User: Mike Smith

gravatar for Mike Smith
Mike Smith3.7k
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EMBL Heidelberg / de.NBI
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http://www.msmith.de/
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2 hours ago
Joined:
9 years, 3 months ago
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g********@gmail.com

Posts by Mike Smith

<prev • 567 results • page 1 of 57 • next >
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Comment: C: BiocManager v. 3.9 - where is it?
... Great explanation Martin, thanks. Perhaps a similar explanation should be included in the BiocVersion package itself, to provide a reference for similar questions in the future. Out of interest, does the `version` argument to `BiocManager::install()` affect the BiocVersion package? I'm wondering ...
written 20 hours ago by Mike Smith3.7k
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Answer: A: BiocManager v. 3.9 - where is it?
... I think you're getting confused between package versions and Bioconductor releases (which occur every 6 months and also have version numbers). All packages within a specific release are expected to work with each other and a specific version of R, but not this is not necessarily true between releas ...
written 1 day ago by Mike Smith3.7k
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Comment: C: The query to the BioMart webservice returned an invalid result: biomaRt expected
... How did you try changing the host? Using one of the mirror sites is usually my go-to solution for this. ...
written 2 days ago by Mike Smith3.7k
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Answer: A: Quiery to biomart returned an invalid result
... The `ensemblRedirect` argument has been deprecated and doesn't do anything anymore. If you're using the latest version of biomaRt there should have been a message printed saying this. To use one of the mirror sites you can do: ``` mart <- useEnsembl(biomart = "ensembl", dat ...
written 2 days ago by Mike Smith3.7k
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Answer: A: Cannot determine whether maintainer is subscribed to the bioc-devel mailing list
... Presumably this is when you are running BiocCheck on your own machine? You don't need to worry about that particular test when checking the package yourself. If you submit a package to Bioconductor the machine that automatically tests your package will have access to the subscription list and will ...
written 3 days ago by Mike Smith3.7k
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Answer: A: Error message: "Request to BioMart web service failed."
... It looks like that regular HTP traffic on port 80 isn't working for you for some reason. Since the second command works you can try those parameter when you setup the mart, something like: ``` mart <- useMart(host = "https://www.ensembl.org", biomart = "ensembl", ...
written 5 days ago by Mike Smith3.7k
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Comment: C: Error message: "Request to BioMart web service failed."
... Do either of these commands work for you? ``` httr::content(httr::GET("http://www.ensembl.org:80/biomart/martservice?type=registry")) httr::content(httr::GET("https://www.ensembl.org:443/biomart/martservice?type=registry")) ``` You should get back a character string that starts with `"\n\n ` ...
written 5 days ago by Mike Smith3.7k
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Comment: C: BiomaRt and phytozome
... I've taken a look at the code, and I think I've actually already removed the parts that relied on **RCurl**. Can you update your version of **biomaRt** to at least version 2.40.0? If I use that on Windows it works fine with Phytozome. ...
written 5 days ago by Mike Smith3.7k
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Comment: C: BiomaRt and phytozome
... Thanks for looking into this in such depth. It's interesting that **RCurl** for Windows ships with such an outdated version of SSL. I don't think there's anyway to force **RCurl** to use the correct version of the protocol without instaling libcurl yourself and building the package from source - t ...
written 6 days ago by Mike Smith3.7k
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Answer: A: Hello ! does anybody failed to convert id using getBM in biomaRt package?
... It might be that the main Ensembl site is being a bit slow today. You can try querying one of the mirror sites e.g. ``` mart <- useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", mirror = "asia") ``` Values for the mirror argument are: `u ...
written 6 days ago by Mike Smith3.7k

Latest awards to Mike Smith

Voter 5 months ago, voted more than 100 times.
Appreciated 5 months ago, created a post with more than 5 votes. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Scholar 5 months ago, created an answer that has been accepted. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Scholar 5 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 5 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: getBM error: The query to the BioMart webservice returned an invalid result
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Scholar 5 months ago, created an answer that has been accepted. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 6 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: getBM error: The query to the BioMart webservice returned an invalid result
Scholar 7 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 7 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
Scholar 9 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 10 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 13 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 13 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 24 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Scholar 24 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 24 months ago, created an answer that has been accepted. For A: BiomaRT URLs down? 404 Not Found
Scholar 24 months ago, created an answer that has been accepted. For A: R: error while reading .h5 files from R using rdhf5 package

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