Ubuntu Cmake: Parse error in command line argument [duplicate]

Ubuntu Cmake: Parse error in command line argument [duplicate] - opencv

-D CMAKE_C_COMPILER is what I use to choose my compiler. However, if I have CMake options that are turned on/off like USEIPHONEFLAG, I need to do -DUSEIPHONEFLAG=1, -D USEIPHONEFLAG=1 does not work. I was wondering how the space after -D works in CMake.

CMake's command line parsing is not very consistent or robust unfortunately.
This issue is probably down to the order in which you pass the arguments.
Internally, CMake iterates over the command line arguments twice. The first time it's looking for non-cache arguments and skips any beginning with -D. Any that don't fit into the list of proper args are assumed to be the path to the CMakeLists.txt file (or the directory, or the CMakeCache.txt).
It's assuming that there will be only one path passed, and does nothing to validate that assumption. Herein lies the problem. If you've passed -D Foo=1, then -D is seen as a complete argument and is skipped, and Foo=1 is seen as a path.
On the second iteration through the args, it now grabs the values given via -D, but on this run it correctly handles spaces after the -D. So it understands that -D Foo=1 is setting Foo to 1.
So, the position of the path in your command line is all-important here.
cmake -D Foo=1 MyProject/CMakeLists.txt # --> Works
cmake MyProject/CMakeLists.txt -D Foo=1 # --> Fails
To complicate things further, you can wrap the space in quotes and have CMake parse it, but the variable name then includes the space and is unusable in the CMakeLists file.
cmake MyProject/CMakeLists.txt "-D Foo=1" # --> Defines the unusable var ${ Foo}
Another inconsistency is that other command line flags work with or without a space (e.g. -G), and others require a space (e.g. -E).
My own advice would be to always avoid adding a space after the flag unless it's required. I guess always passing the path last would help too, although that shouldn't be required if you don't add extra spaces.

Related

Why my rsync scripts do no work on the new mac? [duplicate]

I am making an NW.js app on macOS, and want to run the app in dev mode
by double-clicking on an icon.
In the first step, I'm trying to make my shell script work.
Using VS Code on Windows (I wanted to gain time), I have created a run-nw file at the root of my project, containing this:
#!/bin/bash
cd "src"
npm install
cd ..
./tools/nwjs-sdk-v0.17.3-osx-x64/nwjs.app/Contents/MacOS/nwjs "src" &
but I get this output:
$ sh ./run-nw
: command not found
: No such file or directory
: command not found
: No such file or directory
Usage: npm <command>
where <command> is one of: (snip commands list)
(snip npm help)
npm#3.10.3 /usr/local/lib/node_modules/npm
: command not found
: No such file or directory
: command not found
Some things I don't understand.
It seems that it takes empty lines as commands.
In my editor (VS Code) I have tried to replace \r\n with \n
(in case the \r creates problems) but it changes nothing.
It seems that it doesn't find the folders
(with or without the dirname instruction),
or maybe it doesn't know about the cd command ?
It seems that it doesn't understand the install argument to npm.
The part that really weirds me out, is that it still runs the app
(if I did an npm install manually)...
Not able to make it work properly, and suspecting something weird with
the file itself, I created a new one directly on the Mac, using vim this time.
I entered the exact same instructions, and... now it works without any
issues.
A diff on the two files reveals exactly zero difference.
What can be the difference? What can make the first script not work? How can I find out?
Update
Following the accepted answer's recommendations, after the wrong line
endings came back, I checked multiple things.
It turns out that since I copied my ~/.gitconfig from my Windows
machine, I had autocrlf=true, so every time I modified the bash
file under Windows, it re-set the line endings to \r\n.
So, in addition to running dos2unix (which you will have to
install using Homebrew on a Mac), if you're using Git, check your
.gitconfig file.

Yes. Bash scripts are sensitive to line-endings, both in the script itself and in data it processes. They should have Unix-style line-endings, i.e., each line is terminated with a Line Feed character (decimal 10, hex 0A in ASCII).
DOS/Windows line endings in the script
With Windows or DOS-style line endings , each line is terminated with a Carriage Return followed by a Line Feed character. You can see this otherwise invisible character in the output of cat -v yourfile:
$ cat -v yourfile
#!/bin/bash^M
^M
cd "src"^M
npm install^M
^M
cd ..^M
./tools/nwjs-sdk-v0.17.3-osx-x64/nwjs.app/Contents/MacOS/nwjs "src" &^M
In this case, the carriage return (^M in caret notation or \r in C escape notation) is not treated as whitespace. Bash interprets the first line after the shebang (consisting of a single carriage return character) as the name of a command/program to run.
Since there is no command named ^M, it prints : command not found
Since there is no directory named "src"^M (or src^M), it prints : No such file or directory
It passes install^M instead of install as an argument to npm which causes npm to complain.
DOS/Windows line endings in input data
Like above, if you have an input file with carriage returns:
hello^M
world^M
then it will look completely normal in editors and when writing it to screen, but tools may produce strange results. For example, grep will fail to find lines that are obviously there:
$ grep 'hello$' file.txt || grep -x "hello" file.txt
(no match because the line actually ends in ^M)
Appended text will instead overwrite the line because the carriage returns moves the cursor to the start of the line:
$ sed -e 's/$/!/' file.txt
!ello
!orld
String comparison will seem to fail, even though strings appear to be the same when writing to screen:
$ a="hello"; read b < file.txt
$ if [[ "$a" = "$b" ]]
then echo "Variables are equal."
else echo "Sorry, $a is not equal to $b"
fi
Sorry, hello is not equal to hello
Solutions
The solution is to convert the file to use Unix-style line endings. There are a number of ways this can be accomplished:
This can be done using the dos2unix program:
dos2unix filename
Open the file in a capable text editor (Sublime, Notepad++, not Notepad) and configure it to save files with Unix line endings, e.g., with Vim, run the following command before (re)saving:
:set fileformat=unix
If you have a version of the sed utility that supports the -i or --in-place option, e.g., GNU sed, you could run the following command to strip trailing carriage returns:
sed -i 's/\r$//' filename
With other versions of sed, you could use output redirection to write to a new file. Be sure to use a different filename for the redirection target (it can be renamed later).
sed 's/\r$//' filename > filename.unix
Similarly, the tr translation filter can be used to delete unwanted characters from its input:
tr -d '\r' <filename >filename.unix
Cygwin Bash
With the Bash port for Cygwin, there’s a custom igncr option that can be set to ignore the Carriage Return in line endings (presumably because many of its users use native Windows programs to edit their text files).
This can be enabled for the current shell by running set -o igncr.
Setting this option applies only to the current shell process so it can be useful when sourcing files with extraneous carriage returns. If you regularly encounter shell scripts with DOS line endings and want this option to be set permanently, you could set an environment variable called SHELLOPTS (all capital letters) to include igncr. This environment variable is used by Bash to set shell options when it starts (before reading any startup files).
Useful utilities
The file utility is useful for quickly seeing which line endings are used in a text file. Here’s what it prints for for each file type:
Unix line endings: Bourne-Again shell script, ASCII text executable
Mac line endings: Bourne-Again shell script, ASCII text executable, with CR line terminators
DOS line endings: Bourne-Again shell script, ASCII text executable, with CRLF line terminators
The GNU version of the cat utility has a -v, --show-nonprinting option that displays non-printing characters.
The dos2unix utility is specifically written for converting text files between Unix, Mac and DOS line endings.
Useful links
Wikipedia has an excellent article covering the many different ways of marking the end of a line of text, the history of such encodings and how newlines are treated in different operating systems, programming languages and Internet protocols (e.g., FTP).
Files with classic Mac OS line endings
With Classic Mac OS (pre-OS X), each line was terminated with a Carriage Return (decimal 13, hex 0D in ASCII). If a script file was saved with such line endings, Bash would only see one long line like so:
#!/bin/bash^M^Mcd "src"^Mnpm install^M^Mcd ..^M./tools/nwjs-sdk-v0.17.3-osx-x64/nwjs.app/Contents/MacOS/nwjs "src" &^M
Since this single long line begins with an octothorpe (#), Bash treats the line (and the whole file) as a single comment.
Note: In 2001, Apple launched Mac OS X which was based on the BSD-derived NeXTSTEP operating system. As a result, OS X also uses Unix-style LF-only line endings and since then, text files terminated with a CR have become extremely rare. Nevertheless, I think it’s worthwhile to show how Bash would attempt to interpret such files.

On JetBrains products (PyCharm, PHPStorm, IDEA, etc.), you'll need to click on CRLF/LF to toggle between the two types of line separators (\r\n and \n).

I was trying to startup my docker container from Windows and got this:
Bash script and /bin/bash^M: bad interpreter: No such file or directory
I was using git bash and the problem was about the git config, then I just did the steps below and it worked. It will configure Git to not convert line endings on checkout:
git config --global core.autocrlf input
delete your local repository
clone it again.
Many thanks to Jason Harmon in this link:
https://forums.docker.com/t/error-while-running-docker-code-in-powershell/34059/6
Before that, I tried this, that didn't works:
dos2unix scriptname.sh
sed -i -e 's/\r$//' scriptname.sh
sed -i -e 's/^M$//' scriptname.sh

If you're using the read command to read from a file (or pipe) that is (or might be) in DOS/Windows format, you can take advantage of the fact that read will trim whitespace from the beginning and ends of lines. If you tell it that carriage returns are whitespace (by adding them to the IFS variable), it'll trim them from the ends of lines.
In bash (or zsh or ksh), that means you'd replace this standard idiom:
IFS= read -r somevar # This will not trim CR
with this:
IFS=$'\r' read -r somevar # This *will* trim CR
(Note: the -r option isn't related to this, it's just usually a good idea to avoid mangling backslashes.)
If you're not using the IFS= prefix (e.g. because you want to split the data into fields), then you'd replace this:
read -r field1 field2 ... # This will not trim CR
with this:
IFS=$' \t\n\r' read -r field1 field2 ... # This *will* trim CR
If you're using a shell that doesn't support the $'...' quoting mode (e.g. dash, the default /bin/sh on some Linux distros), or your script even might be run with such a shell, then you need to get a little more complex:
cr="$(printf '\r')"
IFS="$cr" read -r somevar # Read trimming *only* CR
IFS="$IFS$cr" read -r field1 field2 ... # Read trimming CR and whitespace, and splitting fields
Note that normally, when you change IFS, you should put it back to normal as soon as possible to avoid weird side effects; but in all these cases, it's a prefix to the read command, so it only affects that one command and doesn't have to be reset afterward.

Coming from a duplicate, if the problem is that you have files whose names contain ^M at the end, you can rename them with
for f in *$'\r'; do
mv "$f" "${f%$'\r'}"
done
You properly want to fix whatever caused these files to have broken names in the first place (probably a script which created them should be dos2unixed and then rerun?) but sometimes this is not feasible.
The $'\r' syntax is Bash-specific; if you have a different shell, maybe you need to use some other notation. Perhaps see also Difference between sh and bash

Since VS Code is being used, we can see CRLF or LF in the bottom right depending on what's being used and if we click on it we can change between them (LF is being used in below example):
We can also use the "Change End of Line Sequence" command from the command pallet. Whatever's easier to remember since they're functionally the same.

One more way to get rid of the unwanted CR ('\r') character is to run the tr command, for example:
$ tr -d '\r' < dosScript.py > nixScript.py

I ran into this issue when I use git with WSL.
git has a feature where it changes the line-ending of files according to the OS you are using, on Windows it make sure the line endings are \r\n which is not compatible with Linux which uses only \n.
You can resolve this problem by adding a file name .gitattributes to your git root directory and add lines as following:
config/* text eol=lf
run.sh text eol=lf
In this example all files inside config directory will have only line-feed line ending and run.sh file as well.

For Notepad++ users, this can be solved by:

The simplest way on MAC / Linux - create a file using 'touch' command, open this file with VI or VIM editor, paste your code and save. This would automatically remove the windows characters.

If you are using a text editor like BBEdit you can do it at the status bar. There is a selection where you can switch.

For IntelliJ users, here is the solution for writing Linux script.
Use LF - Unix and masOS (\n)

Scripts may call each other.
An even better magic solution is to convert all scripts in the folder/subfolders:
find . -name "*.sh" -exec sed -i -e 's/\r$//' {} +
You can use dos2unix too but many servers do not have it installed by default.

For the sake of completeness, I'll point out another solution which can solve this problem permanently without the need to run dos2unix all the time:
sudo ln -s /bin/bash `printf 'bash\r'`

GNU join overwriting output columns [duplicate]

Yes. Bash scripts are sensitive to line-endings, both in the script itself and in data it processes. They should have Unix-style line-endings, i.e., each line is terminated with a Line Feed character (decimal 10, hex 0A in ASCII).
DOS/Windows line endings in the script
With Windows or DOS-style line endings , each line is terminated with a Carriage Return followed by a Line Feed character. You can see this otherwise invisible character in the output of cat -v yourfile:
$ cat -v yourfile
#!/bin/bash^M
^M
cd "src"^M
npm install^M
^M
cd ..^M
./tools/nwjs-sdk-v0.17.3-osx-x64/nwjs.app/Contents/MacOS/nwjs "src" &^M
In this case, the carriage return (^M in caret notation or \r in C escape notation) is not treated as whitespace. Bash interprets the first line after the shebang (consisting of a single carriage return character) as the name of a command/program to run.
Since there is no command named ^M, it prints : command not found
Since there is no directory named "src"^M (or src^M), it prints : No such file or directory
It passes install^M instead of install as an argument to npm which causes npm to complain.
DOS/Windows line endings in input data
Like above, if you have an input file with carriage returns:
hello^M
world^M
then it will look completely normal in editors and when writing it to screen, but tools may produce strange results. For example, grep will fail to find lines that are obviously there:
$ grep 'hello$' file.txt || grep -x "hello" file.txt
(no match because the line actually ends in ^M)
Appended text will instead overwrite the line because the carriage returns moves the cursor to the start of the line:
$ sed -e 's/$/!/' file.txt
!ello
!orld
String comparison will seem to fail, even though strings appear to be the same when writing to screen:
$ a="hello"; read b < file.txt
$ if [[ "$a" = "$b" ]]
then echo "Variables are equal."
else echo "Sorry, $a is not equal to $b"
fi
Sorry, hello is not equal to hello
Solutions
The solution is to convert the file to use Unix-style line endings. There are a number of ways this can be accomplished:
This can be done using the dos2unix program:
dos2unix filename
Open the file in a capable text editor (Sublime, Notepad++, not Notepad) and configure it to save files with Unix line endings, e.g., with Vim, run the following command before (re)saving:
:set fileformat=unix
If you have a version of the sed utility that supports the -i or --in-place option, e.g., GNU sed, you could run the following command to strip trailing carriage returns:
sed -i 's/\r$//' filename
With other versions of sed, you could use output redirection to write to a new file. Be sure to use a different filename for the redirection target (it can be renamed later).
sed 's/\r$//' filename > filename.unix
Similarly, the tr translation filter can be used to delete unwanted characters from its input:
tr -d '\r' <filename >filename.unix
Cygwin Bash
With the Bash port for Cygwin, there’s a custom igncr option that can be set to ignore the Carriage Return in line endings (presumably because many of its users use native Windows programs to edit their text files).
This can be enabled for the current shell by running set -o igncr.
Setting this option applies only to the current shell process so it can be useful when sourcing files with extraneous carriage returns. If you regularly encounter shell scripts with DOS line endings and want this option to be set permanently, you could set an environment variable called SHELLOPTS (all capital letters) to include igncr. This environment variable is used by Bash to set shell options when it starts (before reading any startup files).
Useful utilities
The file utility is useful for quickly seeing which line endings are used in a text file. Here’s what it prints for for each file type:
Unix line endings: Bourne-Again shell script, ASCII text executable
Mac line endings: Bourne-Again shell script, ASCII text executable, with CR line terminators
DOS line endings: Bourne-Again shell script, ASCII text executable, with CRLF line terminators
The GNU version of the cat utility has a -v, --show-nonprinting option that displays non-printing characters.
The dos2unix utility is specifically written for converting text files between Unix, Mac and DOS line endings.
Useful links
Wikipedia has an excellent article covering the many different ways of marking the end of a line of text, the history of such encodings and how newlines are treated in different operating systems, programming languages and Internet protocols (e.g., FTP).
Files with classic Mac OS line endings
With Classic Mac OS (pre-OS X), each line was terminated with a Carriage Return (decimal 13, hex 0D in ASCII). If a script file was saved with such line endings, Bash would only see one long line like so:
#!/bin/bash^M^Mcd "src"^Mnpm install^M^Mcd ..^M./tools/nwjs-sdk-v0.17.3-osx-x64/nwjs.app/Contents/MacOS/nwjs "src" &^M
Since this single long line begins with an octothorpe (#), Bash treats the line (and the whole file) as a single comment.
Note: In 2001, Apple launched Mac OS X which was based on the BSD-derived NeXTSTEP operating system. As a result, OS X also uses Unix-style LF-only line endings and since then, text files terminated with a CR have become extremely rare. Nevertheless, I think it’s worthwhile to show how Bash would attempt to interpret such files.

On JetBrains products (PyCharm, PHPStorm, IDEA, etc.), you'll need to click on CRLF/LF to toggle between the two types of line separators (\r\n and \n).

I was trying to startup my docker container from Windows and got this:
Bash script and /bin/bash^M: bad interpreter: No such file or directory
I was using git bash and the problem was about the git config, then I just did the steps below and it worked. It will configure Git to not convert line endings on checkout:
git config --global core.autocrlf input
delete your local repository
clone it again.
Many thanks to Jason Harmon in this link:
https://forums.docker.com/t/error-while-running-docker-code-in-powershell/34059/6
Before that, I tried this, that didn't works:
dos2unix scriptname.sh
sed -i -e 's/\r$//' scriptname.sh
sed -i -e 's/^M$//' scriptname.sh

If you're using the read command to read from a file (or pipe) that is (or might be) in DOS/Windows format, you can take advantage of the fact that read will trim whitespace from the beginning and ends of lines. If you tell it that carriage returns are whitespace (by adding them to the IFS variable), it'll trim them from the ends of lines.
In bash (or zsh or ksh), that means you'd replace this standard idiom:
IFS= read -r somevar # This will not trim CR
with this:
IFS=$'\r' read -r somevar # This *will* trim CR
(Note: the -r option isn't related to this, it's just usually a good idea to avoid mangling backslashes.)
If you're not using the IFS= prefix (e.g. because you want to split the data into fields), then you'd replace this:
read -r field1 field2 ... # This will not trim CR
with this:
IFS=$' \t\n\r' read -r field1 field2 ... # This *will* trim CR
If you're using a shell that doesn't support the $'...' quoting mode (e.g. dash, the default /bin/sh on some Linux distros), or your script even might be run with such a shell, then you need to get a little more complex:
cr="$(printf '\r')"
IFS="$cr" read -r somevar # Read trimming *only* CR
IFS="$IFS$cr" read -r field1 field2 ... # Read trimming CR and whitespace, and splitting fields
Note that normally, when you change IFS, you should put it back to normal as soon as possible to avoid weird side effects; but in all these cases, it's a prefix to the read command, so it only affects that one command and doesn't have to be reset afterward.

Coming from a duplicate, if the problem is that you have files whose names contain ^M at the end, you can rename them with
for f in *$'\r'; do
mv "$f" "${f%$'\r'}"
done
You properly want to fix whatever caused these files to have broken names in the first place (probably a script which created them should be dos2unixed and then rerun?) but sometimes this is not feasible.
The $'\r' syntax is Bash-specific; if you have a different shell, maybe you need to use some other notation. Perhaps see also Difference between sh and bash

Since VS Code is being used, we can see CRLF or LF in the bottom right depending on what's being used and if we click on it we can change between them (LF is being used in below example):
We can also use the "Change End of Line Sequence" command from the command pallet. Whatever's easier to remember since they're functionally the same.

One more way to get rid of the unwanted CR ('\r') character is to run the tr command, for example:
$ tr -d '\r' < dosScript.py > nixScript.py

I ran into this issue when I use git with WSL.
git has a feature where it changes the line-ending of files according to the OS you are using, on Windows it make sure the line endings are \r\n which is not compatible with Linux which uses only \n.
You can resolve this problem by adding a file name .gitattributes to your git root directory and add lines as following:
config/* text eol=lf
run.sh text eol=lf
In this example all files inside config directory will have only line-feed line ending and run.sh file as well.

For Notepad++ users, this can be solved by:

The simplest way on MAC / Linux - create a file using 'touch' command, open this file with VI or VIM editor, paste your code and save. This would automatically remove the windows characters.

If you are using a text editor like BBEdit you can do it at the status bar. There is a selection where you can switch.

For IntelliJ users, here is the solution for writing Linux script.
Use LF - Unix and masOS (\n)

Scripts may call each other.
An even better magic solution is to convert all scripts in the folder/subfolders:
find . -name "*.sh" -exec sed -i -e 's/\r$//' {} +
You can use dos2unix too but many servers do not have it installed by default.

For the sake of completeness, I'll point out another solution which can solve this problem permanently without the need to run dos2unix all the time:
sudo ln -s /bin/bash `printf 'bash\r'`

Powershell Docker Command Doesn't Work Like Bat File

I'm trying to create a script that starts a docker container and mounts a local folder that contains spaces in the name. I can get it to work fine when I run a *.bat file with the docker run command:
docker run -p 8081:8081 -v "C:\Test Folder With Blanks":/zzz myimage jupyter lab --notebook-dir=/zzz--ip=0.0.0.0 --port=8081 --allow-root
But when I try to do the same in a Powershell script file, I get an error:
$CMD = 'docker run -p 8081:8081 -v "C:\Test Folder With Blanks":/zzz myimage jupyter lab --notebook-dir=/zzz--ip=0.0.0.0 --port=8081 --allow-root'
Invoke-Expression $CMD
docker: invalid reference format.
See 'docker run --help'.
I'm on Win10 and running Powershell in Visual Studio Code IDE.
Thanks for ideas.

First, the obligatory warning: Unless you have a command line stored as a single string somewhere and you either fully control or trust the content of the string, Invoke-Expression should generally be avoided.
You're seeing an inconsistency in how PowerShell treats compound tokens composed of directly concatenated quoted and unquoted parts.
Specifically, argument "C:\Test Folder With Blanks":/zzz is unexpectedly broken in two, i.e passed as two arguments.
The workaround is to quote the entire argument, i.e.
"C:\Test Folder With Blanks:/zzz"
Note: I'm assuming that docker doesn't actually require partial quoting in its arguments, which it shouldn't; however, there are high-profile CLIs on Windows that do, notably msiexec.
Alternatively, use an expression enclosed in (...) to compose your string; e.g.
("C:\Test Folder With Blanks" + ':/zzz')
There's no good reason to do so in this case, but it could be helpful if you need string interpolation in one part of your string ("..."), but not in another ('...').
General caveats:
Compared to cmd.exe and also POSIX-compatible shells such as bash, PowerShell has several additional metacharacters, notably # (at the start of a token), { / }, and ;. Therefore, you cannot always expect command lines written for these shells to work as-is in PowerShell.
As of PowerShell 7.2.2, passing arguments to external programs (such as docker) is fundamentally broken with respect to arguments that have embedded " characters and empty-string arguments - see this answer.
The general pattern of the inconsistency, as of PowerShell 7.2.2, is as follows:
If an argument:
starts with a quoted token - whether single- ('...') or double-quoted ("...") -
and has additional characters directly following the closing quote,
the first such character starts a separate argument.
E.g. "foo":bar / "foo"=bar / "foo"'bar' are passed as separate arguments foo and :bar / foo and =bar / foo and bar, respectively.
In other words:
You cannot compose a single string argument from a mix of quoted and unquoted / differently quoted tokens if the first token is quoted.
Conversely, it does work if the first token is unquoted, including an unquoted simple variable reference such as $HOME.
# OK: First token is unquoted.
PS> cmd /c echo foo"bar"'baz'last
foobarbazlast
# !! BROKEN: First token is quoted.
# !! Because each successive token is quoted too,
# !! each becomes its own argument.
PS> cmd /c echo 'foo'"bar"'baz'last
foo bar baz last
GitHub issue #6467 discusses this inconsistency; however, it has been closed, because the behavior is - surprisingly - considered by design.
This does not happen if the first token is unquoted; however, there are related bugs that start with unquoted tokens that similarly break arguments in two, related to their looking like named arguments to PowerShell (which is a PowerShell concept that doesn't apply when calling external programs):
GitHub issue #11646: an argument such as -foo=1,2 breaks parsing.
GitHub issue #6291: an argument such as -foo=bar.baz is broken in two at the (first) .

Grep with RegEx Inside a Docker Container?

Dipping my toes into Bash coding for the first time (not the most experienced person with Linux either) and I'm trying to read the version from the version.php inside a container at:
/config/www/nextcloud/version.php
To do so, I run:
docker exec -it 1c8c05daba19 grep -eo "(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?" /config/www/nextcloud/version.php
This uses a semantic versioning RegEx pattern (I know, a bit overkill, but it works for now) to read and extract the version from the line:
$OC_VersionString = '20.0.1';
However, when I run the command it tells me No such file or directory, (I've confirmed it does exist at that path inside the container) and then proceeds to spit out the entire contents of the file it just said doesn't exist?
grep: (0|[1-9]\d*).(0|[1-9]\d*).(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-])(?:.(?:0|[1-9]\d|\d*[a-zA-Z-][0-9a-zA-Z-]))))?(?:+([0-9a-zA-Z-]+(?:.[0-9a-zA-Z-]+)*))?: No such file or directory
/config/www/nextcloud/version.php:$OC_Version = array(20,0,1,1);
/config/www/nextcloud/version.php:$OC_VersionString = '20.0.1';
/config/www/nextcloud/version.php:$OC_Edition = '';
/config/www/nextcloud/version.php:$OC_VersionCanBeUpgradedFrom = array (
/config/www/nextcloud/version.php: 'nextcloud' =>
/config/www/nextcloud/version.php: 'owncloud' =>
/config/www/nextcloud/version.php:$vendor = 'nextcloud';
Anyone able to spot the problem?
Update 1:
For the sake of clarity, I'm trying to run this from a bash script. I just want to fetch the version number from that file, to use it in other areas of the script.
Update 2:
Responding to the comments, I tried to login to the container first, and then run the grep, and still get the same result. Then I cat that file and it shows it's contents no problem.

Many containers don't have the GNU versions of Unix tools and their various extensions. It's popular to base containers on Alpine Linux, which in turn uses a very lightweight single-binary tool called BusyBox to provide the base tools. Those tend to have the set of options required in the POSIX specs, and no more.
POSIX grep(1) in particular doesn't have an -o option. So the command you're running is
grep \
-eo \ # specify "o" as the regexp to match
"(regexps are write-only)" \ # a filename
/config/www/nextcloud/version.php # a second filename
Notice that the grep output in the interactive shell only contains lines with the letter "o", but not for example the line just containing array.
POSIX grep doesn't have an equivalent for GNU grep's -o option
Print only the matched (non-empty) parts of matching lines, with each such part on a separate output line. Output lines use the same delimiters as input....
but it's easy to do that with sed(1) instead. Ask it to match some stuff, the regexp in question, and some stuff, and replace it with the matched group.
sed -e 's/.*\(any regexp here\).*/\1/' input-file
(POSIX sed only accepts basic regular expressions, so you'll have to escape more of the parentheses.)

Well, for any potential future readers, I had no luck getting grep to do it, I'm sure it was my fault somehow and not grep's, but thanks to the help in this post I was able to use awk instead of grep, like so:
docker exec -it 1c8c05daba19 awk '/^\$OC_VersionString/ && match($0,/\047[0-9]+\.[0-9]+\.[0-9]+\047/){print substr($0,RSTART+1,RLENGTH-2)}' /config/www/nextcloud/version.php
That ended up doing exactly what I needed:
It logs into a docker container.
Scans and returns just the version number from the line I am looking for at: /config/www/nextcloud/version.php inside the container.
Exits stage left from the container with just the info I needed.
I can get right back to eating my Hot Cheetos.

PBSPro qsub output error file directed to path with jobid in name

I'm using PBSPro and am trying to use qsub command line to submit a job but can't seem to get the output and error files to be named how I want them. Currently using:
qsub -N ${subjobname_short} \
-o ${path}.o{$PBS_JOBID} -e ${path}.e${PBS_JOBID}
... submission_script.sc
Where $path=fulljobname (i.e. more than 15 characters)
I'm aware that $PBS_JOBID won't be set until after the job is submitted...
Any ideas?
Thanks

The solution I came up with was following the qsub command with a qalter command like so:
jobid=$(qsub -N ${subjobname_short} submission_script.sc)
qalter -o ${path}.o{$jobid} -e ${path}.e${jobid} ${jobid}
This way, PBS Pro does not need to resolve the variables, as it failed to do so in our install (this may be a configuration issue)

If you want the ${PBS_JOBID} to be resolved by PBSPro, you need to escape it on the command line:
qsub -o \$PBS_JOBID
Otherwise, bash will attempt to resolve $PBS_JOBID before it gets to the qsub command. I don't know if $subjobname_short and $path are actual environment variables or ones you want pbs to resolve, but if you want pbs to resolve them you'll also need to escape these ones or place it inside the job script.
NOTE: I also notice that your -o argument says {$PBS_JOBID} and I'm pretty sure you want ${PBS_JOBID}. I don't know if that's a typo in the question or what you tried to pass to qsub.

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