Skip to content

docs: fix typo and malformed .NET link in Windows installation guide #266

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Tanush576 wants to merge 2 commits into
base: develop
Choose a base branch
from
Open

docs: fix typo and malformed .NET link in Windows installation guide #266

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
4e720f4
docs: fix typo and malformed .NET link in Windows installation guide
Rakshi2609 Mar 3, 2026
32e3c57
docs: apply code review suggestions for grammar and punctuation
Tanush576 Mar 3, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
27 changes: 16 additions & 11 deletions docs/about/installation/installation-on-windows.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,17 +1,16 @@
Windows
=======
# Windows

## Install via Windows installer

To Install the binary package of OpenMS & {term}`TOPP`:

1. Download the installer `OpenMS-<version>-Win64.exe` from the [archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/)
1. Download the installer `OpenMS-<version>-Win64.exe` from the [archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/)
2. Execute the installer under the user account that later runs OpenMS and follow its instructions.

You may see a Windows Defender Warning, since our installer is not digitally signed.
Click on "More Info", and then "Run anyways".

Click on "More Info", and then "Run anyway".

![](/_images/installations/win/smartscreen.gif)

When asked for an admin authentication, please enter the credentials (it is not advised to directly invoke the installer using an admin account).
Expand All @@ -23,13 +22,16 @@ The windows installer works with Windows 10 and 11 (older versions might still w
## Known issues

1. During installation, an error message pops up, saying:
>"The installation of the Microsoft .NET 3.5 SP1' package failed!

> "The installation of the Microsoft .NET 3.5 SP1 package failed!"

You must download and install it manually in order for Proteowizard to work.
This should only happen if installion is done by selecting the "Third Party - Proteowizard" components. The reason is
This should only happen if installation is done by selecting the "Third Party - Proteowizard" components. The reason is
Copy link

@coderabbitai coderabbitai bot Mar 3, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ Potential issue | 🟡 Minor

Use consistent product casing for ProteoWizard.

Line 29 says "Third Party - Proteowizard" while Line 55 uses ProteoWizard. Please standardize casing to avoid confusion.

🤖 Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In `@docs/about/installation/installation-on-windows.md` at line 29, The document
uses inconsistent casing for ProteoWizard: change the phrase "Third Party -
Proteowizard" to "Third Party - ProteoWizard" (match the usage on Line 55) so
the product name is consistently capitalized; search for occurrences of
"Proteowizard" in this file and update them to "ProteoWizard" to standardize
casing.

usually that **.NET 3.5 SP1** is already installed (see Windows Control Panel). If it's not installed, follow the
instructions of the error message.

2. During installation, an error message pops up, saying:

> "The installation of the Visual Studio redistributable package ... failed. ..."

This is a known issue with a Microsoft package, we cannot do anything about it.
Expand All @@ -38,13 +40,16 @@ The windows installer works with Windows 10 and 11 (older versions might still w
receive an error message (this is also the reason why the OpenMS setup complained about it). You might have to find
the solution to fix the problem in your local machine. If you're lucky the error message is instructive and the
problem is easy to fix.

3. During installation, an error message pops up saying:
>"Error opening installation log file"

> "Error opening installation log file"

To fix, check the system environment variables. Make sure they are apt. There should a `TMP` and a `TEMP` variable,
and both should contain one directory only, which exists and is writable. Fix accordingly (search the internet on
how to change environment variables on Windows).

4. For Win8 or later, Windows will report an error while installing `.net4` as it's mostly included. But it might occur
that `.net3.5` does not get properly installed during the process.

Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://docs.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows).aspx#ControlPanel) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third party tools (ProteoWizard).
Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://learn.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third-party tools (ProteoWizard).
Copy link

@coderabbitai coderabbitai bot Mar 3, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ Potential issue | 🟡 Minor

Fix list-item continuation formatting for Known issue 4.

Line 55 should be indented as part of list item 4.; currently it can render as a separate paragraph outside the numbered item.

Suggested edit 
-Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://learn.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third-party tools (ProteoWizard).
+   Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://learn.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third-party tools (ProteoWizard).
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://learn.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third-party tools (ProteoWizard).
Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://learn.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third-party tools (ProteoWizard).
🤖 Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In `@docs/about/installation/installation-on-windows.md` at line 55, The sentence
"Fix is to enable the .NET Framework 3.5 yourself through Control Panel..." that
documents Known issue 4 is not indented and renders outside the numbered item;
update the Markdown so that this sentence is a continuation of list item "4." by
indenting that line by four spaces (or one tab) so it is nested under the "4."
list item (edit the paragraph containing the .NET Framework 3.5 guidance in the
Known issue 4 block).

Loading