[Bioc-devel] IgGeneUsage Bioconductor package

Simo Kitanovski @|mo@k|t@nov@k| @end|ng |rom un|-due@de
Tue Oct 20 18:44:17 CEST 2020


Thank you Nitesh!

Some explanation about the problem:

All three Bioconductor packages that depend on CRAN package 'rstan', such as IgGeneUsage (*),
genphen (*) and banocc have cryptic errors on Windows. Hence, this hints at improper
configuration of rstan.

Could someone who has access to the Windows server try to run rstan (e.g. simple examples
are provided here: https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#how-to-use-rstan).

If this returns errors, then we will know that the issues are related to the rstan configuration:
There are also special installation guidelines for rstan on Windows provided at:
https://github.com/stan-dev/rstan/wiki/Installing-RStan-from-source-on-Windows

Please let me know if I can help.

Best,
Simo

* maintained by myself


On 20.10.20 6:31 PM, Turaga, Nitesh wrote:
> Thanks Simo. Since this is a problem we are trying to figure out as a 
> community, I encourage you to cc bioc-devel on your emails.
>
> We are all in the same boat :)
>
> Nitesh
>
>> On Oct 20, 2020, at 12:30 PM, Simo Kitanovski 
>> <simo.kitanovski using uni-due.de <mailto:simo.kitanovski using uni-due.de>> wrote:
>>
>> Thank you!
>>
>> I am only aware of the following instructions: 
>> https://github.com/stan-dev/rstan/wiki/Installing-RStan-from-source-on-Windows
>>
>> Best,
>>
>> Simo
>>
>>
>> On 20.10.20 6:22 PM, Turaga, Nitesh wrote:
>>> 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>
>>>>> *Date:*Friday, October 9, 2020 at 7:09 PM
>>>>> *To:*"Turaga, Nitesh"<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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