M1 apple macbookpro
bigsur 11.0.1
fsl install, then error
(base) -MacBook-Pro ~ fsl
Application initialization failed: couldn't connect to display ":0"
Error in startup script: couldn't connect to display ":0"
while executing
"load /usr/local/fsl/extras/lib/libtk8.4.dylib Tk"
("package ifneeded" script)
invoked from within
"package require Tk"
invoked from within
"if { [ string match -nocase *wish* $MYSHELL ] } {
package require Tk
# tk_focusFollowsMouse
#bind Button <Enter> { focus %W ; tk::ButtonEnter ..."
(file "/usr/local/fsl/tcl/fslstart.tcl" line 18)
invoked from within
"source [ file dirname [ info script ] ]/fslstart.tcl"
(file "/usr/local/fsl/tcl/fsl.tcl" line 71)
invoked from within
"source ${FSLDIR}/tcl/${origname}.tcl"
(file "/usr/local/fsl/bin/fsl" line 22)
then I check my fsl environment,
(base) -MacBook-Pro ~ echo $FSLDIR
/usr/local/fsl
(base) -MacBook-Pro ~ flirt -version
FLIRT version 6.0
(base) -MacBook-Pro ~ which imcp
/usr/local/fsl/bin/imcp
then I check my fsl package, it seems ok, no package missing
(base) -MacBook-Pro ~ cd /usr/local/fsl
(base) -MacBook-Pro /usr/local/fsl ls
LICENCE build data extras lib src
README build.log doc fslpython python tcl
bin config etc include refdoc
then I check my zsh shell config, it seems right.
(base) -MacBook-Pro /usr/local/fsl vim ~/.zshrc
# fsl
FSLDIR=/usr/local/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
(base) -MacBook-Pro /usr/local/fsl source ~/.zshrc
at last, I restart my MacbookPro, but still fsl failed, error info is the same.
and I also tried sudo fsl
(base) ✘ -MacBook-Pro /usr/local/fsl sudo fsl
You need to set the FSLDIR environment variable to point to the FSL installation directory before you can run anything.
So I think the configuration of fsl environment variables may be wrong, but it seems no problem with the related configuration.
Why fsl always fails to start?
What does the error info mean?
Much appreciated.
official web:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/MacOsX
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/ShellSetup
Well, althouth I failed to run fsl in the terminal, but I found that a new App icon appears on my desk. This FSL icon is the exact entrance to start fsl.
FSL icon on the desk
ps: The error info "Application initialization failed: couldn't connect to display “:0” "could be ignored.
I got the same issue on launching fsl using Mac terminal but I can get through with your answer.
Thank you very much.
I right-clicked on the Xquartz icon and choose 'terminal'.
Then I type 'fsl' on Xquartz terminal.
Related
I deleted /nix and started a fresh install of nix, however after installing nix install nix (MACBook Pro M1 arm64 BigSur) with sh <(curl -L https://nixos.org/nix/install) I run $ nix but I get the output zsh: command not found: nix , same for nix-shellalso the /nix volume is not created, I also tried the instruction at https://docs.plutus-community.com/docs/setup/MacOS.html still same issue
Open /etc/zshrc and look for the following lines (probably at the end of the file):
# Nix
if [ -e '/nix/var/nix/profiles/default/etc/profile.d/nix-daemon.sh' ]; then
. '/nix/var/nix/profiles/default/etc/profile.d/nix-daemon.sh'
fi
# End Nix
Copy these lines and delete them from this file.
Open ~/.zshrc and add the above copied lines to the end of this file
Reboot terminal and nix should work now.
~ ll /usr/local/bin| grep vrl
-rwxrwxrwx 1 root root 31K 9月 29 09:38 vrlsubmit
➜ ~ echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
➜ ~ vrlsubmit
zsh: command not found: vrlsubmit
Finally somebody helped me:
Root cause is:
I am trying to exec a 32bit command in 64bit system
Debug:
> file submit # < submit stands for the command >
submit: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux.so.2, for GNU/Linux 2.2.5, not stripped
> ls /lib | grep ld
compat-ld
gold-ld
Based on above "file submit", it tells "interpreter /lib/ld-linux.so.2" needed. But there are no /lib/ld-linux.so.2 file at all!!!
Solution:
sudo apt-get install lib32z1 -y
submit
Error: Missing one or more required arguments.
submit
Finished to resolve this issue!
I'm trying to follow the Fabric Composer Quickstart but failed.
Could you give me hints?
When I tried "sudo npm install", the script was completed with a few warnings.
npm WARN lifecycle getting-started#1.0.0~preinstall: cannot run in wd %s %s (wd=%s) getting-started#1.0.0 composer --version || echo 'Please first run npm install -g composer-cli' /<directory>/sample-applications/packages/getting-started
npm WARN lifecycle getting-started#1.0.0~install: cannot run in wd %s %s (wd=%s) getting-started#1.0.0 scripts/download-hyperledger.sh && scripts/start-hyperledger.sh && npm run deployNetwork /<directory>/sample-applications/packages/getting-started
When I tried "sudo composer network list -n digitalproperty-network --enrollId WebAppAdmin --enrollSecret DJY27pEnl16d",
List business network digitalproperty-network
2017-03-21T22:44:47.360Z ERROR FSConnectionProfileStore :load() Failed to loaded connection profile defaultProfile {"0":{"stack":["{Error}ENOENT: no such file or directory, open '<directory>.composer-connection-profiles/defaultProfile/connection.json' Error: ENOENT: no such file or directory, open '<directory>.composer-connection-profiles/defaultProfile/connection.json'"," at Error (native)"]}}$
Failed to load connection profile defaultProfile
Command completed successfully.
I use
Ubuntu: 16.04
docker: 1.13.1
docker-compose: 1.11.2
node: v6.10.0
npm: 4.4.4
git: 2.11.0
composer:
composer-cli v0.5.5
composer-admin v0.5.5
composer-client v0.5.5
composer-common v0.5.5
composer-runtime-hlf v0.5.5
composer-connector-hlf v0.5.5
It looks like I have .composer-connection-profiles/defaultProfile/ direcotry but the directory don't have connection.js
How can we solve the problem? can i prepare connection.js manually?
Thank you!
This problem occurs when you run the npm install using sudo.
it shouldn't be necessary to run the commands as root so try again without using sudo and see if that helps.
This solves the problem npm install composer-connector-hlf
I am getting an endless stream of errors (as follows) when attempting to start the database server - until I am stopping it with CTRL + C in the terminal. Does anyone have idea what is wrong?
$ rake neo4j:start
Starting Neo4j development...
db/neo4j/development/bin/neo4j: line 147: lsof: command not found
db/neo4j/development/bin/neo4j: line 147: lsof: command not found
db/neo4j/development/bin/neo4j: line 147: lsof: command not found
db/neo4j/development/bin/neo4j: line 147: lsof: command not found
^Crake aborted!
Interrupt:
For me the below worked:
yum install lsof
I solved this after I added /usr/sbin to the PATH.
Here it is:
levi$ echo $PATH
/Users/levi/.rbenv/shims:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/Applications/Sublime Text.app/Contents/SharedSupport/bin
Instead lsof ,,,,,, Try to use
/usr/sbin/lsof $FILE
Where $FILE is path of a file
According to colucix, the lsof command is available only to root.
if you want to run it as a non root user, you can specify its full path.
$ /usr/sbin/lsof /path/to/some/file
Also Philip Reynolds has pointed out that you can specify an sudo alias for lsof if it suites you.
In ubuntu 16.04 it worked after installing lsof
sudo apt-get install lsof
Here's what I've attempted via the Nitrous.IO Console:
wget http://dist.neo4j.org/neo4j-community-1.9.4-unix.tar.gz
tar xvfz neo4j-community-1.9.4-unix.tar.gz
mv neo4j-community-1.9.4 neo4j
neo4j/bin/neo4j start
Here is what it says:
WARNING: Max 512 open files allowed, minimum of 40 000 recommended. See the Neo4j manual.
neo4j/bin/neo4j: line 143: lsof: command not found
Using additional JVM arguments: -server -XX:+DisableExplicitGC -Dorg.neo4j.server.properties=conf/neo4j-server.properties -Djava.util.logging.config.file=conf/log
ging.properties -Dlog4j.configuration=file:conf/log4j.properties -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled
Starting Neo4j Server...WARNING: not changing user
process [1470]... waiting for server to be ready.neo4j/bin/neo4j: line 143: lsof: command not found
.neo4j/bin/neo4j: line 143: lsof: command not found
.neo4j/bin/neo4j: line 143: lsof: command not found
Do I need to install lsof on my box? Are we able to do so ourselves on Nitrous.IO?
The Nitrous box does not include lsof by default, and since you don;t have root access you will want to download and install lsof into your home directory.
Once installed, you will want to add it to your PATH. You can download lsof here http://freshmeat.net/projects/lsof/ .