Re: [Bioc-devel] TCGAbiolinks fails

2023-05-06 Thread Tiago Chedraoui Silva 
Hello,

Sorry for the late reply, I will fix the package this week.
I will also need to do a major change in the code since GDC legacy will be
shut down in the next months.

Best regards,
Tiago Chedraoui Silva


On Fri, Apr 28, 2023 at 10:04 AM Dario Strbenac via Bioc-devel <
bioc-devel@r-project.org> wrote:

> Good day,
>
> The package has checking errors which the developers of it need to fix
> themselves.
>
> Quitting from lines 114-121 (subtypes.Rmd)
> Error: processing vignette 'subtypes.Rmd' failed with diagnostics:
> object 'lgg.gbm.subtype' not found
>
> The installation error simply indicates that the package has never built
> successfully in Bioconductor 3.17.
>
> --
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> ___
> Bioc-devel@r-project.org mailing list
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>

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Re: [Bioc-devel] TCGAbiolinks fails

2023-04-28 Thread Dario Strbenac via Bioc-devel 
Good day,

The package has checking errors which the developers of it need to fix 
themselves.

Quitting from lines 114-121 (subtypes.Rmd) 
Error: processing vignette 'subtypes.Rmd' failed with diagnostics:
object 'lgg.gbm.subtype' not found

The installation error simply indicates that the package has never built 
successfully in Bioconductor 3.17.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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Re: [Bioc-devel] TCGAbiolinks fails

2023-04-28 Thread Vincent Carey 
The problem is that it is in an error state

--- re-building ‘subtypes.Rmd’ using rmarkdown
Quitting from lines 114-121 (subtypes.Rmd)
Error: processing vignette 'subtypes.Rmd' failed with diagnostics:
object 'lgg.gbm.subtype' not found
--- failed re-building ‘subtypes.Rmd’

so the standard installation approach isn't working now.


https://github.com/BioinformaticsFMRP/TCGAbiolinks -- file an issue


In an emergency you might succeed with

BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")




On Fri, Apr 28, 2023 at 9:07 AM Elizabeth Cattaneo <
elizabethcatta...@gmail.com> wrote:

> Hello!
> I was trying to use TCGAbiolinks as usual in a R-Colab notebook but I got
> this error:
>
> Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
> Installing package(s) 'TCGAbiolinks' Warning message: *“package
> ‘TCGAbiolinks’ is not available for *
> *Bioconductor version '3.17'*
>
> What should I do to fix it?
>
> Thanks!
>
> Elizabeth
>
> --
> Bioq. Elizabeth Cattaneo
> Dra Fac. Cs. Exactas, UNLP
> INIBIOLP, Fac. Cs.Médicas, UNLP
> calle 60 y 120 S/N, 1900 La Plata
> Argentina
> Tel. +54 221 4824894
> www.inibiolp.org.ar
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] TCGAbiolinks fails

2023-04-28 Thread Kern, Lori 
We just did our release this week and its possible you caught it while it was 
still running and repopulating. Could you try again and if the problem persists 
please share your sessionInfo()?


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Elizabeth 
Cattaneo 
Sent: Thursday, April 27, 2023 1:25 PM
To: bioc-devel@r-project.org ; 
bioc-devel-requ...@r-project.org 
Subject: [Bioc-devel] TCGAbiolinks fails

Hello!
I was trying to use TCGAbiolinks as usual in a R-Colab notebook but I got
this error:

Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Installing package(s) 'TCGAbiolinks' Warning message: *�package
�TCGAbiolinks� is not available for *
*Bioconductor version '3.17'*

What should I do to fix it?

Thanks!

Elizabeth

--
Bioq. Elizabeth Cattaneo
Dra Fac. Cs. Exactas, UNLP
INIBIOLP, Fac. Cs.M�dicas, UNLP
calle 60 y 120 S/N, 1900 La Plata
Argentina
Tel. +54 221 4824894
<http://secure-web.cisco.com/1m4zKZgGjbumHtMsOTJvLXdnZJxcMtkynUpXhFJ2bWSSohXEOABoui_7MnItDigj9PgmLm0O5LLpDakQAGP5eClAsd4IWzA4EScuC25AgDFF11lqb5lcelrNxXgRJ3hWNELzd74r8f-Sl93eZBPnGN5_QAKU6UkSidxoi3bjEQ6YfrfS2jKnrb_nadaeqlu0IicZ3N24WD33ySeAnRLITSP0KCSRKuZTkd66OwS4VlldIsDpNwsEvfekDhNGKwZc0UYF4G0GQ4LWlvlx14O9yENdBawA2QvXEJyohpTFf8V8w-gBl8Y0zw9X7CurW1t5n/http%3A%2F%2Fwww.inibiolp.org.ar%2F>http://secure-web.cisco.com/1rxyrgnxooM7vnnS_wUX7QPudQKn1lDsS7tCbli34JYlvRUuXHi9yKwchL-JMGjg58EvcSBtboaQLQxEzBHzF1DM0k4p7gus0oI_ZF-vodHoRLuWoO2yTZoIrwhzOAtpyz0sr7ej769MWuuAj-LInsPdyJwIox-fDIhWbw3rXIIgfyFQLbL5irsx12gXWmoy-A27-4DRe1jUlg21MYmEbCmAkkdvKedvBRszsIrv3BblQ2eznCCgEyaTm2OkoDZyafqqekiT6gV0RB2HaPJTekEuXQNYjN2c5T1tuGKF3lKr21C2uDjeje22T-RdPsbXV/http%3A%2F%2Fwww.inibiolp.org.ar

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[Bioc-devel] TCGAbiolinks fails

2023-04-28 Thread Elizabeth Cattaneo 
Hello!
I was trying to use TCGAbiolinks as usual in a R-Colab notebook but I got
this error:

Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Installing package(s) 'TCGAbiolinks' Warning message: *“package
‘TCGAbiolinks’ is not available for *
*Bioconductor version '3.17'*

What should I do to fix it?

Thanks!

Elizabeth

-- 
Bioq. Elizabeth Cattaneo
Dra Fac. Cs. Exactas, UNLP
INIBIOLP, Fac. Cs.Médicas, UNLP
calle 60 y 120 S/N, 1900 La Plata
Argentina
Tel. +54 221 4824894
www.inibiolp.org.ar

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