Why is my debian postinst script not being run? - package

I have made a .deb of my app using fpm:
fpm -s dir -t deb -n myapp -v 9 -a all -x "*.git" -x "*.bak" -x "*.orig" \
--after-remove debian/postrm --after-install debian/postinst \
--description "Automated build." -d mysql-client -d python-virtualenv home
Among other things, the postinst script is supposed to create a user for the app:
#!/bin/sh
set -e
APP_NAME=myapp
case "$1" in
configure)
virtualenv /home/$APP_NAME/local
#supervisorctl start $APP_NAME
;;
# http://www.debian.org/doc/manuals/securing-debian-howto/ch9.en.html#s-bpp-lower-privs
install|upgrade)
# If the package has default file it could be sourced, so that
# the local admin can overwrite the defaults
[ -f "/etc/default/$APP_NAME" ] && . /etc/default/$APP_NAME
# Sane defaults:
[ -z "$SERVER_HOME" ] && SERVER_HOME=/home/$APP_NAME
[ -z "$SERVER_USER" ] && SERVER_USER=$APP_NAME
[ -z "$SERVER_NAME" ] && SERVER_NAME=""
[ -z "$SERVER_GROUP" ] && SERVER_GROUP=$APP_NAME
# Groups that the user will be added to, if undefined, then none.
ADDGROUP=""
# create user to avoid running server as root
# 1. create group if not existing
if ! getent group | grep -q "^$SERVER_GROUP:" ; then
echo -n "Adding group $SERVER_GROUP.."
addgroup --quiet --system $SERVER_GROUP 2>/dev/null ||true
echo "..done"
fi
# 2. create homedir if not existing
test -d $SERVER_HOME || mkdir $SERVER_HOME
# 3. create user if not existing
if ! getent passwd | grep -q "^$SERVER_USER:"; then
echo -n "Adding system user $SERVER_USER.."
adduser --quiet \
--system \
--ingroup $SERVER_GROUP \
--no-create-home \
--disabled-password \
$SERVER_USER 2>/dev/null || true
echo "..done"
fi
# … and a bunch of other stuff.
It seems like the postinst script is being called with configure, but not with install, and I am trying to understand why. In /var/log/dpkg.log, I see the lines I would expect:
2012-06-30 13:28:36 configure myapp 9 9
2012-06-30 13:28:36 status unpacked myapp 9
2012-06-30 13:28:36 status half-configured myapp 9
2012-06-30 13:28:43 status installed myapp 9
I checked that /etc/default/myapp does not exist. The file /var/lib/dpkg/info/myapp.postinst exists, and if I run it manually with install as the first parameter, it works as expected.
Why is the postinst script not being run with install? What can I do to debug this further?

I think the example script you copied is simply wrong. postinst is not
supposed to be called with any install or upgrade argument, ever.
The authoritative definition of the dpkg format is the Debian Policy
Manual. The current version describes postinst in chapter
6
and only lists configure, abort-upgrade, abort-remove,
abort-remove, and abort-deconfigure as possible first arguments.
I don't have complete confidence in my answer, because your bad example
is still up on debian.org and it's hard to believe such a bug could slip
through.

I believe the answer provided by Alan Curry is incorrect, at least as of 2015 and beyond.
There must be some fault with the way the that your package is built or an error in the postinst file which is causing your problem.
You can debug your install by adding the -D (debug) option to your command line i.e.:
sudo dpkg -D2 -i yourpackage_name_1.0.0_all.deb
-D2 should sort out this type of issue
for the record the debug levels are as follows:
Number Description
1 Generally helpful progress information
2 Invocation and status of maintainer scripts
10 Output for each file processed
100 Lots of output for each file processed
20 Output for each configuration file
200 Lots of output for each configuration file
40 Dependencies and conflicts
400 Lots of dependencies/conflicts output
10000 Trigger activation and processing
20000 Lots of output regarding triggers
40000 Silly amounts of output regarding triggers
1000 Lots of drivel about e.g. the dpkg/info dir
2000 Insane amounts of drivel
The install command calls the configure option and in my experience the postinst script will always be run. One thing that may trip you up is that the postrm script of the "old" version, if upgrading a package, will be run after your current packages preinst script, this can cause havoc if you don't realise what is going on.
From the dpkg man page:
Installation consists of the following steps:
1. Extract the control files of the new package.
2. If another version of the same package was installed before
the new installation, execute prerm script of the old package.
3. Run preinst script, if provided by the package.
4. Unpack the new files, and at the same time back up the old
files, so that if something goes wrong, they can be restored.
5. If another version of the same package was installed before
the new installation, execute the postrm script of the old pack‐
age. Note that this script is executed after the preinst script
of the new package, because new files are written at the same
time old files are removed.
6. Configure the package.
Configuring consists of the following steps:
1. Unpack the conffiles, and at the same time back up the old
conffiles, so that they can be restored if something goes wrong.
2. Run postinst script, if provided by the package.

This is an old issue that has been resolved, but it seems to me that the accepted solution is not totally correct and I believe that it is necessary to provide information for those who, like me, are having this same problem.
Chapter 6.5 details all the parameters with which the preinst and postinst files are called
At https://wiki.debian.org/MaintainerScripts the installation and uninstallation flow is detailed.
Watch what happens in the following case:
apt-get install package
- It runs preinst install and then postinst configure
apt-get remove package
- Execute postrm remove and the package will be set to "Config Files"
For the package to actually be in the "not installed" state it must be used:
apt-get purge package
That's the only way we'll be able to run preinst install and postinst configure the next time the package is installed.

Related

i run npm start and it showing this pls how do i solve this problem [duplicate]

I have setup a new blank react native app.
After installing few node modules I got this error.
Running application on PGN518.
internal/fs/watchers.js:173
throw error;
^
Error: ENOSPC: System limit for number of file watchers reached, watch '/home/badis/Desktop/react-native/albums/node_modules/.staging'
at FSWatcher.start (internal/fs/watchers.js:165:26)
at Object.watch (fs.js:1253:11)
at NodeWatcher.watchdir (/home/badis/Desktop/react-native/albums/node modules/sane/src/node watcher. js:175:20)
at NodeWatcher.<anonymous> (/home/badis/Desktop/react-native/albums/node modules/sane/src/node watcher. js:310:16)
at /home/badis/Desktop/react-native/albums/node modules/graceful-fs/polyfills.js:285:20
at FSReqWrap.oncomplete (fs.js:154:5)
I know it's related to no enough space for watchman to watch for all file changes.
I want to know what's the best course of action to take here ?
Should I ignore node_modules folder by adding it to .watchmanconfig ?
Linux uses the inotify package to observe filesystem events, individual files or directories.
Since React / Angular hot-reloads and recompiles files on save it needs to keep track of all project's files. Increasing the inotify watch limit should hide the warning messages.
You could try editing
# insert the new value into the system config
echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf && sudo sysctl -p
# check that the new value was applied
cat /proc/sys/fs/inotify/max_user_watches
# config variable name (not runnable)
fs.inotify.max_user_watches=524288
The meaning of this error is that the number of files monitored by the system has reached the limit!!
Result: The command executed failed! Or throw a warning (such as executing a react-native start VSCode)
Solution:
Modify the number of system monitoring files
Ubuntu
sudo gedit /etc/sysctl.conf
Add a line at the bottom
fs.inotify.max_user_watches=524288
Then save and exit!
sudo sysctl -p
to check it
Then it is solved!
You can fix it, that increasing the amount of inotify watchers.
If you are not interested in the technical details and only want to get Listen to work:
If you are running Debian, RedHat, or another similar Linux distribution, run the following in a terminal:
$ echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf && sudo sysctl -p
If you are running ArchLinux, run the following command instead
$ echo fs.inotify.max_user_watches=524288 | sudo tee /etc/sysctl.d/40-max-user-watches.conf && sudo sysctl --system
Then paste it in your terminal and press on enter to run it.
The Technical Details
Listen uses inotify by default on Linux to monitor directories for changes. It's not uncommon to encounter a system limit on the number of files you can monitor. For example, Ubuntu Lucid's (64bit) inotify limit is set to 8192.
You can get your current inotify file watch limit by executing:
$ cat /proc/sys/fs/inotify/max_user_watches
When this limit is not enough to monitor all files inside a directory, the limit must be increased for Listen to work properly.
You can set a new limit temporary with:
$ sudo sysctl fs.inotify.max_user_watches=524288
$ sudo sysctl -p
If you like to make your limit permanent, use:
$ echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf
$ sudo sysctl -p
You may also need to pay attention to the values of max_queued_events and max_user_instances if listen keeps on complaining.
From the official document:
"Visual Studio Code is unable to watch for file changes in this large workspace" (error ENOSPC)
When you see this notification, it indicates that the VS Code file watcher is running out of handles because the workspace is large and contains many files. The current limit can be viewed by running:
cat /proc/sys/fs/inotify/max_user_watches
The limit can be increased to its maximum by editing
/etc/sysctl.conf
and adding this line to the end of the file:
fs.inotify.max_user_watches=524288
The new value can then be loaded in by running
sudo sysctl -p
Note that Arch Linux works a little differently, See Increasing the amount of inotify watchers for details.
While 524,288 is the maximum number of files that can be watched, if you're in an environment that is particularly memory constrained, you may wish to lower the number. Each file watch takes up 540 bytes (32-bit) or ~1kB (64-bit), so assuming that all 524,288 watches are consumed, that results in an upper bound of around 256MB (32-bit) or 512MB (64-bit).
Another option
is to exclude specific workspace directories from the VS Code file watcher with the files.watcherExclude setting. The default for files.watcherExclude excludes node_modules and some folders under .git, but you can add other directories that you don't want VS Code to track.
"files.watcherExclude": {
"**/.git/objects/**": true,
"**/.git/subtree-cache/**": true,
"**/node_modules/*/**": true
}
delete react node_modules
rm -r node_modules
yarn or npm install
yarn start or npm start
if error occurs use this method again
Firstly you can run every time with root privileges
sudo npm start
Or you can delete node_modules folder and use npm install to install again
or you can get permanent solution
echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf && sudo sysctl -p
It happened to me with a node app I was developing on a Debian based distro. First, a simple restart solved it, but it happened again on another app.
Since it's related with the number of watchers that inotify uses to monitors files and look for changes in a directory, you have to set a higher number as limit:
I was able to solve it from the answer posted here
(thanks to him!)
So, I ran:
echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf && sudo sysctl -p
Read more about what’s happening at https://github.com/guard/listen/wiki/Increasing-the-amount-of-inotify-watchers#the-technical-details
Hope it helps!
Remembering that this question is a duplicated: see this answer at original question
A simple way that solve my problem was:
npm cache clear
best practice today is
npm cache verify
npm or a process controlled by it is watching too many files. Updating max_user_watches on the build node can fix it forever. For debian put the following on terminal:
echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf && sudo sysctl -p
If you want know how Increase the amount of inotify watchers only click on link.
I use ubuntu 20 server and i add in the file : /etc/sysctl.conf the below line
fs.inotify.max_user_watches=524288
Then save the file and run sudo sysctl -p
After that all is works fine!
I solved this issue by using sudo
ie
sudo yarn start
or
sudo npm start
Use sudo to solve this issue will force the number of watchers to be increased without apply any modifications in system settings. Use sudo to solve this kind of issue is never recommended, although it's a choice that have to be made by you, hope you choose wisely.
Root cause
Most answers above talk about raising the limit, not about taking away the root cause which is typically just a matter redundant watches, typically for files in node_modules.
Webpack
The answer is in the webpack 5 docs:
watchOptions: { ignored: /node_modules/ }
Simply read here: https://webpack.js.org/configuration/watch/#watchoptionsignored
The docs even mention this as a "tip", quote:
If watching does not work for you, try out this option. This may help
issues with NFS and machines in VirtualBox, WSL, Containers, or
Docker. In those cases, use a polling interval and ignore large
folders like /node_modules/ to keep CPU usage minimal.
VS Code
VS Code or any code editor creates lots of file watches too. By default many of them are completely redundant. Read more about it here: https://code.visualstudio.com/docs/setup/linux#_visual-studio-code-is-unable-to-watch-for-file-changes-in-this-large-workspace-error-enospc
Generally we don't need to increase count of filewatchers
In this case we will have more watchers
We need to remove redundant watchers what became zombie
The issue is that we have many filewatchers that are filling out our memory
We just need remove these filewatchers (in case of node)
killall node
In react.js show me same error i fix this way hope work in react native too
echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf
sudo sysctl -p
Now you can run npm start again.
npm start
Using the sysctl -p approach after setting fs.inotify.max_user_watches did not work for me (by the way this setting was already set to a high value, likely from me trying to fix this issue a while back ago, using the commonly recommended workaround(s) above).
The best solution to the problem I found here, and below I share the performed steps in solving it - in my case the issue was spotted while running visual studio code, but solving the issue should be the same in other instances, like yours:
Use this script to identify which processes are requiring the most file watchers in your session.
You can then query the current max_user_watches value with sysctl fs.inotify.{max_queued_events,max_user_instances,max_user_watches} and then set it to a different value (a lower value may do it)
sudo sysctl -w fs.inotify.max_user_watches=16384
Or you can simply kill the process you found in (1) that consumes the most file watchers (in my case, baloo_file)
The above, however, will likely need to be done again when restarting the system - the process we identified as responsible for taking much of the file watchers will (in my case - baloo_file) - will again so the same in the next boot. So to permanently fix the issue - either disable or remove this service/package. I disabled it: balooctl disable.
Now run sudo code --user-data-dir and it should open vscode with admin privileges this time. (by the way when it does not - run sudo code --user-data-dir --verbose to see what the problem is - that's how I figured out it had to do with file watchers limit).
Update:
You may configure VS code file watcher exclusion patterns as described here. This may prove to be the ultimate solution, I am just not sure you will always know beforehand which files you are NOT interested watching.
Easy Solution
I found, that a previous solution work well in my case. I removed node_modules and clear the yarn / npm cache.
Long Tail Solution
If you want to have a long-tail solution - e.g. if you often be catched by this error - you can increase the value of allowed watchers (depending on your available memory)
To figure out the current used amount of watchers, instead of only guessing, you can use this handy bash-script:
https://github.com/fatso83/dotfiles/blob/master/utils/scripts/inotify-consumers
I suggest to set the max_user_watches temporary to a high value:
sudo sysctl fs.inotify.max_user_watches=95524288 and run the script.
How to calculate how much you can use
Each watcher needs
540 bytes (32-bit system), or
1 kB (double - on 64-bit OS
So if you will allow to use 512MB (on 64Bit), you set something 524288 as value.
Other way around, you can take the amount of memory you will set, and multiply it by 1024.
Example:
512 * 1024 = 52488
1024 * 1024 = 1048576
It shows you the exact amount of the current used inotify-consumers. So you might have an better Idea, how much you should increase the limit.
If you are running your project in Docker, you should do the echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf and all other commands in the host machine, since the container will inherit that setting automatically (and doing it directly inside it will not work).
Late answer, and there are many good answers already.
In case you want a simple script to check if the maximum file watches is big enough, and if not, increase the limit, here it is:
#!/usr/bin/env bash
let current_watches=`sysctl -n fs.inotify.max_user_watches`
if (( current_watches < 80000 ))
then
echo "Current max_user_watches ${current_watches} is less than 80000."
else
echo "Current max_user_watches ${current_watches} is already equal to or greater than 80000."
exit 0
fi
if sudo sysctl -w fs.inotify.max_user_watches=80000 && sudo sysctl -p && echo fs.inotify.max_user_watches=80000 | sudo tee /etc/sysctl.d/10-user-watches.conf
then
echo "max_user_watches changed to 80000."
else
echo "Could not change max_user_watches."
exit 1
fi
The script increases the limit to 80000, but feel free to set a limit that you want.
As already pointed out by #snishalaka, you can increase the number of inotify watchers.
However, I think the default number is high enough and is only reached when processes are not cleaned up properly. Hence, I simply restarted my computer as proposed on a related github issue and the error message was gone.
Another simple and good solution is just to add this to jest configuration:
watchPathIgnorePatterns: ["<rootDir>/node_modules/", "<rootDir>/.git/"]
This ignores the specified directories to reduce the files being scanned
In my case in Angular 13, I added in tsconfig.spec.json
"exclude": [
"node_modules/",
".git/"
]
thanks #Antimatter it gaves me the trick.
echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf && sudo sysctl -p
Run This Code In Project Terminal After Run Npm Run Dev
Please refer this link[1]. Visual Studio code has mentioned a brief explanation for this error message. I also encountered the same error. Adding the below parameter in the relavant file will fix this issue.
fs.inotify.max_user_watches=524288
[1] https://code.visualstudio.com/docs/setup/linux#_visual-studio-code-is-unable-to-watch-for-file-changes-in-this-large-workspace-error-enospc
While almost everyone suggests to increase a number of watchers, I couldn't agree that it is a solution.
In my case I wanted to disable watcher completely, because of the tests running on CI using vui-cli plugin which starts web-pack-dev server for each test.
The problem was: when a few builds are running simultaneously they would fail because watchers limit is reached.
First things first I've tried to add the following to the vue.config.js:
module.exports = {
devServer: {
hot: false,
liveReload: false
}
}
Ref.: https://github.com/vuejs/vue-cli/issues/4368#issuecomment-515532738
And it worked locally but not on CI (apparently it stopped working locally the next day as well for some ambiguous reason).
After investigating web-pack-dev server documentation I found this:
https://webpack.js.org/configuration/watch/#watch
And then this:
https://github.com/vuejs/vue-cli/issues/2725#issuecomment-646777425
Long story short this what eventually solved the problem:
vue.config.js
module.exports = {
publicPath: process.env.PUBLIC_PATH,
devServer: {
watchOptions: {
ignored: process.env.CI ? "./": null,
},
}
}
Vue version 2.6.14
if you working with vs code editor any editor that error due to large number of files in projects. node_modules and build not required in it so remove in list. that all open in vs code files menu
You have to filter unnecessary folders file sidebar
Goes to Code > Preferences > settings
in search setting search keyword "files:exclude"
Add pettern
**/node_modules
**/build
That's it
Try this , I was facing it for very long time but at the end it is solved by this,
echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf && sudo sysctl -p
The most important step after that is restart your system.
2 fixes if you've already added: fs.inotify.max_user_watches=524288
Reboot the machine, things will work again
Rename the folder that is causing the issue (for me node_modules) to an arbitrary name (node_modilesa) and then rename right back. This will remove the watches that linux had put on those folders. Allowing you code as normal again.
I encountered this issue on a linuxmint distro. It appeared to have happened when there was so many folders and subfolders/files I added to the /public folder in my app.
I applied this fix and it worked well...
$ echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf
change directory into the /etc folder:
cd /etc
then run this:
sudo systcl -p
You may have to close your terminal and npm start again to get it to work.
If this fails i recommend installing react-scripts globally and running your application directly with that.
$ npm i -g --save react-scripts
then instead of npm start run react-scripts start to run your application.
I tried increasing number as suggested but it didn't work.
I saw that when I login to my VM, it displayed "restart required"
I rebooted VM and it worked
sudo reboot
it is to easy to fix this
echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf
and run your project.
if there is fs.inotify.max_user_watches=524288 in your /etc/sysctl.conf,
run same command(echo fs.inotify.max_user_watches=524288 | sudo tee -a /etc/sysctl.conf). and run your project
For vs code, see detailed instructions here:
https://code.visualstudio.com/docs/setup/linux#_visual-studio-code-is-unable-to-watch-for-file-changes-in-this-large-workspace-error-enospc

How to completely download Anaconda Cloud bz2 files and dependencies for offline package installation? [duplicate]

I want to create a Python environment with the data science libraries NumPy, Pandas, Pytorch, and Hugging Face transformers. I use miniconda to create the environment and download and install the libraries. There is a flag in conda install, --download-only to download the required packages without installing them and install them afterwards from a local directory. Even when conda just downloads the packages without installing them, it also extracts them.
Is it possible to download the packages without extracting them and extract them afterwards before installation?
There is no simple command in the CLI to prevent the extraction step. The extraction is regarded as part of the FETCH operation to populate the package cache before running the LINK operation to transfer the package to the specified environment.
The alternative would be to do something manually. Naively, one could search Anaconda Cloud and manually download, however, it would probably be better to go through the solver to ensure package compatibility. All the info for operations to be run can be viewed by including the --json flag. This could be filtered to just the tarball URLs and then downloaded directly. Here's a script along these lines (assuming Linux/Unix):
File: conda-download.sh
#!/bin/bash -l
conda create -dn null --json "$#" |\
grep '"url"' | grep -oE 'https[^"]+' |\
xargs wget -c
which can be used as
./conda-download.sh -c conda-forge -c pytorch numpy pandas pytorch transformers
that is, it accepts all arguments conda create would, and will download all the tarballs locally.
Ignoring Cached Packages
If you already have some packages cached then the above will not redownload them. Instead, if you wish to download all tarballs needed for an environment, then you could use this alternate version which overrides the package cache using an empty temporary directory:
File: conda-download-all.sh
#!/bin/bash -l
tmp_dir=$(mktemp -d)
CONDA_PKGS_DIRS=$tmp_dir conda create -dn null --json "$#" |\
grep '"url"' | grep -oE 'https[^"]+' |\
xargs wget -c
rm -r $tmp_dir
Do you really want to use conda-pack? That lets you archive a conda-environment for reproducing without using the internet or re-solving for dependencies. To just prevent re-solving you can also use conda env export --explict but that still ties you to the source (internet or local disk repository).
If you have a static environment (read-only) and want to really reduce docker size, you can volume mount the environment at runtime. You would need to match the file paths (ie: /opt/anaconda => /opt/anaconda).

How do I solve the following git error: No such file or directory [duplicate]

I get this error when I try to commit.
OS - Latest OSX
Git version - git version 2.11.0 (Apple Git-81)
.git/hooks/pre-commit: line 2: ./node_modules/pre-commit/hook: No such file or directory
pre-commit hook runs first when you try to commit changes, it can be used to do certain checks, tests, conditions. In this case, clearly, you don't have it, that's why it's complaining.
Go to .git/hooks directory and remove pre-commit file, as its trying to reference to node_modules/pre-commit/hook. It should resolve it.
Other option is append your commit with option: --no-verify, it will make the commit without checking.
You should delete node_modules folder and install again running npm install or yarn install. After it, you probably solve the problem.
If the script files are actually present, then the cause may be that the first line of the script should be something like:
#!/bin/sh
Otherwise you get the same error.
Any file will work -- e.g., /bin/bash, /usr/local/bin/python3 -- as long as it exists and is executable.
Following #Mutant tip, the simple answer for me was:
rm .git/hooks/pre-commit
Working from macOS, my issue was that Python3 was originally installed via Homebrew, and after I upgraded Python3 via brew update && brew upgrade, I got the same error.
To fix this, I needed to update the symbolic links in the directory that the shebang (#!) line in the .git/hooks/pre-commit file points to.
Here's how I fixed this in my environment:
Look at the contents of the .git/hooks/pre-commit:
cat .git/hooks/pre-commit
The first few lines should look something like:
#!/usr/local/opt/pre-commit/libexec/bin/python3
# File generated by pre-commit: https://pre-commit.com
# ID: 0123456789abcdef0123456789abcdef
import os
import sys
Take note of the path to the python3 executable in the shebang line:
/usr/local/opt/pre-commit/libexec/bin/
cd into that directory.
cd /usr/local/opt/pre-commit/libexec/bin/
Take at look at the Python symlinks:
ls -l | grep python
You'll see some symlinks that are probably broken:
lrwxr-xr-x 1 user group 91 Apr 5 13:33 python -> /usr/local/Cellar/python#3.9/3.9.2_4/Frameworks/Python.framework/Versions/3.9/bin/python3.9
lrwxr-xr-x 1 user group 91 Apr 5 13:33 python3.9 -> /usr/local/Cellar/python#3.9/3.9.2_4/Frameworks/Python.framework/Versions/3.9/bin/python3.9
lrwxr-xr-x 1 user group 91 Apr 5 13:33 python3 -> /usr/local/Cellar/python#3.9/3.9.2_4/Frameworks/Python.framework/Versions/3.9/bin/python3.9
Quick note: In case something goes wrong or my answer isn't the solution, you might want to back up these symlinks first by running:
mv python python.bak
mv python3.9 python3.9.bak
mv python3 python3.bak
Update the symbolic links using ln -s [PATH] [LINK], where [PATH] is the location of the Homebrew-updated Python3 executable and [LINK] is python, python3.9, and python3:
ln -s /usr/local/Cellar/python#3.9/3.9.4/Frameworks/Python.framework/Versions/3.9/bin/python3.9 python
ln -s /usr/local/Cellar/python#3.9/3.9.4/Frameworks/Python.framework/Versions/3.9/bin/python3.9 python3.9
ln -s /usr/local/Cellar/python#3.9/3.9.4/Frameworks/Python.framework/Versions/3.9/bin/python3.9 python3
When you've done that, list your Python symlinks again.
ls -l | grep python
You should see the updated symlinks, and git commit should now work.
lrwxr-xr-x 1 user group 89 Apr 6 13:58 python -> /usr/local/Cellar/python#3.9/3.9.4/Frameworks/Python.framework/Versions/3.9/bin/python3.9
lrwxr-xr-x 1 user group 89 Apr 6 13:58 python3 -> /usr/local/Cellar/python#3.9/3.9.4/Frameworks/Python.framework/Versions/3.9/bin/python3.9
lrwxr-xr-x 1 user group 89 Apr 6 13:58 python3.9 -> /usr/local/Cellar/python#3.9/3.9.4/Frameworks/Python.framework/Versions/3.9/bin/python3.9
I got that error after I was played with brew to make yarn work in Webstorm.
The fix is just re-install pre-commit again.
brew install pre-commit
https://pre-commit.com/
For anyone who is having this problem with husky, for me what solved it is running:
husky install
(which I forgot to run) The docs talk about it under usage, aka npm run prepare for one time after you set up husky. usage
Nothing helps me but remove local repo and clone it again. This kinda error appears when I accidentically tried commit and push changes to master..
If you look at your package.json you will get a better idea about the problem.
Husky is npm dependency so basically you got the error because for some reason it's not available.
So, option one run
npm i
Or if you already did that
rm -rf node_modules
npm i
I had installed pre-commit using homebrew, and installed the pre-commit-vscode extension and got this error.
What solved this was to also run pre-commit install from the root of the git repo.
In my case in Mac OS, upgrading python3 via brew somehow messed up python3 location whereas the shebang in pre-commit was was still pointing to the old python3 location. So finding new python3 location via which python3 and updating same in pre-commit and other scripts under .githooks folder did fixed the issue.
INGW64 ~/code/ingestor-gdelt (test-build)
$ git commit -m "your comment"
.git/hooks/pre-commit: line 9: py: command not found
.git/hooks/pre-commit: line 10: py: command not found
git commit --no-verify -m "your comment"
This command resolved my issue !!
just make sure you have hooks folder inside of .git . if not make one.
Deleting pre-commit from hooks inside .git worked for me

Installing TinyTeX in a Singularity container

I'm writing a paper in RMarkdown and for better reproducibility, I want to containerize all required software in a singularity container. Unfortunately, when I try to install TinyTeX (which is recommended for Rmarkdown and I would prefer over TeXLive to not inflate the container more than needed), it fails with the following error message (the full build log is pasted here):
Can't locate TeXLive/TLConfig.pm in #INC (you may need to install the TeXLive::TLConfig module) (#INC contains: /~/.TinyTeX/texmf-dist/scripts/texlive /~/.TinyTeX/tlpkg /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at ~/.TinyTeX/bin/x86_64-linux/tlmgr line 100.
BEGIN failed--compilation aborted at ~/.TinyTeX/bin/x86_64-linux/tlmgr line 100.
This is the build definition file, basically it uses a very slimmed down ubuntu 18.04 and then executes the %post section to install software
BootStrap: library
From: ubuntu:18.04
%post
# Add universe repository
echo "deb http://us.archive.ubuntu.com/ubuntu bionic universe" >> /etc/apt/sources.list
apt -y update
# Install utilites
apt install -y wget
# Install R
apt install -y r-base-core
## Install RMarkdown and TinyTeX
R --slave -e 'install.packages(c("rmarkdown","tinytex")); tinytex::install_tinytex()'
# Clean
apt-get clean
%environment
export LC_ALL="en_US.UTF-8"
%labels
Author DP
I have also tried tinytex::install_tinytex(dir="/opt/tinytex") but that didn't seem to change anything. Does anyone have an idea what's wrong?
That error message is complaining that your image (or, more likely, your path) is missing the TeXLive::TLConfig perl module.
My guess is that the path contents are not being rehashed with the installed modules after the install. The simplest solution is to break it into two commands:
R --slave -e 'install.packages(c("rmarkdown","tinytex"))'
R --slave -e 'tinytex::install_tinytex()'
Installation succeeds when I try that locally.
A potentially useful alternative, if the image is just for document generation, could be converting a docker image with rmarkdown and tex (e.g. https://hub.docker.com/r/rocker/verse) to a singularity one.
With singularity pull docker://rocker/verse you can do that for the latest version, or for a specific version with verse:version_number.

How to fake macports into using my build script for ffmpeg?

I have my own bash script to configure ffmpeg which successfully updates my git repo, builds, tests and installs everything correctly.
Basically I want to bypass macports env and configuration but recognize my build but only for ffmpeg, I don't want macports to look in /usr/local or another location, I want it installed in /opt/local
So it probably boils down to, how to completely disable all the macports env and just launch a subshell with my script?
Created tarball, checksums, etc
PortSystem 1.0
PortGroup muniversal 1.0
name ffmpeg
epoch 1
version 9.9.9
revision 9
license LGPL-2.1+
categories multimedia
maintainers nomaintainer
platforms darwin
homepage http://www.ffmpeg.org/
master_sites file:///Volumes/Apps_Media/my_repo
use_zip yes
checksums {they work}
depends_build port:pkgconfig \
port:gmake \
port:texinfo
use_configure no
build.cmd $HOME/bin/configFFMPEG
macports chokes on these lines in ffmpeg's configure
FFmpeg/configure: line 3596: ffbuild/config.log: Operation not permitted
FFmpeg/configure: line 3597: ffbuild/config.log: Operation not permitted
echo "# $0 $FFMPEG_CONFIGURATION" > $logfile
set >> $logfile
MacPorts runs builds as the macports user, not yoru normal user or root. Make sure that user can both read your script and write to the locations where your script is trying to write.
Even though you invoke MacPorts with superuser privileges, it will not use these privileges while building software.

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