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Downloads:

8,053

Downloads of v 3.9.1.20230227:

14

Last Update:

27 Feb 2023

Package Maintainer(s):

Software Author(s):

  • Cytoscape Consortium

Tags:

cytoscape graph visualization analysis

cytoscape

Downloads:

8,053

Downloads of v 3.9.1.20230227:

14

Maintainer(s):

Software Author(s):

  • Cytoscape Consortium

cytoscape

  • 1
  • 2
  • 3

All Checks are Passing

3 Passing Tests


Validation Testing Passed


Verification Testing Passed

Details

Scan Testing Successful:

No detections found in any package files

Details
WARNING

This package was rejected on 13 May 2023. The reviewer chocolatey-ops has listed the following reason(s):

awatcha (maintainer) on 27 Feb 2023 09:42:35 +00:00:

User 'awatcha' (maintainer) submitted package.

chocolatey-ops (reviewer) on 27 Feb 2023 10:18:29 +00:00:

cytoscape has passed automated validation. It may have or may still fail other checks like testing (verification).
NOTE: No required changes that the validator checks have been flagged! It is appreciated if you fix other items, but only Requirements will hold up a package version from approval. A human review could still turn up issues a computer may not easily find.

Guidelines

Guidelines are strong suggestions that improve the quality of a package version. These are considered something to fix for next time to increase the quality of the package. Over time Guidelines can become Requirements. A package version can be approved without addressing Guideline comments but will reduce the quality of the package.

  • Package contains dependencies with no specified version. You should at least specify a minimum version of a dependency. More...
  • Title (title) matches id exactly. Please consider using something slightly more descriptive for the title in the nuspec. More...

chocolatey-ops (reviewer) on 27 Feb 2023 10:46:57 +00:00:

cytoscape has passed automated package testing (verification). The next step in the process is package scanning.
Please visit https://gist.github.com/1e52a6ac22b87ad6b72f7d17e585b713 for details.
This is an FYI only. There is no action you need to take.

chocolatey-ops (reviewer) on 27 Feb 2023 10:57:36 +00:00:

cytoscape has passed automated virus scanning.

Pauby (reviewer) on 08 Apr 2023 16:22:20 +00:00:

Hi, a couple of issues / suggestions / questions:

  1. Can you use a static CDN for your <iconUrl> - githack.com and jsdelivr.com are popular. See https://docs.chocolatey.org/en-us/create/create-packages#package-icon-guidelines
  2. You are taking a dependency on a specific flavour and version of Java. Does this application need a specific flavour or version of Java? If not, my suggestion would be to check for the installation of Java, or a specific version of Java using inside the chocolateyInstall.ps1 script. That way you can allows the end users to have any flavour of Java they need rather than installing a specific one, for this, that isn't needed.
  3. On line 4 of your chocolateyInstall.ps1 you have hard coded a path. Please don't do this. You don't know where that Java flavour is actually installed (could be the D: or E: drive for example, or another path entirely). You are also setting the JAVA_HOME variable to this path which will override whatever the user has already set. Please don't do this.

Thanks.

Paul

chocolatey-ops (reviewer) on 28 Apr 2023 16:24:30 +00:00:

We've found cytoscape v3.9.1.20230227 in a submitted status and waiting for your next actions. It has had no updates for 20 or more days since a reviewer has asked for corrections. Please note that if there is no response or fix of the package within 15 days of this message, this package version will automatically be closed (rejected) due to being stale.

Take action:

  • Log in to the site and respond to the review comments.
  • Resubmit fixes for this version.
  • If the package version is failing automated checks, you can self-reject the package.

If your package is failing automated testing, you can use the chocolatey test environment to manually run the verification and determine what may need to be fixed.

Note: We don't like to see packages automatically rejected. It doesn't mean that we don't value your contributions, just that we can not continue to hold packages versions in a waiting status that have possibly been abandoned. If you don't believe you will be able to fix up this version of the package within 15 days, we strongly urge you to log in to the site and respond to the review comments until you are able to.

chocolatey-ops (reviewer) on 13 May 2023 16:26:22 +00:00:

Unfortunately there has not been progress to move cytoscape v3.9.1.20230227 towards an approved status within 15 days after the last review message, so we need to close (reject) the package version at this time. If you want to pick this version up and move it towards approval in the future, use the contact site admins link on the package page and we can move it back into a submitted status so you can submit updates.

Status Change - Changed status of package from 'submitted' to 'rejected'.

Description

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.


tools\chocolateyinstall.ps1

$ErrorActionPreference = 'Stop';

$zulu11 = "c:\program files\zulu\zulu-11"

$packageArgs = @{
  packageName    = 'cytoscape'
  softwareName   = 'Cytoscape*'

  unzipLocation  = "$(Split-Path -parent $MyInvocation.MyCommand.Definition)"
  fileType       = 'exe'

  url64bit       = 'https://github.com/cytoscape/cytoscape/releases/download/3.9.1/Cytoscape_3_9_1_windows_64bit.exe'

  silentArgs     = '-q'
  validExitCodes = @(0)

  checksum64     = '4A9073F2480FDBECB945C9A76838EC1E93FAD027F36EFD44AE2C779040F317F0'
  checksumType64 = 'sha256'
}

setx /m JAVA_HOME "$zulu11"

Install-ChocolateyPackage @packageArgs
tools\chocolateyuninstall.ps1
$ErrorActionPreference = 'Stop';

$packageName = 'cytoscape'
$softwareName = 'Cytoscape*'
$installerType = 'EXE' 

$silentArgs = '/qn /norestart'
$validExitCodes = @(0, 3010, 1605, 1614, 1641)
if ($installerType -ne 'MSI') {
  $silentArgs = '-q'
  $validExitCodes = @(0)
}

[array]$key = Get-UninstallRegistryKey -SoftwareName $softwareName

if ($key.Count -eq 1) {
  $key | % { 
    $file = "$($_.UninstallString)"

    if ($installerType -eq 'MSI') {
      $silentArgs = "$($_.PSChildName) $silentArgs"

      $file = ''
    }

    Uninstall-ChocolateyPackage -PackageName $packageName `
                                -FileType $installerType `
                                -SilentArgs "$silentArgs" `
                                -ValidExitCodes $validExitCodes `
                                -File "$file"
  }
} elseif ($key.Count -eq 0) {
  Write-Warning "$packageName has already been uninstalled by other means."
} elseif ($key.Count -gt 1) {
  Write-Warning "$key.Count matches found!"
  Write-Warning "To prevent accidental data loss, no programs will be uninstalled."
  Write-Warning "Please alert package maintainer the following keys were matched:"
  $key | ForEach-Object {Write-Warning "- $_.DisplayName"}
}




Log in or click on link to see number of positives.

In cases where actual malware is found, the packages are subject to removal. Software sometimes has false positives. Moderators do not necessarily validate the safety of the underlying software, only that a package retrieves software from the official distribution point and/or validate embedded software against official distribution point (where distribution rights allow redistribution).

Chocolatey Pro provides runtime protection from possible malware.

Add to Builder Version Downloads Last Updated Status
cytoscape (Install) 3.7.1 863 Sunday, February 24, 2019 Approved
cytoscape (Install) 3.4.0 678 Monday, September 19, 2016 Approved
Discussion for the cytoscape Package

Ground Rules:

  • This discussion is only about cytoscape and the cytoscape package. If you have feedback for Chocolatey, please contact the Google Group.
  • This discussion will carry over multiple versions. If you have a comment about a particular version, please note that in your comments.
  • The maintainers of this Chocolatey Package will be notified about new comments that are posted to this Disqus thread, however, it is NOT a guarantee that you will get a response. If you do not hear back from the maintainers after posting a message below, please follow up by using the link on the left side of this page or follow this link to contact maintainers. If you still hear nothing back, please follow the package triage process.
  • Tell us what you love about the package or cytoscape, or tell us what needs improvement.
  • Share your experiences with the package, or extra configuration or gotchas that you've found.
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