Question

DMRcate

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yr542 • 0

@yr542-17045

Last seen 7 months ago

United States

My goal: I am trying to use DMRcate to find some differentially methylated regions.

Issue Description: When I run the following code it does not give the expected result even when I try localHub = TRUE or localHub = FALSE it still gives and error:

My sessionInfo (only some of it below):

R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Attempt 1:

# Converting DMR list
results.ranges <- extractRanges(dmrcoutput, genome = "hg19")

The error is below:

Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead

Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use

snapshotDate(): 2023-01-30

Error: File not previously downloaded. Run with 'localHub=FALSE' Traceback:

extractRanges(dmrcoutput, genome = "hg19")

eh[["EH3132"]]

eh[["EH3132"]]

.local(x, i, j = j, ...)

stop("File not previously downloaded.\n", " Run with 'localHub=FALSE'", . call. = FALSE)

Attempt 2 (with localHub = TRUE):

# Converting DMR list
results.ranges <- extractRanges(dmrcoutput, genome = "hg19", localHub=TRUE)

It gives the error:

Error in extractRanges(dmrcoutput, genome = "hg19", localHub = TRUE): unused argument (localHub = TRUE) Traceback:

Attempt 3 (with localHub = FALSE):

# Converting DMR list
results.ranges <- extractRanges(dmrcoutput, genome = "hg19", localHub=FALSE)

It gives the error:

Error in extractRanges(dmrcoutput, genome = "hg19", localHub = FALSE): unused argument (localHub = FALSE) Traceback:

This seems to be associated with what I believe might be an issue with the DMRcate software itself. Is there a way around this?

DMRcate R DMRcatedata Markdown • 1.7k views

ADD COMMENT • link 14 months ago yr542 • 0

James W. MacDonald · Answer 1 · 2023-02-10

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 11 hours ago

United States

The error is coming from ExperimentHub, which is trying to download some data. Since there isn't an ellipsis argument ... to extractRanges, you won't be able to pass in the localHub argument anyway, but you could still use setExperimentHubOption with LOCAL = TRUE, although that won't help unless you have already downloaded the object.

If you can't connect to ExperimentHub, it may be due to a firewall, in which case you may be able to use a proxy connection. See ?setExperiementHubOption and talk to your IT person to see if there is a proxy URL that you can use to get through your firewall.

ADD COMMENT • link 14 months ago James W. MacDonald 65k

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Could you perchance give a sample of the code showing how to use this setExperimentHubOption as I cannot seem to find it online?

ADD REPLY • link 14 months ago yr542 • 0

1

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> library(ExperimentHub)
> ?setExperimentHubOption

ADD REPLY • link 14 months ago James W. MacDonald 65k

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I found the command description online (https://rdrr.io/bioc/ExperimentHub/man/getExperimentHubOption.html) I am not sure how to do this exactly it does seem to allow someone to specify a proxy however, the command seems to fail due to something I believe I am writing incorrectly?

Attempt 1:

library(ExperimentHub)
setExperimentHubOption(“PROXY”, "my_proxy_not_mentioned_here")

The error is below:

> Error in parse(text = x, srcfile = src): <text>:2:24: unexpected input
> 1: library(ExperimentHub) 
2: setExperimentHubOption(“
>                           ^ Traceback:

Attempt 2:

library(ExperimentHub)
setExperimentHubOption(PROXY, "my_proxy_not_mentioned_here")

The error is below:

> Error in stopifnot(is.character(arg), length(arg) == 1L): object
> 'PROXY' not found Traceback:
> 
> 1. setExperimentHubOption(PROXY, "my_proxy_not_mentioned_here")
> 2. stopifnot(is.character(arg), length(arg) == 1L)

I definitely use this proxy - why would it say the proxy is not found?

ADD REPLY • link updated 14 months ago by James W. MacDonald 65k • written 14 months ago by yr542 • 0

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Why are you searching online for help pages that you can get within R? There is no guarantee that the help you find online is current with the version of the package you are using. I pointed you to ?setExperimentHubOption for a reason, which is that it is guaranteed (unless the maintainer forgot to update or whatever) to be current with the package.

The error you see in your first iteration (Error in parse(text = x, srcfile = src): <text>:2:24: unexpected input) indicates you provided some input gibberish that R couldn't process. It's not clear from what you provided what that was, but if formatted correctly it should work. As an example (that won't work, btw, it's just an example)

> setExperimentHubOption("PROXY", "http://www.bioconductor.org")
> getExperimentHubOption("PROXY")
<request>
Options:
* proxy: http://www.bioconductor.org
* proxyauth: 1

Your second error is because the first argument is meant to be a character string, but you provided what R took to be an object (PROXY without quotations will be interpreted as an object). You could have a character object called PROXY that is simply "PROXY".

> PROXY
Error: object 'PROXY' not found
> PROXY <- "PROXY"
> setExperimentHubOption(PROXY, "http://www.bioconductor.org")
> getExperimentHubOption(PROXY)
<request>
Options:
* proxy: http://www.bioconductor.org
* proxyauth: 1

But there's hardly a point to that.

ADD REPLY • link 14 months ago James W. MacDonald 65k

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For some reason the ? command you gave did not work in R Markdown. What about the error with the rmSNPandCH command?

When I correct PROXY to be in single quotes I get an odd error. The proxy seems to work here but why is the rmSNPandCH command not working. I am not very good at programming and this is why I am still positing the next question. Why is this occurring?

Attempt 1:

library(ExperimentHub)
setExperimentHubOption('PROXY', "my_proxy_not_mentioned_here")

m.noSNPs <- rmSNPandCH(m, dist=2, mafcut=0.05)

Error:

Assuming valid proxy connection through 'my_proxy_not_mentioned_here' If you experience connection issues consider using 'localHub=TRUE'

Warning message: "Could not check database for updates. Database source currently unreachable. This should only be a temporary interruption. Using previously cached version." Error in value[3L]: failed to connect reason: error:1408F10B:SSL routines:ssl3_get_record:wrong version number Consider rerunning with 'localHub=TRUE' Traceback:

rmSNPandCH(m, dist = 2, mafcut = 0.05)

ExperimentHub()

.Hub("ExperimentHub", hub, cache, proxy, localHub, ask, ...)

tryCatch({ . db_date <- .restrictDateByVersion(db_path) . }, error = function(err) { . stop("failed to connect", "\n reason: ", conditionMessage(err), . "\n Consider rerunning with 'localHub=TRUE'") . })

tryCatchList(expr, classes, parentenv, handlers)

tryCatchOne(expr, names, parentenv, handlers[[1L]])

value[3L]

stop("failed to connect", "\n reason: ", conditionMessage(err), . "\n Consider rerunning with 'localHub=TRUE'")

localHub = TRUE and localHub = FALSE do not solve this issue. Why would this occur? The error seems to effect some code down stream as well?

ADD REPLY • link 14 months ago yr542 • 0