I have installed opam 2.1.0 on a Linux Virtualbox VM. When I try opam init, I get the following error:
<><> Fetching repository information ><><><><><><><><><><><><><><><><><><><><><>
[ERROR] Could not update repository "default": OpamDownload.Download_fail(_, "Curl
failed: \"/snap/bin/curl --write-out %{http_code}\\\\n --retry 3
--retry-delay 2 --user-agent opam/2.1.0 -L -o
/tmp/opam-32196-d33843/index.tar.gz.part --
https://opam.ocaml.org/index.tar.gz\" exited with code 23")
[ERROR] Initial download of repository failed.
Running with --disable-sandboxing doesn't help. I know that its a problem creating/writing to /tmp/opam-... directory because if I replace that with my current directory or home directory the command by itself runs fine. It also runs fine with /tmp/opam-... if I use the --create-dirs option in curl but I don't have any way of getting opam init to use that option. Any ideas?
thanks
Update
The reason opam init failed for me was because curl was installed with snap on my system. This exactly what is going on with your VM.
Try to run opam init -verbose and that could reveal more about why you ran into an error.
In my case I needed to install other things with opam and it kept failing every time. So snap uninstall curl and then sudo apt install curl fixed things. (Was only able to figure this out with help from my professor)
Workaround
I ran into the same issue and I found a workaround on the OCaml forum: here. (Credits to UnixJunkie)
You can run:
opam init github git+https://github.com/ocaml/opam-repository.git
This should avoid the certificate issues. This worked for me.
I tried to fix the certificate issues using this answer as well. You could try doing that, but it seems complicated when the workaround is to simply point it to the github repo directly.
This question is similar to this one.
I tried to import the biopython package in Spyder and got the error message:
ModuleNotFoundError: No module named 'biopython'
although biopython is installed.
I also checked the PYTHONPATH: there is a path set into the directory where the packages are stored.
Can somebody help? Did I miss something? Thanks for your help!
If you're using Anaconda, it's best to install all the packages you want from Anaconda if possible. You can check if a package is available with (e.g.):
conda search biopython
When I try that command it shows that biopython is available, so assuming you have access to the standard conda channels you should be able to get it this way.
Assuming you haven't already created a conda environment to work with, start by creating a new one with the packages you want to use:
conda create -n myenvname spyder biopython
where myenvname is the name you want to give the environment - call it whatever you like. If you want to use other packages as well, add their names to the end of this command. Then once the env is completed, activate it:
activate myenvname
or if this doesn't work, on Mac or Linux:
source activate myenvname
and start Spyder in this environment:
spyder
Each time you want to use this environment in future you will need to activate it first. You may also be able to do some of these tasks through the Anaconda Navigator or via Start menu shortcuts but the command line version will always work.
If there's a package you want that isn't available from conda but is available via pip, just use the pip command after creating and activating the environment.
If you are using Anaconda, a solution could be
conda install -c main biopython
following https://anaconda.org/main/biopython.
The official repository page helped me when I got your error message because numpy was not in place.
For the following commands to work, make sure you have "ant", "mvn", and "git" in your environment PATH.
pls I need to add the following to the environment part.
$ git clone https://github.com/shannah/cn1-iap-demo-server
$ cd cn1-iap-demo-server
$ ant install-deps.
I dont know how to locate environment path on my system. pls help
That's Unix/Linux and unrelated to Codename One. One would setup an environment path as such:
export PATH=/path/to/ant/binary:$PATH
I am using custom Nagios plugins for the first time and am running into this error when I create a service for the plugin.
(No output on stdout) stderr: execvp(/usr/local/nagios/libexec/check_load.py, ...) failed. errno is 2: No such file or directory
The plugin works when I run it on the command line, however does not work when it runs within Nagios.
I followed these steps to get the plugin into Nagios
https://assets.nagios.com/downloads/nagiosxi/docs/Managing-Plugins-in-Nagios-XI.pdf
Here is what it looks like in the Nagios UI
The plugin is in the correct path: /usr/local/nagios/libexec and the resource.cfg file has the same path within it.
I tried two separate plugins, both which work on the command line, and the result is the same error.
The error indicates the file location is incorrect, however the plugin is in the specified directory and runs with no errors within that directory.
I am totally stumped and appreciate any help.
For anyone reading this, I solved the problem.
The first time I added the plugin, I forgot to add the python extension. When I updated the already created plugin, Nagios still threw the error.
Once I completely deleted the plugin and re-created it the 'file not found', error went away.
I faced a similar issue when I was trying to add a custom plugin ( I had custom plugins in ruby and python ).
The issue was the missing shebang line at the start of the script (which determines the script's ability to be executed like a standalone executable).
For example, if you have a python plugin custom-plugin.py then make sure this script has shebang at the start of script #!/usr/bin/env python3. Also if you have other scripts (ruby, bash etc.) make sure to add the appropriate path at the start of your scripts.
Also, check the path for plugins Nagios version. For my setup path was /usr/local/nagios/libexec/ and make sure your custom plugin is executable and has correct ownership permissions.
Sample custom template I used :
define command {
command_name check_switch_health
command_line /usr/local/nagios/libexec/check_snmp.rb --host $HOSTADDRESS$ --model "$ARG1$" --community "$ARG2$"
}
The above workaround worked for me.
I am trying to selfupdate my Macports, but I am getting the following message:
Error: /opt/local/bin/port: port selfupdate failed: Error synchronizing
MacPorts sources: command execution failed
I checked my /opt/local/bin/macports and the directory does not exist. Instead, it is in /opt/local/var. Could that be the issue?
Running with -dt, I get the following:
[Users/user] > selfupdate
DEBUG: MacPorts sources location: /opt/local/var/macports/sources/rsync.macports.org/release/base
---> Updating MacPorts base sources using rsync
rsync: failed to connect to rsync.macports.org: Connection refused (61)
rsync error: error in socket IO (code 10) at /SourceCache/rsync/rsync-42/rsync/clientserver.c(105) [receiver=2.6.9]
Command failed: /usr/bin/rsync -rtzv --delete-after rsync://rsync.macports.org/release/base/ /opt/local/var/macports/sources/rsync.macports.org/release/base
Exit code: 10
DEBUG: Error synchronizing MacPorts sources: command execution failed
while executing
"macports::selfupdate [array get global_options] base_updated"
Error: /opt/local/bin/port: port selfupdate failed: Error synchronizing MacPorts sources: command execution failed
What is error 61? Any ideas how I can fix that?
I had this same problem recently, and I forgot to run the command under root. If anyone else is having the problem, be sure to run command as so:
sudo port selfupdate
I was behind a firewall. Tried on a different network and it worked.
There is no /opt/local/bin/macports. The executable you need is /opt/local/bin/port. (Port files are in /opt/local/var/..., which is correct.)
Based on the command execution failed:
you might have forgotten to run as root.
port forks the following programs: rsync, tclsh, openssl, tar, chmod, chown.
Are these executable and in the PATH? (Is /opt/local/bin in your PATH as well?)
If that doesn't help, run port with -dt to get all sorts of debug info. That might help with finding the problem. Append the interesting parts to your question, maybe.
I faced the same issue.But I used to this method in the after.
Go to:
$prefix/etc/macports/sources.conf
(my path is like this):
/opt/local/etc/macports/sources.conf
comment out the rsync entry, and add a new entry as follows:
#rsync://rsync.macports.org/release/tarballs/ports.tar [default]
https://distfiles.macports.org/ports.tar.gz [default]
After that you can run:
sudo port -d sync
It's also explained on MacPorts.com.
Update for Mavericks: to ensure the XCode command line tools are installed, open a terminal and run xcode-select –-install, then follow the instructions in the resulting pop-up window:
accept license
Of course, this is in addition to the other tips such as making sure to run sudo port selfupdate.
If anybody else is having this issue and they've recently updated XCode, the root of my problem was that Command Line Tools had been omitted from the latest build.
Opening XCode and installing Command Line Tools via the XCode preference panel fixed this error being thrown by MacPorts.
If your company block the access via rsync you can use the http tarball. Explained here
Hope this helps.
EDIT: Now prefer to use homebrew
I too had the same error. It is because the network connection is rejected. If you are using University/Company WiFi or public connection, firewall would be refusing the connection.
As you can see from the output of -dt "rsync: failed to connect to rsync.macports.org: Connection refused (61)"
There are workarounds available which are provided on the macports site:
1) Using svn.
2) If svn fails too, you can try using Daily tarball.
You can test the changes by running "sudo port -d sync"
Note: If the https fails, you can replace it with http. But doing so is not recommended, as you will be fetching from insecure connection.
I faced the same issue.
The main problem was my network. Because the NETWORK Port was blocked for;
rsync://rsync.macports.org/release/tarballs/ports.tar
Try to use use another network.
for someone who's problem still exists, maybe you've forgot agree the Xcode license:
# sudo xcodebuild license
remember to look through and type 'agree' in the end.
In my case, the problem was internal to Macports! I updated rsync (the one delivered by Apple is old) with Macports and then Macports failed to use it (/opt/local/bin/rsync) but asked instead to use /usr/bin/rsync which does not exist (or has been erased to force using Macports rsync ?). I created a soft link between the two and now it works again.