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 <jmac...@uw.edu>
Sent: Monday, August 2, 2021 1:34 PM
To: Bhattacharya, Surajit <sbhatta...@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-boun...@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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