[Bioc-devel] Regarding package nanotatoR

Bhattacharya, Surajit @bh@tt@ch2 @end|ng |rom ch||dren@n@t|on@|@org
Fri Aug 6 20:20:29 CEST 2021


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.


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

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Perhaps this helps explain things?

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

> 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 

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



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


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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