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List:       bioc-devel
Subject:    Re: [Bioc-devel] Regarding  package nanotatoR
From:       "Bhattacharya, Surajit via Bioc-devel" <bioc-devel () r-project ! org>
Date:       2021-08-06 18:20:29
Message-ID: DM6PR15MB2778584A51D436463E8146D290F39 () DM6PR15MB2778 ! namprd15 ! prod ! outlook ! com
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Hello, 

Thanks a lot for your help. I removed the example, and also added an additional check \
to not proceed if there is a failure to extract data from entrez_search function. It \
passes my local checks and travis check. I am facing issues to update the data to \
Bioconductor as I am having issues with ssh key. Due to changes in my current system, \
I had provided a new ssh key on the BiocCredentials \
(https://git.bioconductor.org/BiocCredentials), added the keys to my git page, and \
also have a config file created, but am still getting a permission error. Is it \
because I changed it yesterday and I should wait for some time, or am I doing some \
thing wrong?

Please guide me on this and let me know, if you need more information.

Thanks,
Surajit

-----Original Message-----
From: James W. MacDonald <jmacdon@uw.edu> 
Sent: Monday, August 2, 2021 1:34 PM
To: Bhattacharya, Surajit <sbhattach2@childrensnational.org>
Subject: [EXT] RE: Regarding package nanotatoR

ATTENTION: External Email! Do not click attachments/links unless sender is known.

----------------------------------------------------------------------
Perhaps this helps explain things?

> z <- entrez_search("gtr","muscle_weakness", retmax = 99999999)$id 
> any(z %in% keys(org.Hs.eg.db))
[1] FALSE

> zz <- entrez_summary("gene", z)
> table(do.call(c,sapply(extract_from_esummary(zz, "organism"), 
> function(x) x$scientificname)))

               Apis mellifera                    Bos taurus 
                           11                           118 
                  Danio rerio       Drosophila melanogaster 
                           96                             1 
                  Glycine max               Hordeum vulgare 
                            2                             2 
                 Mus musculus             Rattus norvegicus 
                           20                            13 
         Solanum lycopersicum Strongylocentrotus purpuratus 
                            4                            35 
            Triticum aestivum            Xenopus tropicalis 
                            3                             1 
                     Zea mays 
                            6

Apparently, muscle weakness no longer returns human IDs from GTR?

Best,

Jim



-----Original Message-----
From: Bioc-devel <bioc-devel-bounces@r-project.org> On Behalf Of Bhattacharya, \
                Surajit via Bioc-devel
Sent: Friday, July 30, 2021 3:48 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Regarding package nanotatoR

Hello,


I am the maintainer for the package nanotatoR. I have been facing an issue for a \
couple of weeks, where the package is failing in the build stage in all the platform, \
and throwing an error (attached error report for Linux platform). The error seems to \
show, that the package is failing at the vignette build stage and looking at the \
error "None of the keys entered are valid keys for 'ENTREZID'. Please use the keys \
method to see a listing of valid arguments.", it seems like a org.Hs.eg.db error. I \
am using that package to convert from entrez id to gene symbol. I was not able to \
replicate this error, either in my local system nor was I able to replicate it on \
Travis CI(attached). Is it an issue with the version being used?  Are other people \
using org.Hs.eg.db facing similar issue, and is there any workaround ?



Please let mknow, in case you have any further questions.
With Regards,
Surajit Bhattacharya
Research Postdoctoral Fellow
Eric Vilain Lab
Center for Genetic Medicine Research
Children's National Medical Center

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