checkForRemoteErrors(val) : one node produced an error: could not find function "rmultinom"

[kanefos]

Hi authors,

Love the tool, can't want to use. Having issue with getting run.Ted() to work. I have formatted my data as laid out in vignette, and started to run, but then encounter this error:

Start run... This may take a while 
Loading required package: utils
R Version:  R version 4.1.0 (2021-05-18) 

snowfall 1.84-6.1 initialized (using snow 0.4-4): parallel execution on 1 CPUs.

Error in checkForRemoteErrors(val) : 
  one node produced an error: could not find function "rmultinom"

I played with some of this code to try and get rmultinom onto the snowfall cluster, but didn't get anywhere.

Thanks,

[tinyi]

Hi Kane,

Thank you for your interest in our work. Can I ask the OS you use? Linux/Mac OS or Windows? rmultinom should be loaded in base R from stats, so this issue might be related to the specific R environment.

Best,

Tinyi

On Tue, May 17, 2022 at 2:52 PM Kane @.***> wrote:

Hi authors,

Love the tool, can't want to use. Having issue with getting run.Ted() to work. I have formatted my data as laid out in vignette, and started to run, but then encounter this error:

Start run... This may take a while Loading required package: utils R Version: R version 4.1.0 (2021-05-18)

snowfall 1.84-6.1 initialized (using snow 0.4-4): parallel execution on 1 CPUs.

Error in checkForRemoteErrors(val) : one node produced an error: could not find function "rmultinom"

I played with some of this https://stackoverflow.com/questions/47197566/r-get-list-and-environment-of-all-variables-and-functions-within-a-given-functi code to try and get rmultinom onto the snowfall cluster, but didn't get anywhere.

Thanks,

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[tinyi]

I have added stats and utils in the namespace and description. You may try reinstalling the package.

Best,

Tinyi

On Tue, May 17, 2022 at 3:09 PM Tinyi Chu @.***> wrote:

Hi Kane,

Thank you for your interest in our work. Can I ask the OS you use? Linux/Mac OS or Windows? rmultinom should be loaded in base R from stats, so this issue might be related to the specific R environment.

Best,

Tinyi

On Tue, May 17, 2022 at 2:52 PM Kane @.***> wrote:

Hi authors,

Love the tool, can't want to use. Having issue with getting run.Ted() to work. I have formatted my data as laid out in vignette, and started to run, but then encounter this error:

Start run... This may take a while Loading required package: utils R Version: R version 4.1.0 (2021-05-18)

snowfall 1.84-6.1 initialized (using snow 0.4-4): parallel execution on 1 CPUs.

Error in checkForRemoteErrors(val) : one node produced an error: could not find function "rmultinom"

I played with some of this https://stackoverflow.com/questions/47197566/r-get-list-and-environment-of-all-variables-and-functions-within-a-given-functi code to try and get rmultinom onto the snowfall cluster, but didn't get anywhere.

Thanks,

— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/TED/issues/22, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHS62GQL2EKDEVG4JF2TVKPTHJANCNFSM5WF4GN2Q . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[kanefos]

Hi Tinyi. Thanks for such a quick reply, really appreciate it. I'm on macOS Catalina v 10.15.7.

I reinstalled the packaged, and am not encountering the previous error. However, now I encounter this error message upon running run.Ted().

snowfall 1.84-6.1 initialized (using snow 0.4-4): parallel execution on 1 CPUs.

Error in checkForRemoteErrors(val) : 
  one node produced an error: invalid second argument 'size'

I am not sure what snowfall does under the hood, but I have not installed any JavaScript or CSS materials on this machine, if this is relevant (no idea). Is there something I need to do to my CPU to make it friendly with snowfall?

Any ideas would be great, thank youKane

[tinyi]

Do you have negative values or NA values in your bulk input X?

[kanefos]

Aha yes NAs were the issue. My mistake should have looked. Thanks again for all the help, really appreciate it

[tinyi]

Hi Kane,

Thank you for your reply. In theory, the run.Ted function should be able to exclude genes with NA values. Do you mind sending me your bulk matrix or the exact value that causes the issue, so that I can troubleshoot to adjust the function that does the filtering to prevent similar issues?

Many thanks.

Best,

Tinyi

On Thu, May 19, 2022 at 10:21 AM Kane @.***> wrote:

Aha yes NAs were the issue. My mistake should have looked. Thanks again for all the help, really appreciate it

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[kanefos]

Hi Tinyi, sorry I should have edited my comment to say I was also using normalise expression (with negative values), but I simply checked for NAs first then replied. So error on my part understanding required input data. Thanks again for all the help, much appreciated

[tinyi]

Hi Kane,

I see. I will add an assertion for not allowing negative values then. Thank you for your feedback.

Best,

Tinyi

On Thu, May 19, 2022 at 1:24 PM Kane @.***> wrote:

Hi Tinyi, sorry I should have edited my comment to say I was also using normalise expression (with negative values), but I simply checked for NAs first then replied. So error on my part understanding required input data. Thanks again for all the help, much appreciated

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[Frank-Xuran]

My bulk input X donot have negative values or NA values.But, Still Error in checkForRemoteErrors(val) : 16 node produced an error: invalid second argument 'size'

[tinyi]

My bulk input X donot have negative values or NA values.But, Still Error in checkForRemoteErrors(val) : 16 node produced an error: invalid second argument 'size'

Hi Frank. Do you mind if sending me your bulk data in Rdata format. I shall be able to help troubleshoot.