Error: attempt to set an attribute on NULL

[rfernan1]

We are running SCAFFoLD for the first time. We can successfully Run Clustering (files are generated) but when we try to Run SCAFFoLD Analysis we get an error message (Error: attempt to set an attribute on NULL). We have tried selecting different samples and marker combinations but same message. Could you suggest what we need to change, please? Thank you!

[ShaunJiao]

I have the same problem, can anyone help?

[treizandouric]

We are running SCAFFoLD for the first time.

I obtained these warning :

Warning: replacing previous import ‘flowCore::normalize’ by ‘igraph::normalize’ when loading ‘scaffold’ Warning: replacing previous import ‘flowCore::tree’ by ‘igraph::tree’ when loading ‘scaffold’ Warning: replacing previous import ‘flowCore::parent’ by ‘igraph::parent’ when loading ‘scaffold’ Warning: replacing previous import ‘plyr::rename’ by ‘reshape::rename’ when loading ‘scaffold’ Warning: replacing previous import ‘plyr::round_any’ by ‘reshape::round_any’ when loading ‘scaffold’

Could you suggest me what to do ?

Thank You

[zinagood]

This generally means that the definitions of those functions have been updated by the scaffold R library. You don't need to worry about these warning messages. Disclaimer: I'm not one one the SCAFFoLD developers, but use it often.

Zina

-- Zinaida Good 415-290-8944

On Sun, Dec 3, 2017 at 1:46 PM, treizandouric notifications@github.com wrote:

We are running SCAFFoLD for the first time.

I obtained these warning :

Warning: replacing previous import ‘flowCore::normalize’ by ‘igraph::normalize’ when loading ‘scaffold’ Warning: replacing previous import ‘flowCore::tree’ by ‘igraph::tree’ when loading ‘scaffold’ Warning: replacing previous import ‘flowCore::parent’ by ‘igraph::parent’ when loading ‘scaffold’ Warning: replacing previous import ‘plyr::rename’ by ‘reshape::rename’ when loading ‘scaffold’ Warning: replacing previous import ‘plyr::round_any’ by ‘reshape::round_any’ when loading ‘scaffold’

Could you suggest me what to do ?

Thank You

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nolanlab/scaffold/issues/8#issuecomment-348817386, or mute the thread https://github.com/notifications/unsubscribe-auth/AIDe2x_D2JihtZ7chnu_x_MEqL0k92ABks5s8xaygaJpZM4Pvkoz .

[treizandouric]

Thank you Zina for your response.

I start in bioinformatics and I try to use and understand scaffold and x-shift.

Kind regard

Hélène

Le 04-12-2017 19:45, Zinaida Good a écrit :

This generally means that the definitions of those functions have been updated by the scaffold R library. You don't need to worry about these warning messages. Disclaimer: I'm not one one the SCAFFoLD developers, but use it often.

Zina

-- Zinaida Good 415-290-8944

On Sun, Dec 3, 2017 at 1:46 PM, treizandouric notifications@github.com wrote:

We are running SCAFFoLD for the first time.

I obtained these warning :

Warning: replacing previous import 'flowCore::normalize' by 'igraph::normalize' when loading 'scaffold' Warning: replacing previous import 'flowCore::tree' by 'igraph::tree' when loading 'scaffold' Warning: replacing previous import 'flowCore::parent' by 'igraph::parent' when loading 'scaffold' Warning: replacing previous import 'plyr::rename' by 'reshape::rename' when loading 'scaffold' Warning: replacing previous import 'plyr::round_any' by 'reshape::round_any' when loading 'scaffold'

Could you suggest me what to do ?

Thank You

-- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nolanlab/scaffold/issues/8#issuecomment-348817386, or mute the thread https://github.com/notifications/unsubscribe-auth/AIDe2x_D2JihtZ7chnu_x_MEqL0k92ABks5s8xaygaJpZM4Pvkoz .

-- You are receiving this because you commented. Reply to this email directly, view it on GitHub [1], or mute the thread [2].

Links:

[1] https://github.com/nolanlab/scaffold/issues/8#issuecomment-349062883 [2] https://github.com/notifications/unsubscribe-auth/AgooXq9gW6fZtvT9Kg4CT8PiZVa6XGeAks5s9D2vgaJpZM4Pvkoz

[treizandouric]

Dear Zina,

When I launch Scaffold, I arrived to do the first step, Run the clustering.

When I Try to run the Scaffold analysis, I obtained this error

attempt to set an attribute on NULL

Could you help me . I work with a fcs file (cytometry).

Kind Regards

Hélène

Le 04-12-2017 19:45, Zinaida Good a écrit :

This generally means that the definitions of those functions have been updated by the scaffold R library. You don't need to worry about these warning messages. Disclaimer: I'm not one one the SCAFFoLD developers, but use it often.

Zina

-- Zinaida Good 415-290-8944

On Sun, Dec 3, 2017 at 1:46 PM, treizandouric notifications@github.com wrote:

We are running SCAFFoLD for the first time.

I obtained these warning :

Warning: replacing previous import 'flowCore::normalize' by 'igraph::normalize' when loading 'scaffold' Warning: replacing previous import 'flowCore::tree' by 'igraph::tree' when loading 'scaffold' Warning: replacing previous import 'flowCore::parent' by 'igraph::parent' when loading 'scaffold' Warning: replacing previous import 'plyr::rename' by 'reshape::rename' when loading 'scaffold' Warning: replacing previous import 'plyr::round_any' by 'reshape::round_any' when loading 'scaffold'

Could you suggest me what to do ?

Thank You

-- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nolanlab/scaffold/issues/8#issuecomment-348817386, or mute the thread https://github.com/notifications/unsubscribe-auth/AIDe2x_D2JihtZ7chnu_x_MEqL0k92ABks5s8xaygaJpZM4Pvkoz .

-- You are receiving this because you commented. Reply to this email directly, view it on GitHub [1], or mute the thread [2].

Links:

[1] https://github.com/nolanlab/scaffold/issues/8#issuecomment-349062883 [2] https://github.com/notifications/unsubscribe-auth/AgooXq9gW6fZtvT9Kg4CT8PiZVa6XGeAks5s9D2vgaJpZM4Pvkoz

[zinagood]

Hi Helene, I'm not sure what causes this error. Perhaps one one the scaffold developers can help. You can also troubleshoot using R function definitions. Zina

-- Zinaida Good 415-290-8944

On Wed, Dec 6, 2017 at 12:25 AM, treizandouric notifications@github.com wrote:

Dear Zina,

When I launch Scaffold, I arrived to do the first step, Run the clustering.

When I Try to run the Scaffold analysis, I obtained this error

attempt to set an attribute on NULL

Could you help me . I work with a fcs file (cytometry).

Kind Regards

Hélène

Le 04-12-2017 19:45, Zinaida Good a écrit :

This generally means that the definitions of those functions have been updated by the scaffold R library. You don't need to worry about these warning messages. Disclaimer: I'm not one one the SCAFFoLD developers, but use it often.

Zina

-- Zinaida Good 415-290-8944 <(415)%20290-8944>

On Sun, Dec 3, 2017 at 1:46 PM, treizandouric notifications@github.com wrote:

We are running SCAFFoLD for the first time.

I obtained these warning :

Warning: replacing previous import 'flowCore::normalize' by 'igraph::normalize' when loading 'scaffold' Warning: replacing previous import 'flowCore::tree' by 'igraph::tree' when loading 'scaffold' Warning: replacing previous import 'flowCore::parent' by 'igraph::parent' when loading 'scaffold' Warning: replacing previous import 'plyr::rename' by 'reshape::rename' when loading 'scaffold' Warning: replacing previous import 'plyr::round_any' by 'reshape::round_any' when loading 'scaffold'

Could you suggest me what to do ?

Thank You

-- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nolanlab/scaffold/issues/8#issuecomment-348817386, or mute the thread https://github.com/notifications/unsubscribe- auth/AIDe2x_D2JihtZ7chnu_x_MEqL0k92ABks5s8xaygaJpZM4Pvkoz .

-- You are receiving this because you commented. Reply to this email directly, view it on GitHub [1], or mute the thread [2].

Links:

[1] https://github.com/nolanlab/scaffold/issues/8#issuecomment-349062883 [2] https://github.com/notifications/unsubscribe-auth/ AgooXq9gW6fZtvT9Kg4CT8PiZVa6XGeAks5s9D2vgaJpZM4Pvkoz

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nolanlab/scaffold/issues/8#issuecomment-349568648, or mute the thread https://github.com/notifications/unsubscribe-auth/AIDe2x2S8RjAxdCO6Kn-LQTK0aZm7T28ks5s9k91gaJpZM4Pvkoz .

[Kprice21]

Hi there, I am having a similar issue, we are getting an error message trying to run scaffold, it says attempt to set an attribute on NULL.

I have ensured there are plenty of events in the exported gate, that the file name is labelled correctly and that I have the latest version of everything I need. The RData and clustered txt files are made without issue but I cannot analyse them without this error.

Any tips would be greatly appreciated Cheers Kylie

Here's the error I see in R:

Warning: Error in <-: attempt to set an attribute on NULL Stack trace (innermost first): 89: load_attractors_from_gated_data 88: scaffold:::run_analysis_gated 81: isolate 80: renderText [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/scaffold/shinyGUI/server.R#352] 79: func 78: origRenderFunc 77: output$analysisui_empty 2: runApp 1: scaffold.run

[ShaunJiao]

Put the gated subsets(cd4/cd8) in the same folder with your data files before running scaffold.

On Mon, Dec 18, 2017 at 8:54 PM, Kprice21 notifications@github.com wrote:

Hi there, I am having a similar issue, we are getting an error message trying to run scaffold, it says attempt to set an attribute on NULL.

I have ensured there are plenty of events in the exported gate, that the file name is labelled correctly and that I have the latest version of everything I need. The RData and clustered txt files are made without issue but I cannot analyse them without this error.

Any tips would be greatly appreciated Cheers Kylie

Here's the error I see in R:

Warning: Error in <-: attempt to set an attribute on NULL Stack trace (innermost first): 89: load_attractors_from_gated_data 88: scaffold:::run_analysis_gated 81: isolate 80: renderText [/Library/Frameworks/R.framework/Versions/3.4/ Resources/library/scaffold/shinyGUI/server.R#352] 79: func 78: origRenderFunc 77: output$analysisui_empty 2: runApp 1: scaffold.run

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nolanlab/scaffold/issues/8#issuecomment-352624798, or mute the thread https://github.com/notifications/unsubscribe-auth/Adanmx_5MsUj3x4_6cQ2RfJUi5J6vsx3ks5tByVkgaJpZM4Pvkoz .

[mhspitzer]

Hi everyone. Apologies for the delayed responses here. As Shaun mentioned, if you are running Scaffold in the "gated" mode, make sure your landmark gated files are in a subdirectory called "gated" that lives within the working directory with your FCS files (see the README for more detailed instructions). If you are still getting an error message, there may be a syntax issue with your gated files. You can use the updatePanel function in cytofCore to make sure that your gated files and your FCS files for analysis have the same nomenclature for each channel.

[pfgherardini]

This is probably due to some weirdness in your marker names. Did you manage to solve the problem? If not I can help