Version 1.10 of spade appears to be non-compatible with Cytoscape 2.8.x

[mlinderm]

This came via bioconductor...

Running spade 1.10 produces outputs that contain a folder of CSV tables, whereas 1.8 produced a folder of pdf files. The latter works with Cytoscape 2.8.x and the prior produces empty boxes.

I prefer sticking with Cytoscape 2.8 as opposed to moving up to 3.x as the documentation seems much better so far, so is there a place where spade 1.8 is still available for download?

-- output of sessionInfo():

R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

Sent via the guest posting facility at bioconductor.org.

[zbjornson]

Known issue, which has naught to do with the tables vs PDFs folders. Any way to communicate to the buoconductor asker?

[johnquinn]

Zach,

I'm the bioconductor asker. Can you tell me a little more about what the actual problem is and what the recommended work around is?

John Quinn

[zbjornson]

Hello John,

Installing vintage SPADE is rather tricky because at least one legacy dependency has been removed from CRAN and bioconductor. The steps would be something like:

1. Obtain igraph0 from the archive http://cran.r-project.org/src/contrib/Archive/igraph0/
2. Run a version of R near 2.15.1 (3.x.x won't work)
3. Reinstall Biobase and flowCore packages
4. Build and install this ZIP of SPADE 1.6/1.8 https://github.com/nolanlab/spade/archive/bf9a81d182cc7186f674c1e6ed6d7c0f466467ae.zip

Cytoscape 2.8.x is the only version that supports the plugin right now (3.0 definitely doesn't work with the plugin), but it has a number of bugs unrelated to our plugin that cause issues like what you described with rectangles instead of circles and VizMapper randomly not working.

Sometime we might get the plugin working in Cytoscape 3.0 and resolve the gross compatibility/upgrade issues, but this remains a low priority because the Cytobank interface offers a ton of advantages of Cytoscape.

Hope that helps and sorry for the trouble.
Zach

[zbjornson]

... note that Cytoscape 2.8 should actually be able to open SPADE 1.10 output, as long as Cytoscape bugs don't prevail. Ensure the current SPADE 1.10 cytoscape.jar file is installed in your Cytoscape plugins directory. There's an issue with running SPADE from Cytoscape however.

[johnquinn]

Zach,

 Thanks, I appreciate you taking the time to write this out!

John

John Quinn, Ph.D.
Application Scientist
Tree Star, Inc.
www.flowjo.com
john@treestar.com

On 3/23/2014 4:03 PM, Zach Bjornson wrote:

Hello John,

Installing vintage SPADE is rather tricky because at least one legacy
dependency has been removed from CRAN and bioconductor. The steps
would be something like:

1. Obtain igraph0 from the archive
   http://cran.r-project.org/src/contrib/Archive/igraph0/
2. Run a version of R near 2.15.1 (3.x.x won't work)
3. Reinstall Biobase and flowCore packages
4. Build and install this ZIP of SPADE 1.6/1.8
   https://github.com/nolanlab/spade/archive/bf9a81d182cc7186f674c1e6ed6d7c0f466467ae.zip

Cytoscape 2.8.x is the only version that supports the plugin right now
(3.0 definitely doesn't work with the plugin), but it has a number of
bugs unrelated to our plugin that cause issues like what you described
with rectangles instead of circles and VizMapper randomly not working.

Sometime we might get the plugin working in Cytoscape 3.0 and resolve
the gross compatibility/upgrade issues, but this remains a low
priority because the Cytobank interface offers a ton of advantages of
Cytoscape.

Hope that helps and sorry for the trouble.
Zach

—
Reply to this email directly or view it on GitHub
#91 (comment).

[johnquinn]

Zach,

 I need a bit more help here, installing vintage SPADE has been too 

tricky for my users and I am far from an R expert. I put up a page
documenting how to run SPADE 1.8 through FlowJo back when 1.8 was
current and now I've got a small mountain of support e-mails coming
through from folks trying to run 1.10 unsuccessfully.

First off the igraph0 link leads to a download page with many choices.
I assumed that the most recent is best and further that the R commands -
install.packages("igraph") and library(igraph) would achieve the goal.
Have I assumed wrong and if so, can you give me the baby steps
instruction of which tar.gz file to tell folks to get and how to install it?

Then if possible, could you give the baby steps instructions on 'build
and install the SPADE from a Zip'. I had folks follow the Read Me file
inside it, but I haven't had anyone have success yet.

Sorry to trouble you again, but I get 3-4 more folks each day asking the
same question so I want to get this workaround ironed out.

John

John Quinn, Ph.D.
Application Scientist
Tree Star, Inc.
www.flowjo.com
john@treestar.com

On 3/23/2014 4:03 PM, Zach Bjornson wrote:

Hello John,

Installing vintage SPADE is rather tricky because at least one legacy
dependency has been removed from CRAN and bioconductor. The steps
would be something like:

1. Obtain igraph0 from the archive
   http://cran.r-project.org/src/contrib/Archive/igraph0/
2. Run a version of R near 2.15.1 (3.x.x won't work)
3. Reinstall Biobase and flowCore packages
4. Build and install this ZIP of SPADE 1.6/1.8
   https://github.com/nolanlab/spade/archive/bf9a81d182cc7186f674c1e6ed6d7c0f466467ae.zip

Cytoscape 2.8.x is the only version that supports the plugin right now
(3.0 definitely doesn't work with the plugin), but it has a number of
bugs unrelated to our plugin that cause issues like what you described
with rectangles instead of circles and VizMapper randomly not working.

Sometime we might get the plugin working in Cytoscape 3.0 and resolve
the gross compatibility/upgrade issues, but this remains a low
priority because the Cytobank interface offers a ton of advantages of
Cytoscape.

Hope that helps and sorry for the trouble.
Zach

—
Reply to this email directly or view it on GitHub
#91 (comment).

[zbjornson]

Since the Cytoscape issues aren't going away... I started working on the Cytoscape 3 upgrade yesterday. If I can get that to work, that will be a far easier solution than dealing with the above. Hope to get back to you soon.

[johnquinn]

Awesome, and good luck :)

John

John Quinn, Ph.D.
Application Scientist
Tree Star, Inc.
www.flowjo.com
john@treestar.com

On 4/9/2014 4:32 PM, Zach Bjornson wrote:

Since the Cytoscape issues aren't going away... I started working on
the Cytoscape 3 upgrade yesterday. If I can get that to work, that
will be a far easier solution than dealing with the above. Hope to get
back to you soon.

—
Reply to this email directly or view it on GitHub
#91 (comment).

[johnquinn]

Any update?

[zbjornson]

As of last week, we finally hired someone to work on this. Sorry for the continuing delays.

[johnquinn]

Thanks for the update.

John Quinn, Ph.D.
Application Scientist
Tree Star, Inc.
www.flowjo.com
john@treestar.com

On 7/11/2014 2:06 PM, Zach Bjornson wrote:

As of last week, we finally hired someone to work on this. Sorry for
the continuing delays.

—
Reply to this email directly or view it on GitHub
#91 (comment).

[zbjornson]

Sorry for the on-going delays John. We've run out of resources to try to finish upgrading the cytoscape package and are no longer supporting it.