Re: Please vendor version tarball for destiny on bioconductor page

I spent some time with the destiny package this morning. It is the first package I've come across that composes

vignettes as jupyter notebooks. This is interesting and it is nice that R can support this. To make progress, I found that I

needed to enhance my latex/font setup with tinytex::tlmgr_install for these packages

Tue Sep 14 06:37:07 2021] install: tcolorbox
[Tue Sep 14 06:41:49 2021] install: oberdiek
[Tue Sep 14 06:43:02 2021] install: eurosym
[Tue Sep 14 06:45:09 2021] install: ucs
[Tue Sep 14 06:46:24 2021] install: adjustbox
[Tue Sep 14 06:52:54 2021] install: collectbox
[Tue Sep 14 06:57:37 2021] install: ulem
[Tue Sep 14 07:01:51 2021] install: jknapltx
[Tue Sep 14 07:49:25 2021] install: rsfs

After this, I still ran into

--- re-building ‘Global-Sigma.ipynbmeta’ using nbconvert
Error: processing vignette 'Global-Sigma.ipynbmeta' failed with diagnostics:
Running 'texi2dvi' on 'Global-Sigma.tex' failed.
LaTeX errors:
! Package inputenc Error: Unicode character σ (U+03C3)
(inputenc) not set up for use with LaTeX.

which seems solvable but I am out of time.

It is mainly up to the destiny developer/maintainer to solve these problems, and as Lori Kern noted

the package is currently slated for removal.

If you are willing to work with the source to get it to build for your use, you can clone the source

from git (not github) at https://git.bioconductor.org/packages/destiny, until it is removed.

On Tue, Sep 14, 2021 at 7:28 AM Kern, Lori <Lori.Shepherd@roswellpark.org> wrote:

Destiny is currently marked as deprecated and scheduled to be removed in the next Bioconductor release as the maintainers were unresponsive to our requests to fix their package. The package is failing in both release and devel version of Bioconductor and we tried numerous times to reach the maintainer. If you know the maintainer we encourage you to reach out to them to fix the package.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Andreas Tille <andreas@an3as.eu>
Sent: Tuesday, September 14, 2021 2:52 AM
To: Debian R <debian-r@lists.debian.org>; Bioconductor Package Maintainer <maintainer@bioconductor.org>
Cc: Philipp A <flying-sheep@web.de>
Subject: Re: Please vendor version tarball for destiny on bioconductor page

Hi Bioconductor Package Maintainers,

I just want to bring this issue to your attention. May be the
maintainer of destiny is on vacation. It would be great if this could
be solved quickly since it might also affect other consumers of
this Bioconductor source package.

Kind regards

     Andreas.

On Sat, Sep 11, 2021 at 09:46:33PM +0530, Nilesh Patra wrote:
> Hi Phil,
>
> Thanks for your work on the destiny software.
> I was trying to update the package to latest release 3.6.0 in Debian for bioconductor 3.13 transition,
> but the bioconductor page[1]
> does not vendor the corresponding .tar.gz
>
> and I cannot find that version tagged in the github repo either[2]
> It'd be great if you could fix the corresponding bioconductor.org page to vendor .tar.gz
>
> [1]:https://bioconductor.org/packages/release/bioc/html/destiny.html
> [2]: https://secure-web.cisco.com/1b8BeOzjsmvAB0eJ5F0vfrct2Krwh_fgkjn4S4HDwHeVnUZq-7KpCdowDMicdEjSriRn0GRAwZKHa_tT7tbrY_HR7AEcQ8dpSoRX2kVai53eufXfbh6EetkRvUlYWcHeNbnj-PyC8Cd8L0ZXuzJpMbMO0SbmAO8xBv_-jPiJUgPtYqo9bcUFXwT1OL5yrDjQ8O-ROj5Frb_1G_UKQijmZ3nedTc_uAd8U-rKpWIUe7ddi5b8wbRxtXEw_sACM2oPZb__CECo1xusuv3ItNRpxqG5-qU9KVEi9OxTWRbsrd_oSDUCdEP7oPLLL-aWV51pq/https%3A%2F%2Fgithub.com%2Ftheislab%2Fdestiny%2Ftags
>
> Cheers,
>
> --
> Nilesh Patra
>
> Debian Developer, Uploading
>   ⢀⣴⠾⠻⢶⣦⠀
>   ⣾⠁⢠⠒⠀⣿⡁
>   ⢿⡄⠘⠷⠚⠋   nilesh@debian.org / nileshpatra.info
>   ⠈⠳⣄
>

--
http://secure-web.cisco.com/1C529ZmJ7RNksoUOQtP9EiVELV8_MC48-fgkrqWwWd5sPnVALduRAYkoF26RJngMlYE9Jb9p6n6x9K7x3HH2_jO9EiMACAH5Z08lovxCHXrcSoKyV8dDJ27oN09kVfMLZVNMuVGIxdzkdpB8_LydhAqyeqnP5tX3jBSUZZg1osDfQRkS1DaBeuDTsTOQo55T716bXuDGj10JKxl6m9kFKZsNVvJ0QwvH_c0yI1YJEEoG3SJk2Dtow4-J-F-jSQzVUwcP-JmRfaAkAws5_uD82yd9pSQ1heAnZ8AbIVXihRJaBtLvK2sy_E-LJlWerOl9D/http%3A%2F%2Ffam-tille.de

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