[Bioc-devel] Can we still patch a broken package in 3_11

[Christian Mertes]

Dear Bioc team,

I'm very sorry to ask you this, since it is release time and you fixed
already the 3_11 branch.

But during the last 3 days, Nature decided to change their URLs and
hence it broke our OUTRIDER package and the last build of 3_11.

http://bioconductor.org/checkResults/release/bioc-LATEST/OUTRIDER/

Would it be still possible to patch it to make it work again? I can
understand if the branch 3_11 is fixed and you do not want to touch it
again.

I attached the patch if you decide to change it. 

Best,
Christian


-- 
Christian Mertes | PhD Student / Lab Administrator

Gagneur Lab | Computation Molecular Medicine
I29 - Department of Informatics
Technical University of Munich
Boltzmannstr. 3, 85748, Garching, Germany

mer...@in.tum.de | https://in.tum.de/gagneurlab/



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Re: [Bioc-devel] IgGeneUsage Bioconductor package

[Simo Kitanovski]

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 
>> mailto:simo.kitanov...@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 
 mailto:simo.kitanov...@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
>  
> .
>  
> Try setting mcmc.cores = 1.
> Best,
> Nitesh
> *From:*Simo Kitanovski
> *Date:*Friday, October 9, 2020 at 7:09 PM
> *To:*"Turaga, Nitesh"
> *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.tur...@roswellpark.orgwrote:
>
>
>   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://bioconductor.org/checkResults/devel/bioc-LATEST/IgGeneUsage/

Re: [Bioc-devel] IgGeneUsage Bioconductor package

[Turaga, Nitesh]

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 
mailto:simo.kitanov...@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 
mailto:simo.kitanov...@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
 . Try setting mcmc.cores = 1.

Best,

Nitesh

From: Simo Kitanovski 

Date: Friday, October 9, 2020 at 7:09 PM
To: "Turaga, Nitesh" 

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.tur...@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://bioconductor.org/checkResults/devel/bioc-LATEST/IgGeneUsage/

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

This email message may contain legally privileged and/or confidential 
information. If you are not the intended recipient(s), or the employee or agent 
responsible for the delivery of this message to the intended recipient(s), 

Re: [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 
mailto:simo.kitanov...@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
 . Try setting mcmc.cores = 1.

Best,

Nitesh

From: Simo Kitanovski 

Date: Friday, October 9, 2020 at 7:09 PM
To: "Turaga, Nitesh" 

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.tur...@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://bioconductor.org/checkResults/devel/bioc-LATEST/IgGeneUsage/

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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[Bioc-devel] Access denied to lpNet package

[Prof.Dr. Lars Kaderali]

Dear Bioconductor team,

I changed institution and my old email address @tu-dresden.de no longer 
exists. The packages RNAither and RCASPAR are properly associated with my new 
email address, however, I apparently failed to do the same for the lpNet 
package.

As I no longer have access to the TU dresden email (in fact, the address 
exists no more), I cannot get write acces to the lpNet repository and cannot 
update the package.

Can you help and associate the package with my git account under the new Email 
address @uni-greifswald.de ?

Thanks
Lars

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Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

[Mike Smith]

Thanks for the self contained example Gordon.  Just to add to the
confusion, I'm unable to replicate this on my Windows machine.  Both the
toy example and running R CMD check on limma or Biobase fail to produce the
NOTE.

I've tried within RStudio, RGui and at the command line.

The only differences I can see in our systems are the locale and a 1 digit
change in the Windows build.

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C

[5] LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] devtools_2.3.2 usethis_1.6.3

loaded via a namespace (and not attached):
 [1] rstudioapi_0.11   magrittr_1.5  rcmdcheck_1.3.3   pkgload_1.1.0
  R6_2.4.1
 [6] rlang_0.4.8   fansi_0.4.1   tools_4.0.3   pkgbuild_1.1.0
 xopen_1.0.0
[11] sessioninfo_1.1.1 cli_2.1.0 withr_2.3.0   ellipsis_0.3.1
 remotes_2.2.0
[16] assertthat_0.2.1  digest_0.6.25 rprojroot_1.3-2   crayon_1.3.4
 processx_3.4.4
[21] callr_3.5.1   fs_1.5.0  ps_1.4.0  testthat_2.3.2
 memoise_1.1.0
[26] glue_1.4.2compiler_4.0.3desc_1.2.0backports_1.1.10
 prettyunits_1.1.1

On Mon, 19 Oct 2020 at 23:03, Gordon K Smyth  wrote:

> Sorry, there was mistype in previous email. Here is the reproducible
> example again. This code produces the NOTE when run in a fresh R 4.0.3 for
> Windows session:
>
>   library(Rcpp)
>   Rcpp.package.skeleton("TestPack", example_code = TRUE)
>   library(devtools)
>   check("TestPack")
>
>
> > -Original Message-
> > From: Gordon K Smyth
> > Sent: Tuesday, 20 October 2020 7:58 AM
> > To: Martin Morgan ; bioc-devel@r-project.org
> > Subject: RE: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'
> >
> > If you're interested, here is a small reproducible example. This example
> uses
> > Rcpp, but I think that any src code will give the same NOTE:
> >
> >   library(Rcpp)
> >   Rcpp.package.skeleton("TestPack", example_code = TRUE)
> >   library(devtools)
> >   install.package("devtools")
> >   check("TestPack")
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