trouble installing R packages for Ubuntu 18.04 AFNI install

alfarmer8 · October 25, 2019, 2:06pm

Hi, I’m having trouble installing AFNI for Ubuntu 18.04. I’ve followed the instructions for AFNI installation on the NIH page, but I can’t get past the R packages install. It looks like the dependencies for the required R packages aren’t installing, but when I try to install the dependencies manually in R it says they aren’t available. Any help would be much appreciated!

-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 5.0.0-31-generic
version: #33~18.04.1-Ubuntu SMP Tue Oct 1 10:20:39 UTC 2019
distribution: Ubuntu 18.04 bionic
number of CPUs: 12
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/anna/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Oct 21 2019
: AFNI_19.3.08 ‘Nero’
AFNI_version.txt : AFNI_19.3.08, linux_ubuntu_16_64, Oct 21 2019
which python : /usr/bin/python
python version : 2.7.15+
which R : /usr/bin/R
R version : R version 3.4.4 (2018-03-15) – “Someone to Lean On”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/anna/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/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
3dMVM : success

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

    oo Warning: 
       These packages are not installed on the computer: afex!
    These packages are not installed on the computer: phia!
    These packages are not installed on the computer: brms!
    These packages are not installed on the computer: metafor!

R RHOME : /usr/lib/R

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

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib/python2.7/dist-packages/PyQt4/init.pyc

** failed to load module matplotlib.pyplot
– matplotlib.pyplot is not required, but is desirable

– python binaries under /usr/local/bin:
/usr/local/bin/python2.7

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/anna/abin

PYTHONPATH =
R_LIBS = /home/anna/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ 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 /home/anna/abin

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.12 (amd64)

have Ubuntu system: Ubuntu 18.04 bionic
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Oct 21 2019

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

login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
missing R packages (see rPkgsInstall)
insufficient data for AFNI bootcamp

ptaylor · October 25, 2019, 3:57pm

Hi-

I think the problem is that your version of R is too old:


R version : R version 3.4.4 (2018-03-15) -- "Someone to Lean On"

It should be at least 3.5., and probably on Linux even 3.6. is standard now.

Under the Ubuntu 18.04 setup instructions, there is a description of using a startup script to update your R:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu18.html#install-r
… but please note that this will purge your current R and install a newer version with the desired packages-- if you have special packages or something to save, then another route might be easier. (However, updating R and packages is often tricky; the “full removal + update of repo list + reinstall newer R” often seems the easiest.)

–pt

alfarmer8 · October 25, 2019, 4:32pm

When I run these scripts, it installs R version 3.4.4 . Do you have any other thoughts? Thanks again for your help.

ptaylor · October 25, 2019, 9:30pm

That’s weird.

What is the output of this:


grep -H cloud /etc/apt/sources.list

?

–pt

pereanez · December 31, 2019, 7:03pm

Hi,
I have followed the installation guide for Ubuntu 18.04, however, four libraries continue to be missing “afex”, “phia”, “brms”, and “metafor”. I see from the message board history that user alfarmer8 had the same issue a couple of months ago, and I’m wondering whether a solution was found. Thank you, and happy new year! :)o

-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 5.0.0-37-generic
version: #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 UTC 2019
distribution: elementary 5.1 hera
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/pereanez/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Dec 27 2019
: AFNI_19.3.18 ‘Nero’
AFNI_version.txt : AFNI_19.3.18, linux_ubuntu_16_64, Dec 27 2019
which python : /usr/bin/python
python version : 2.7.15+
which R : /usr/bin/R
R version : R version 3.6.2 (2019-12-12) – “Dark and Stormy Night”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/pereanez/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/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
3dMVM : success

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

    oo Warning: 
       These packages are not installed on the computer: afex!
    These packages are not installed on the computer: phia!
    These packages are not installed on the computer: brms!
    These packages are not installed on the computer: metafor!

R RHOME : /usr/lib/R

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

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib/python2.7/dist-packages/PyQt4/init.pyc

** failed to load module matplotlib.pyplot
– matplotlib.pyplot is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/pereanez/abin

PYTHONPATH =
R_LIBS = /home/pereanez/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: …2019 [ptaylor]: updated FT_analysis/results.QC_FT.05
data dir : found AFNI_demos under $HOME
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer 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/pereanez/abin

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.12 (amd64)

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

login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
shell bash: consider sourcing (non-login) .bashrc from (login) .profile
missing R packages (see rPkgsInstall)

ptaylor · December 31, 2019, 8:33pm

Hi-

I’m guessing that is on Windows Subsystem Linux-- is that right?

Did you try this solution:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,162604,162604#msg-162604
?

–pt

chammo20 · August 25, 2020, 1:20pm

I’m having similar problems installing R packages for Ubuntu 18.04.
I’ve tried the different solutions presented in this thread without sucess.

What do you recommend I try next.

I’ve posted below my output results when running system check.

Thank you for your help

-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 4.4.0-18362-Microsoft
version: #836-Microsoft Mon May 05 16:04:00 PST 2020
distribution: Ubuntu 18.04 bionic
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/chammo20/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Aug 21 2020
: AFNI_20.2.14 ‘Aulus Vitellius’
AFNI_version.txt : AFNI_20.2.14, linux_ubuntu_16_64, Aug 21 2020
which python : /usr/bin/python
python version : 2.7.15rc1
which R : /usr/bin/R
R version : R version 3.6.3 (2020-02-29) – “Holding the Windsock”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/chammo20/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/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
3dMVM : success

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

    oo Warning:
       These packages are not installed on the computer: brms!

R RHOME : /usr/lib/R

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

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib/python2.7/dist-packages/PyQt4/init.pyc

++ module loaded: matplotlib.pyplot
module file : /usr/lib/python2.7/dist-packages/matplotlib/pyplot.pyc

-------------------------------- 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.UbuntuonWindows_2004.2020.812.0_x64__79rhkp1fndgsc:/mnt/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/iCLS/:/mnt/c/Program Files/Intel/Intel(R) Management Engine Components/iCLS/:/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 (x86)/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Program Files/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/IPT:/mnt/c/Program Files/Intel/Intel(R) Management Engine Components/IPT:/mnt/c/Program Files/Intel/WiFi/bin/:/mnt/c/Program Files/Common Files/Intel/WirelessCommon/:/mnt/c/Program Files/IBM/SPSS/Statistics/Subscription/JRE/bin:/mnt/c/Program Files/IBM/SPSS/Statistics/25/JRE/bin:/mnt/c/Users/bmc/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/bmc/AppData/Local/Polycom/RealPresence Desktop/:/snap/bin:/home/chammo20/abin:/home/chammo20/abin

PYTHONPATH =
R_LIBS = /home/chammo20/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer 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/chammo20/abin

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.3 (amd64)

have Ubuntu system: Ubuntu 18.04 bionic
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Aug 21 2020

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

just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
missing R packages (see rPkgsInstall)video

ptaylor · August 25, 2020, 2:10pm

Ugh, R… I don’t know why life is so difficult with it… But anyways…

Can you please try copy+pasting each of these lines? (I would copy+paste the first one, and you will be asked for your administrative password, and then you can copy+paste the others all at once, if you want, and the admin password will be saved to apply to the others for a short interval):


sudo add-apt-repository -y "ppa:marutter/rrutter3.5"
sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"

sudo apt update

sudo apt install -y r-cran-brms

–pt

chammo20 · August 25, 2020, 6:22pm

Just tried it.
I got an error message with the last command “sudo apt install -y r-cran-brms” stating:

Reading package lists… Done
Building dependency tree
Reading state information… Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
r-cran-brms : Depends: r-cran-rstan but it is not going to be installed
Depends: r-cran-shinystan but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

Ideas?
Thanks.

ptaylor · August 25, 2020, 7:00pm

Hmm, I think that error message "Unable to correct problems, you have held broken packages. " means that a previous install of something didn’t complete successfully.

What is the output of:


apt-mark showhold

?

–pt

chammo20 · August 25, 2020, 8:01pm

I don’t get any output when I enter that command.
The output is as follows:

chammo20@DESKTOP-BB7NQKM:~$ apt-mark showhold
chammo20@DESKTOP-BB7NQKM:~$ apt-mark hold
E: No packages found
chammo20@DESKTOP-BB7NQKM:~$ apt-mark unhold
E: No packages found
chammo20@DESKTOP-BB7NQKM:~$
chammo20@DESKTOP-BB7NQKM:~$ apt-mark showauto
adwaita-icon-theme
aspell
aspell-en
at-spi2-core
avahi-daemon
binutils
binutils-common
binutils-x86-64-linux-gnu
blt
bubblewrap
bzip2-doc
cpp
cpp-7
dbus-user-session
dconf-gsettings-backend
dconf-service
desktop-file-utils
dictionaries-common
dpkg-dev
emacsen-common
enchant
evince-common
fakeroot
fontconfig
fontconfig-config
fonts-dejavu-core
fonts-droid-fallback
fonts-lyx
fonts-noto-mono
g++
g+±7
gcc
gcc-6-base
gcc-7
gcc-7-base
gcr
gedit-common
geoclue-2.0
gfortran
gfortran-7
ghostscript
gir1.2-atk-1.0
gir1.2-freedesktop
gir1.2-gdesktopenums-3.0
gir1.2-gdkpixbuf-2.0
gir1.2-gnomedesktop-3.0
gir1.2-gtk-3.0
gir1.2-gtksource-3.0
gir1.2-harfbuzz-0.0
gir1.2-notify-0.7
gir1.2-pango-1.0
gir1.2-peas-1.0
gir1.2-soup-2.4
glib-networking
glib-networking-common
glib-networking-services
gnome-desktop3-data
gnome-icon-theme
gnome-keyring
gnome-keyring-pkcs11
gnome-settings-daemon
gnome-settings-daemon-schemas
gnome-shell-common
gnome-terminal-data
gnome-tweaks
gsettings-desktop-schemas
gsfonts
gstreamer1.0-gl
gstreamer1.0-plugins-base
gstreamer1.0-plugins-good
gstreamer1.0-pulseaudio
gstreamer1.0-x
gtk-update-icon-cache
gvfs
gvfs-backends
gvfs-common
gvfs-daemons
gvfs-libs
hicolor-icon-theme
humanity-icon-theme
hunspell-en-us
icu-devtools
iio-sensor-proxy
javascript-common
libaa1
libalgorithm-diff-perl
libalgorithm-diff-xs-perl
libalgorithm-merge-perl
libarchive13
libasan4
libasound2
libasound2-data
libasound2-plugins
libaspell15
libasyncns0
libatasmart4
libatk-bridge2.0-0
libatk1.0-0
libatk1.0-data
libatomic1
libatspi2.0-0
libaudio2
libauthen-sasl-perl
libavahi-client3
libavahi-common-data
libavahi-common3
libavahi-core7
libavahi-glib1
libavc1394-0
libbinutils
libblas-dev
libblas3
libblockdev-crypto2
libblockdev-fs2
libblockdev-loop2
libblockdev-part-err2
libblockdev-part2
libblockdev-swap2
libblockdev-utils2
libblockdev2
libbrotli1
libbz2-dev
libc-dev-bin
libc6-dev
libcaca0
libcairo-gobject2
libcairo2
libcanberra-gtk3-0
libcanberra-gtk3-module
libcanberra0
libcc1-0
libcdio-cdda2
libcdio-paranoia2
libcdio17
libcdparanoia0
libcilkrts5
libcolord2
libcroco3
libcups2
libcupsfilters1
libcupsimage2
libdaemon0
libdata-dump-perl
libdatrie1
libdbus-glib-1-2
libdbusmenu-glib4
libdbusmenu-gtk3-4
libdconf1
libdee-1.0-4
libdjvulibre-text
libdjvulibre21
libdpkg-perl
libdrm-amdgpu1
libdrm-dev
libdrm-intel1
libdrm-nouveau2
libdrm-radeon1
libdv4
libegl-mesa0
libegl1
libenchant1c2a
libencode-locale-perl
libepoxy0
libevdocument3-4
libevview3-3
libexempi3
libexif12
libfakeroot
libfile-basedir-perl
libfile-desktopentry-perl
libfile-fcntllock-perl
libfile-listing-perl
libfile-mimeinfo-perl
libflac8
libfont-afm-perl
libfontconfig1
libfontenc1
libfreetype6
libgail-3-0
libgbm1
libgcc-7-dev
libgck-1-0
libgcr-base-3-1
libgcr-ui-3-1
libgd3
libgdata-common
libgdata22
libgdk-pixbuf2.0-0
libgdk-pixbuf2.0-bin
libgdk-pixbuf2.0-common
libgeoclue-2-0
libgeocode-glib0
libgfortran-7-dev
libgfortran4
libgl1
libgl1-mesa-dev
libgl1-mesa-dri
libgl1-mesa-glx
libglapi-mesa
libgles1
libgles2
libglib2.0-bin
libglib2.0-dev
libglib2.0-dev-bin
libglu1-mesa
libglvnd-core-dev
libglvnd-dev
libglvnd0
libglx-mesa0
libglx0
libgnome-autoar-0-0
libgnome-desktop-3-17
libgoa-1.0-0b
libgoa-1.0-common
libgomp1
libgpgme11
libgphoto2-6
libgphoto2-l10n
libgphoto2-port12
libgraphene-1.0-0
libgraphite2-3
libgraphite2-dev
libgs9
libgs9-common
libgsl23
libgslcblas0
libgspell-1-1
libgspell-1-common
libgstreamer-gl1.0-0
libgstreamer-plugins-base1.0-0
libgstreamer-plugins-good1.0-0
libgstreamer1.0-0
libgtk-3-0
libgtk-3-bin
libgtk-3-common
libgtksourceview-3.0-1
libgtksourceview-3.0-common
libgudev-1.0-0
libgweather-3-15
libgweather-common
libgxps2
libharfbuzz-dev
libharfbuzz-gobject0
libharfbuzz-icu0
libharfbuzz0b
libhtml-form-perl
libhtml-format-perl
libhtml-parser-perl
libhtml-tagset-perl
libhtml-tree-perl
libhttp-cookies-perl
libhttp-daemon-perl
libhttp-date-perl
libhttp-message-perl
libhttp-negotiate-perl
libhunspell-1.6-0
libhyphen0
libice6
libicu-dev
libicu-le-hb-dev
libicu-le-hb0
libiculx60
libiec61883-0
libijs-0.35
libimobiledevice6
libio-html-perl
libio-socket-ssl-perl
libipc-system-simple-perl
libisl19
libitm1
libjack-jackd2-0
libjansson4
libjavascriptcoregtk-4.0-18
libjbig0
libjbig2dec0
libjpeg-dev
libjpeg-turbo8
libjpeg-turbo8-dev
libjpeg8
libjpeg8-dev
libjs-jquery
libjs-jquery-ui
libjson-glib-1.0-0
libjson-glib-1.0-common
libkpathsea6
liblapack-dev
liblapack3
liblcms2-2
libldb1
libllvm7
liblsan0
libltdl7
liblwp-mediatypes-perl
liblwp-protocol-https-perl
liblzma-dev
libmailtools-perl
libmbim-glib4
libmbim-proxy
libmm-glib0
libmng2
libmotif-common
libmp3lame0
libmpc3
libmpg123-0
libmpx2
libmtp-common
libmtp-runtime
libmtp9
libmysqlclient20
libnautilus-extension1a
libncurses5-dev
libnet-dbus-perl
libnet-http-perl
libnet-smtp-ssl-perl
libnet-ssleay-perl
libnetpbm10
libnl-3-200
libnl-genl-3-200
libnm0
libnotify4
libnspr4
libnss-mdns
libnss3
liboauth0
libogg0
libopengl0
libopus0
liborc-0.4-0
libpam-gnome-keyring
libpango-1.0-0
libpangocairo-1.0-0
libpangoft2-1.0-0
libpangoxft-1.0-0
libpaper-utils
libpaper1
libparted-fs-resize0
libpciaccess0
libpcre16-3
libpcre2-16-0
libpcre2-32-0
libpcre2-8-0
libpcre2-dev
libpcre2-posix0
libpcre3-dev
libpcre32-3
libpcrecpp0v5
libpcsclite1
libpeas-1.0-0
libpeas-common
libpixman-1-0
libplist3
libpng-dev
libpng-tools
libpoppler-glib8
libpoppler73
libproxy1v5
libpthread-stubs0-dev
libpulse-mainloop-glib0
libpulse0
libpulsedsp
libpython-stdlib
libpython2.7
libpython2.7-minimal
libpython2.7-stdlib
libqmi-glib5
libqmi-proxy
libqt4-dbus
libqt4-declarative
libqt4-designer
libqt4-help
libqt4-network
libqt4-script
libqt4-scripttools
libqt4-sql
libqt4-sql-mysql
libqt4-svg
libqt4-test
libqt4-xml
libqt4-xmlpatterns
libqtassistantclient4
libqtcore4
libqtdbus4
libqtgui4
libquadmath0
libraw1394-11
libreadline-dev
librest-0.7-0
librsvg2-2
librsvg2-common
libsamplerate0
libsecret-1-0
libsecret-common
libsensors4
libshout3
libsm6
libsmbclient
libsndfile1
libsoup-gnome2.4-1
libsoup2.4-1
libspectre1
libspeex1
libspeexdsp1
libssl-doc
libstartup-notification0
libstdc+±7-dev
libstemmer0d
libtag1v5
libtag1v5-vanilla
libtalloc2
libtcl8.6
libtdb1
libtevent0
libthai-data
libthai0
libtheora0
libtie-ixhash-perl
libtiff5
libtimedate-perl
libtinfo-dev
libtk8.6
libtracker-sparql-2.0-0
libtry-tiny-perl
libtsan0
libtwolame0
libubsan0
libudisks2-0
libunity-protocol-private0
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ebtables
ed
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file
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ftp
fuse
gawk
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gedit
geoip-database
gettext-base
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git
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irqbalance
isc-dhcp-client
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klibc-utils
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libaccountsservice0
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openssl
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pciutils
perl
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python-matplotlib
python-qt4
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python3-attr
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python3-certifi
python3-cffi-backend
python3-chardet
python3-click
python3-colorama
python3-commandnotfound
python3-configobj
python3-constantly
python3-cryptography
python3-dbus
python3-debconf
python3-debian
python3-distro-info
python3-distupgrade
python3-gdbm
python3-gi
python3-httplib2
python3-hyperlink
python3-idna
python3-incremental
python3-jinja2
python3-json-pointer
python3-jsonpatch
python3-jsonschema
python3-jwt
python3-markupsafe
python3-minimal
python3-newt
python3-oauthlib
python3-openssl
python3-pam
python3-pkg-resources
python3-problem-report
python3-pyasn1
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python3-requests
python3-requests-unixsocket
python3-serial
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python3-urllib3
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python3-zope.interface
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r-base-dev
readline-common
rsync
rsyslog
run-one
screen
sed
sensible-utils
shared-mime-info
snapd
software-properties-common
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squashfs-tools
ssh-import-id
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systemd
systemd-sysv
sysvinit-utils
tar
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time
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ubuntu-release-upgrader-core
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ucf
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uidmap
unattended-upgrades
update-manager-core
update-notifier-common
ureadahead
usbutils
util-linux
uuid-runtime
vim
vim-common
vim-runtime
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wget
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xauth
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xfonts-100dpi
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xkb-data
xterm
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xxd
xz-utils
zerofree
zlib1g

chammo20 · August 27, 2020, 4:36pm

Any other thoughts?
Thank you again

ptaylor · August 27, 2020, 5:37pm

Can you try running this:


sudo apt-get install -f

to see if that will fix your broken installation? What output/final lines does that give?

–pt

chammo20 · August 27, 2020, 6:28pm

It didn’t fix it.
the output is:

chammo20@DESKTOP-BB7NQKM:~$ sudo apt-get install -f
Reading package lists… Done
Building dependency tree
Reading state information… Done
The following packages were automatically installed and are no longer required:
libstartup-notification0 libxcb-util1
Use ‘sudo apt autoremove’ to remove them.
0 upgraded, 0 newly installed, 0 to remove and 377 not upgraded.

ptaylor · August 27, 2020, 6:50pm

OK, so it doesn’t appear like there is something broken in the apt install, which is good.

Since the initial message said it wouldn’t install some dependencies, can you try installing those explicitly first:


sudo apt install -y r-cran-rstan r-cran-shinystan

and if those go well (note: those unfortunately take a long time to build), then try the:


sudo apt install -y r-cran-brms

again?

–pt

chammo20 · August 27, 2020, 7:02pm

I’m now getting the following error message (shown below)
It states that I can’t install r-cran-stan b/c I don’t have r-cran-v8
In trying to install r-cran-v8 it states that I don’t have libnode64 and it won’t let me install libnode64

See below error message:

chammo20@DESKTOP-BB7NQKM:~$ sudo apt install -y r-cran-rstan r-cran-shinystan
[sudo] password for chammo20:
Reading package lists… Done
Building dependency tree
Reading state information… Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
r-cran-rstan : Depends: r-cran-v8 but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
chammo20@DESKTOP-BB7NQKM:~$ sudo apt install -y r-cran-v8 r-cran-rstan r-cran-shinystan
Reading package lists… Done
Building dependency tree
Reading state information… Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
r-cran-v8 : Depends: libnode64 but it is not installable
E: Unable to correct problems, you have held broken packages.
chammo20@DESKTOP-BB7NQKM:~$ sudo apt install -y libnode64 r-cran-v8 r-cran-rstan r-cran-shinystan
Reading package lists… Done
Building dependency tree
Reading state information… Done
Package libnode64 is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package ‘libnode64’ has no installation candidate

ptaylor · August 27, 2020, 7:21pm

Crisis…

Just to check your sources list, what is the output of:


grep -H cloud /etc/apt/sources.list

?

–pt

chammo20 · August 27, 2020, 9:10pm

Output:

chammo20@DESKTOP-BB7NQKM:~$ grep -H cloud /etc/apt/sources.list
/etc/apt/sources.list:deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/
/etc/apt/sources.list:deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/

ptaylor · August 27, 2020, 9:22pm

Yeah, that seems fine (only one of those lines is necessary to have in that file, but having 2 shouldn’t be a problem).

Ummm, I pinged our R installation expert (=Justin) about this to see if he has any ideas about this… Sorry, I am not sure why things are so problematic.

One question: did you upgrade your R from a previous existing version, or was this a clean system and you installed R v3.6 from the start?

–pt

chammo20 · August 28, 2020, 4:17pm

I tried to install AFNI sometime last year ran into errors and then decided to delay taking the bootcamp till this year.
So I could have partially installed an older version of R.