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1

hello there i need FATCAT for resting-state fmri analysis. i am using WSL Ubuntu 20.04
when i run command @afni_R_package_install -shiny -circos
i get this output:
osman@DESKTOP-A849Q2J:~$ @afni_R_package_install -shiny -circos
Installing: c(‘shiny’,‘shinydashboard’,‘plotly’,‘colourpicker’,‘data.table’,‘gplots’,‘RColorBrewer’,‘psych’)

Installing packages into ‘/home/osman/R’
(as ‘lib’ is unspecified)
trying URL ‘https://cloud.r-project.org/src/contrib/shiny_1.7.1.tar.gz’
Content type ‘application/x-gzip’ length 2963486 bytes (2.8 MB)

downloaded 2.8 MB

trying URL ‘https://cloud.r-project.org/src/contrib/shinydashboard_0.7.2.tar.gz’
Content type ‘application/x-gzip’ length 239254 bytes (233 KB)

downloaded 233 KB

trying URL ‘https://cloud.r-project.org/src/contrib/plotly_4.10.0.tar.gz’
Content type ‘application/x-gzip’ length 3842199 bytes (3.7 MB)

downloaded 3.7 MB

trying URL ‘https://cloud.r-project.org/src/contrib/colourpicker_1.1.1.tar.gz’
Content type ‘application/x-gzip’ length 1233214 bytes (1.2 MB)

downloaded 1.2 MB

trying URL ‘https://cloud.r-project.org/src/contrib/data.table_1.14.2.tar.gz’
Content type ‘application/x-gzip’ length 5301817 bytes (5.1 MB)

downloaded 5.1 MB

trying URL ‘https://cloud.r-project.org/src/contrib/gplots_3.1.1.tar.gz’
Content type ‘application/x-gzip’ length 520248 bytes (508 KB)

downloaded 508 KB

trying URL ‘https://cloud.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz’
Content type ‘application/x-gzip’ length 11532 bytes (11 KB)

downloaded 11 KB

trying URL ‘https://cloud.r-project.org/src/contrib/psych_2.1.9.tar.gz’
Content type ‘application/x-gzip’ length 2068413 bytes (2.0 MB)

downloaded 2.0 MB

  • installing source package ‘shiny’ …
    ** package ‘shiny’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    *** copying figures
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (shiny)
  • installing source package ‘data.table’ …
    ** package ‘data.table’ successfully unpacked and MD5 sums checked
    ** using staged installation
    gcc -std=gnu99 -std=gnu11 9.3.0
    zlib 1.2.11 is available ok
    R CMD SHLIB supports OpenMP without any extra hint
    ** libs
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c assign.c -o assign.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c between.c -o between.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bmerge.c -o bmerge.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chmatch.c -o chmatch.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cj.c -o cj.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c coalesce.c -o coalesce.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dogroups.c -o dogroups.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastmean.c -o fastmean.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fcast.c -o fcast.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fifelse.c -o fifelse.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmelt.c -o fmelt.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c forder.c -o forder.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c frank.c -o frank.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fread.c -o fread.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c freadR.c -o freadR.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c froll.c -o froll.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c frollR.c -o frollR.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c frolladaptive.c -o frolladaptive.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fsort.c -o fsort.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fwrite.c -o fwrite.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fwriteR.c -o fwriteR.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gsumm.c -o gsumm.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ijoin.c -o ijoin.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inrange.c -o inrange.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nafill.c -o nafill.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nqrecreateindices.c -o nqrecreateindices.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c openmp-utils.c -o openmp-utils.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c quickselect.c -o quickselect.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbindlist.c -o rbindlist.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reorder.c -o reorder.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c shift.c -o shift.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c snprintf.c -o snprintf.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subset.c -o subset.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c transpose.c -o transpose.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c types.c -o types.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uniqlist.c -o uniqlist.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c vecseq.c -o vecseq.o
    gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c wrappers.c -o wrappers.o
    gcc -std=gnu99 -std=gnu11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz -L/usr/lib/R/lib -lR
    PKG_CFLAGS = -fopenmp
    PKG_LIBS = -fopenmp -lz
    if [ “data.table.so” != “datatable.so” ]; then mv data.table.so datatable.so; fi
    if [ “” != “Windows_NT” ] && [ uname -s = ‘Darwin’ ]; then install_name_tool -id datatable.so datatable.so; fi
    installing to /home/osman/R/00LOCK-data.table/00new/data.table/libs
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded from temporary location
    ** checking absolute paths in shared objects and dynamic libraries
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (data.table)
  • installing source package ‘gplots’ …
    ** package ‘gplots’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** R
    ** data
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (gplots)
  • installing source package ‘RColorBrewer’ …
    ** package ‘RColorBrewer’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (RColorBrewer)
  • installing source package ‘psych’ …
    ** package ‘psych’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (psych)
  • installing source package ‘shinydashboard’ …
    ** package ‘shinydashboard’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (shinydashboard)
  • installing source package ‘plotly’ …
    ** package ‘plotly’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** demo
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    *** copying figures
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (plotly)
  • installing source package ‘colourpicker’ …
    ** package ‘colourpicker’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (colourpicker)

The downloaded source packages are in
‘/tmp/RtmpsJq7wK/downloaded_packages’
Installing: OmicCircos

Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install
Execution halted

2

Hi,
What version of R do you have installed?
If it is greater 4 or greater, you can run this from R:

(you should be able to start R at the terminal by typing):


R

Then run this in R


install.packages("BiocManager",repos="https://cloud.r-project.org")
BiocManager::install("OmicCircos")

then to quit R:


q()

I’ll put in a check for this in the next release.

Thanks, Justin

3

i installed the BiocManager and then the OmicCircos.
but i still get the same error:

The downloaded source packages are in
‘/tmp/RtmpBOscMN/downloaded_packages’
Installing: OmicCircos

Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install
Execution halted

4

Hi,
Can you post the output of:?


afni_system_check.py -check_all

Thanks

5

osman@DESKTOP-A849Q2J:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.4.0-19041-Microsoft
version: #1237-Microsoft Sat Sep 11 14:32:00 PST 2021
distribution: ubuntu 20.04 focal
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/osman/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Feb 18 2022
: AFNI_22.0.11 ‘Hadrian’
AFNI_version.txt : AFNI_22.0.11, linux_ubuntu_16_64, Feb 18 2022
which python : /usr/bin/python
python version : 3.8.10
which R : /usr/bin/R
R version : R version 4.1.2 (2021-11-01) – “Bird Hippie”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/osman/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.8)
python2 : 0
python3 : 1 (/usr/bin/python3.8)

** 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 : /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 = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.Ubuntu20.04onWindows_2004.2022.8.0_x64__79rhkp1fndgsc:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0/:/mnt/c/Windows/System32/OpenSSH/:/mnt/c/Program Files/Polyspace/R2020a/runtime/win64:/mnt/c/Program Files/Polyspace/R2020a/bin:/mnt/c/Program Files/Polyspace/R2020a/polyspace/bin:/mnt/c/Program Files/NVIDIA Corporation/NVIDIA NvDLISR:/mnt/c/Program Files (x86)/NVIDIA Corporation/PhysX/Common:/mnt/c/Users/Lab/AppData/Local/Microsoft/WindowsApps:/snap/bin:/home/osman/abin

PYTHONPATH =
R_LIBS = /home/osman/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (475207M 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/osman/abin

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.6 (amd64)

have Ubuntu system: ubuntu 20.04 focal
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Feb 18 2022

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

  • just be aware: login shell ‘bash’, but our code examples use ‘tcsh’