hi guys
i'm working on a centos cluster that had afni built in a somewhat piecemeal way but it's been okay until now. we've run @SUMA_Make_Spec and parts of afni_procs before without issue. however recently we began running a full normal afni_proc and we've noticed the QC_* directories are not created. this happens whether "pythonic" or "basic" is specified to -html_review_style.
the apqc_make_tcsh.py and apqc_make_html.py programs both appear to be installed correctly, but i did notice some weirdness in the out.ss_review.sub001.txt file; that file contains all the normal stuff at first, up through line 37 ("final DF fraction") but then line 39 says:
rc: Subscript out of range.
any ideas? let me know if you need any more files or info and THANKS. here's the afni_system_check.py output for the system:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 3.10.0-1160.105.1.el7.x86_64
version: #1 SMP Thu Dec 7 15:39:45 UTC 2023
distribution: CentOS Linux 7.9.2009 Core
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)--------------------- AFNI and related program tests ---------------------
which afni : /opt/afni/abin/afni
afni version : Precompiled binary linux_centos_7_64: Sep 7 2023
: AFNI_23.2.08 'Marcus Didius Severus Julianus'
AFNI_version.txt : AFNI_23.2.08, linux_centos_7_64, Sep 07 2023, local
which python : /usr/bin/python
python version : 3.6.8
which R : /opt/R/bin/R
R version :instances of various programs found in PATH:
afni : 1 (/opt/afni/abin/afni)
R : 2
/opt/R/r-wrapper.sh
/usr/bin/R
python : 2
/usr/bin/python2.7
/usr/bin/python3.6
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.6)testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : success------------------------ dependent program tests -------------------------
checking for dependent programs...which tcsh : /usr/bin/tcsh
which Xvfb : /usr/bin/Xvfbchecking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
/mnt/c7_opt/afni/abin/@global_parse: Command not found.R RHOME : You must set the RVERSION environment variable before using this command.
export RVERSION=NAvailable versions:
3.6.0
4.2.1
4.3.1
4.3.2------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /opt/afni/AFNI_23.2.08/venv/lib64/python3.6/site-packages/matplotlib/pyplot.py
matplotlib version : 3.3.4-------------------------------- env vars --------------------------------
PATH = /opt/grid7/sge/bin:/opt/grid7/sge/bin/lx-amd64:/opt/mico/mico-build/:/opt/muse/muse-3.0.5/bin/:/opt/mass/mass-1.1.1/bin/:/opt/dramms/1.5.1/bin/:/opt/SPM/bin:/usr/local/bin/slicer:/opt/grid7/sge/bin:/opt/grid7/sge/bin/lx-amd64:/opt/qit/qit-build-linux-latest/bin:/opt/nodejs/v12.18.3/bin:/home/vhasfctorris/.npm-packages/bin:/opt/mipav/mipav:/opt/mathworks/bin:/opt/itk-snap:/opt/grid_tools/cnt_qstat/build/bin:/opt/fsl/bin:/opt/freesurfer/bin:/opt/fmriprep/bin:/opt/dcmtk/3.6.0/bin:/opt/ants/bin:/opt/afni/abin:/opt/R/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin/mricron:/opt/pijp-fs/bin:/opt/pijp-nnicv/bin:/opt/pijp-dti/bin:/opt/pijp-asl/bin:/opt/pijp-ants/bin:/opt/pijp-fwe/bin:/opt/pijp-matasl/bin:/opt/pijp-mriqc/bin:/opt/pijp-multiatlas/bin:/opt/pijp-spmseg/bin:/opt/pijp-oxasl/bin:/opt/pijp-asl-mot/bin:/opt/pijp-wmls/bin:/opt/pijp-export/bin:/opt/pycharm/pycharm-community-2022.1.3/bin:/opt/python/3.10.5/bin:/opt/python/3.9.13/bin:/home/vhasfctorris/.local/bin:/home/vhasfctorris/binPYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found .sumarc : found .afni/help/all_progs.COMP : found--------- shell startup files ----------
-- no .tcshrc, will create one as a follower of .cshrc
-- considered operations: path, flatdir, apsearch
(not on a mac, should skip flatdir)-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)dot file test : want 4 modifications across 3 files:
file path flatdir apsearch follower --------------- ---- ------- -------- -------- .cshrc 1 0 1 0 .tcshrc 0 0 0 1 .bashrc 1 0 1 0------------------------------ 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 /opt/afni/abin------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3========================= summary, please fix: =========================
- just be aware: login shell 'bash', but our code examples use 'tcsh'
- 'afni' executable is owned by root
- missing R packages (see rPkgsInstall)
- dot file test : want 4 modifications across 3 files:
- insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)