc \
4009 con pic 4009_money_pic+tlrc \
4010 con pic 4010_money_pic+tlrc \
4012 con pic 4012_money_pic+tlrc \
4013 con pic 4013_money_pic+tlrc \
4014 con pic 4014_money_pic+tlrc \
4015 con pic 4015_money_pic+tlrc \
4016 con pic 4016_money_pic+tlrc \
4017 con pic 4017_money_pic+tlrc \
4018 con pic 4018_money_pic+tlrc \
4019 con pic 4019_money_pic+tlrc \
4020 con pic 4020_money_pic+tlrc \
4021 con pic 4021_money_pic+tlrc \
4022 con pic 4022_money_pic+tlrc \
4023 con pic 4023_money_pic+tlrc \
4025 con pic 4025_money_pic+tlrc \
4026 con pic 4026_money_pic+tlrc \
4027 con pic 4027_money_pic+tlrc \
4028 con pic 4028_money_pic+tlrc \
4029 con pic 4029_money_pic+tlrc \
4030 con pic 4030_money_pic+tlrc \
4031 con pic 4031_money_pic+tlrc \
4033 con pic 4033_money_pic+tlrc \
4034 con pic 4034_money_pic+tlrc \
4035 con pic 4035_money_pic+tlrc \
3002 sz outcome 3002_money_outcome+tlrc \
3004 sz outcome 3004_money_outcome+tlrc \
3005 sz outcome 3005_money_outcome+tlrc \
3006 sz outcome 3006_money_outcome+tlrc \
3010 sz outcome 3010_money_outcome+tlrc \
3011 sz outcome 3011_money_outcome+tlrc \
3014 sz outcome 3014_money_outcome+tlrc \
3015 sz outcome 3015_money_outcome+tlrc \
3016 sz outcome 3016_money_outcome+tlrc \
3017 sz outcome 3017_money_outcome+tlrc \
3018 sz outcome 3018_money_outcome+tlrc \
3020 sz outcome 3020_money_outcome+tlrc \
3021 sz outcome 3021_money_outcome+tlrc \
3023 sz outcome 3023_money_outcome+tlrc \
3026 sz outcome 3026_money_outcome+tlrc \
3029 sz outcome 3029_money_outcome+tlrc \
3030 sz outcome 3030_money_outcome+tlrc \
3033 sz outcome 3033_money_outcome+tlrc \
3034 sz outcome 3034_money_outcome+tlrc \
3036 sz outcome 3036_money_outcome+tlrc \
3037 sz outcome 3037_money_outcome+tlrc \
3039 sz outcome 3039_money_outcome+tlrc \
3040 sz outcome 3040_money_outcome+tlrc \
3041 sz outcome 3041_money_outcome+tlrc \
3043 sz outcome 3043_money_outcome+tlrc \
3044 sz outcome 3044_money_outcome+tlrc \
3046 sz outcome 3046_money_outcome+tlrc \
3052 sz outcome 3052_money_outcome+tlrc \
3053 sz outcome 3053_money_outcome+tlrc \
3054 sz outcome 3054_money_outcome+tlrc \
4002 con outcome 4002_money_outcome+tlrc \
4003 con outcome 4003_money_outcome+tlrc \
4004 con outcome 4004_money_outcome+tlrc \
4005 con outcome 4005_money_outcome+tlrc \
4006 con outcome 4006_money_outcome+tlrc \
4007 con outcome 4007_money_outcome+tlrc \
4008 con outcome 4008_money_outcome+tlrc \
4009 con outcome 4009_money_outcome+tlrc \
4010 con outcome 4010_money_outcome+tlrc \
4012 con outcome 4012_money_outcome+tlrc \
4013 con outcome 4013_money_outcome+tlrc \
4014 con outcome 4014_money_outcome+tlrc \
4015 con outcome 4015_money_outcome+tlrc \
4016 con outcome 4016_money_outcome+tlrc \
4017 con outcome 4017_money_outcome+tlrc \
4018 con outcome 4018_money_outcome+tlrc \
4019 con outcome 4019_money_outcome+tlrc \
4020 con outcome 4020_money_outcome+tlrc \
4021 con outcome 4021_money_outcome+tlrc \
4022 con outcome 4022_money_outcome+tlrc \
4023 con outcome 4023_money_outcome+tlrc \
4025 con outcome 4025_money_outcome+tlrc \
4026 con outcome 4026_money_outcome+tlrc \
4027 con outcome 4027_money_outcome+tlrc \
4028 con outcome 4028_money_outcome+tlrc \
4029 con outcome 4029_money_outcome+tlrc \
4030 con outcome 4030_money_outcome+tlrc \
4031 con outcome 4031_money_outcome+tlrc \
4033 con outcome 4033_money_outcome+tlrc \
4034 con outcome 4034_money_outcome+tlrc \
4035 con outcome 4035_money_outcome+tlrc

afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 5.4.0-132-generic
version: #148-Ubuntu SMP Mon Oct 17 16:02:06 UTC 2022
distribution: linuxmint 20.3 una
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/jay/software/afni/abin_22.3.03/afni
afni version : Precompiled binary linux_ubuntu_16_64: Nov 9 2022
: AFNI_22.3.05 'Lucius Verus'
AFNI_version.txt : AFNI_22.3.05, linux_ubuntu_16_64, Nov 09 2022
which python : /usr/bin/python
python version : 3.8.10
which R : /usr/bin/R
R version : R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting"
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/jay/software/afni/abin_22.3.03/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.8)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.8)


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 : /usr/lib/R

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 : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
matplotlib version : 3.1.2

-------------------------------- env vars --------------------------------
PATH = /home/jay/software/afni/abin_22.3.03:/usr/lib/R/site-library:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

PYTHONPATH =
R_LIBS = /usr/lib/R/site-library

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (99714M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: ...ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /home/jay/software/afni/abin_22.3.03

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.9 (amd64)


========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'