[Bioc-devel] IgGeneUsage Bioconductor package

[Turaga, Nitesh]

Hi Simo,

I need more details about “rstan” and the configuration.

I’m trying to figure it out.

Nitesh

On Oct 20, 2020, at 12:20 PM, Simo Kitanovski <simo.kitanovski using uni-due.de<mailto:simo.kitanovski using uni-due.de>> wrote:


Dear Nitesh,

as mentioned in my previous email the error persists in devel.

Best,

Simo

On 13.10.20 4:58 PM, Turaga, Nitesh wrote:
Hi Simo,

Can you tell me how you configured rstan on your windows machine?

Either way, don’t worry about the release version on Windows, there seems to be a version which has propagated through. But the issue persists in devel, which you’ll need to fix.

The issue seems to be in

--- failed re-building 'IgUsageCaseStudies.Rmd'


In that windows machine it’s likely because it exceeds the number of cores availablehttps://github.com/snaketron/IgGeneUsage/blob/master/vignettes/IgUsageCaseStudies.Rmd#L227<https://secure-web.cisco.com/16nzh5XsG1ICN95000rvtRhEBdGFGmQe3m6sfr0t0oiipFiGIfBOdR-PR04cwWWJZKVoBleA3_MCwY2_0v5jhunj5yIQhdTBonlczxdnhs7tFuASIDqTNfGmwdjrgq3phbrsryzWq_v7wO0TlT0BiFfTf0MTEssb0NRKa8UnwlktkOmLhxUgtvFj8X3Lx_XFdtNqgz3fuMak5T3M3fu_-DdPADPJslb_njxjFvpWxVxzckwzpHsyJLKMkwAMmrcvuFokgCEPKLLS776ygsMAKWJc8aECoq2HHcJ39S9Bv6Fn9ItP4FAnNQb1WOGXMEy_oxRPNBr269xQnaEMkmfvoGQ/https%3A%2F%2Fgithub.com%2Fsnaketron%2FIgGeneUsage%2Fblob%2Fmaster%2Fvignettes%2FIgUsageCaseStudies.Rmd%23L227> . Try setting mcmc.cores = 1.

Best,

Nitesh

From: Simo Kitanovski <simo.kitanovski using uni-due.de><mailto:simo.kitanovski using uni-due.de>
Date: Friday, October 9, 2020 at 7:09 PM
To: "Turaga, Nitesh" <Nitesh.Turaga using RoswellPark.org><mailto:Nitesh.Turaga using RoswellPark.org>
Subject: Re: IgGeneUsage Bioconductor package


Dear Nitesh Turaga,



I did not hear back from you concerning IgGeneUsage and genphen and

their problem with the CRAN package rstan.



Given that I cannot solve the errors with my packages without reconfiguring

how rstan was installed on tokay2, I am stuck with the errors. Any suggestions?



Best,

Simo



On 06.10.20 2:33 AM, nitesh.turaga using roswellpark.org<mailto:nitesh.turaga using roswellpark.org> wrote:
IgGeneUsage Bioconductor Package Report

Nitesh Turaga1

1Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA

October 05, 2020
Package: IgGeneUsage
________________________________

Dear Simo Kitanovski,

I am contacting you concerning the IgGeneUsage package, on the release and devel branch of Bioconductor, for which you are listed as the maintainer.

The latest build/check report shows that your package is failing on one or more platforms. Please resolve the issues for your package’s continued inclusion in Bioconductor.

https://bioconductor.org/checkResults/release/bioc-LATEST/IgGeneUsage/<https://secure-web.cisco.com/1cWWSuKaXaMm3z3KPV0uvEgXX5KrrDc5F5EBaDgP7m7UQdi9GMiYNdp4TWyDwaIZDLMdDexBU00Man6r6F0uCZv6h5lPvljhg599tYojoJ8V59ePQDEbQfgk8MnKGgU7zDAaJcL03A0kfqyg53LcasowRRa3svhOPSF4HSz7OVYpR_h2E9YXCiRRcEPiKFtWAkO49joC1EYtzNYwj7PNZt6-6HOYDfvH2vHpVKe2YjdgMttdWB97juGLcc7FGZfo-ZvQoq92IohzJgU8jlpebMXB7prg5is4zycXW3bdrxZ2yGwvQqGPIQfXWRGQoXJCxDytnzSmer3-7MN-uDnY6fw/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FIgGeneUsage%2F>https://bioconductor.org/checkResults/devel/bioc-LATEST/IgGeneUsage/<https://secure-web.cisco.com/17rFifncearVbAJ9PKNWi1raZSOGuyxLunr6pqjFdiSpJu1nz9ZC2ektotS-uVE7rGQ5_Z8wqpcu4cNvE-xKiW5xB2Pk85nReNrVMf-YJmdgf_hNVOt-IgZtmunNkIGaxyYij9njKQqOv6oI3m0E3U-koNXZJDQtUc5LqHcSyUxq_ySmgMQuoB7gLOdwqD4pZBSCCtlQPaKZy5hLaiNGzFbLdsiyxxCugdUqIu1fYcCz28xBJAfumV1UswxPX5Gao_yOMdrEh3u5BT_FWAFOo4uMm_NFkyKzc08DLGhyhVWsAkr8-WLS3NGiulQntAOT1JK_bsRIssKS56lFafEL7zA/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FIgGeneUsage%2F>

Please let me know if you have any questions.

Regards,

Nitesh

________________________________

Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263

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