[R-pkg-team] Bug#1058613: [External] Re: Source archive of DSS missing

Thu Jan 11 03:22:13 GMT 2024

Thanks. Just done that. Hopefully it’ll work this time.

Hao

From: "Shepherd, Lori" <Lori.Shepherd at RoswellPark.org>
Date: Wednesday, January 10, 2024 at 8:30 PM
To: "Wu, Hao" <hao.wu at emory.edu>, Andreas Tille <andreas at an3as.eu>, Harry Feng <hxf155 at case.edu>
Cc: "1058613 at bugs.debian.org" <1058613 at bugs.debian.org>, Debian R <debian-r at lists.debian.org>, Bioconductor Package Maintainer <maintainer at bioconductor.org>
Subject: Re: [External] Re: Source archive of DSS missing

Two points:
1.      You need a valid version bump for it to propagate on Bioconductor systems. so it devel you would need to push a bump to 1.51.1
2.       There are always two active branches in Bioconductor. devel and the current release found currently on branch RELEASE_3_18.  You would have to push to RELEASE_3_18 branch in order fo the change to be active in release. (with a valid version bump of 1.50.1)

Hope this helps!
Cheers,

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Wu, Hao <hao.wu at emory.edu>
Sent: Tuesday, January 9, 2024 5:29 PM
To: Kern, Lori <Lori.Shepherd at RoswellPark.org>; Andreas Tille <andreas at an3as.eu>; Hao Feng <hxf155 at case.edu>
Cc: 1058613 at bugs.debian.org <1058613 at bugs.debian.org>; Debian R <debian-r at lists.debian.org>; Bioconductor Package Maintainer <maintainer at bioconductor.org>
Subject: Re: [External] Re: Source archive of DSS missing

I thought I have fixed this. Just checked, at least from my end I have added edgeR to suggests, and have pushed the change. What else can I do?

@Lori, if the change is not there, could you please help me to make this change? DSS is pretty widely used and I certainly don’t want it to be deprecated. Thank you so much.

Regards,

Hao

From: "Shepherd, Lori" <Lori.Shepherd at RoswellPark.org>
Date: Tuesday, January 9, 2024 at 11:51 PM
To: Andreas Tille <andreas at an3as.eu>, "Wu, Hao" <hao.wu at emory.edu>, Harry Feng <hxf155 at case.edu>
Cc: "1058613 at bugs.debian.org" <1058613 at bugs.debian.org>, Debian R <debian-r at lists.debian.org>, Bioconductor Package Maintainer <maintainer at bioconductor.org>
Subject: [External] Re: Source archive of DSS missing

DSS is unavailable because it has yet to build this release.  The DSS maintainers have been notified multiple times but have yet to fix the package; DSS is currently at risk of deprecation if it is not fixed.

https://bioconductor.org/checkResults/release/bioc-LATEST/DSS/<https://secure-web.cisco.com/10v_7NJ8sPgXorW2rpTNuQ9cK8B04xcbNiWYaEpjmbsc71G0WySa4wDrOpxI0DHBSnGbKriM05uWWGln-Yr1FI79EQyZnT9klBdkr6DcuA2wt0-8mALjxcZ2jk2M5D27fqNvA3Y-oBp-qnzOEanGJxDCujwi9u6to15e3KOHYFVjaa7IsAkHnvI30UnDIeZkbvyEVmTqQstL6EDmo8BfZhKeJYWlpFZEo6mfyhpLp7Ptw4_VwLc2hGZTXjbFw4gYNMwVHym_goTU4xM8_JlK1PxmbbpwaOGWVLswtLQw_38GaUGLKUcgtpcpFlVF-xeTh/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FDSS%2F>

Per the build report the solution is very simple. DSS needs to add the needed dependency edgeR to the list of Suggests package in the DESCRIPTION and push a valid version bump.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________

From: Andreas Tille <andreas at an3as.eu>
Sent: Tuesday, January 9, 2024 10:32 AM
To: Hao Wu <hao.wu at emory.edu>; Hao Feng <hxf155 at case.edu>
Cc: 1058613 at bugs.debian.org <1058613 at bugs.debian.org>; Debian R <debian-r at lists.debian.org>; Bioconductor Package Maintainer <maintainer at bioconductor.org>
Subject: Re: Source archive of DSS missing

Hi again,

putting Bioconductor Package Maintainer in CC since I can not yet find
the source archive of DSS 2.50.0 neither at

   https://secure-web.cisco.com/1IXs1DXRx2Y9dsRzzvLX84yK4Ym9eNeMVhLE8Z1rSs1XEmkvc9TlBtwJTB7DOPYrI0g0KgeG9hBwAaYvDvLqRK1ebqhCu939zH8_Ck55gAkqlcowiWK7FEtyGnoy96fpqFd5u8Kq4cTsmPqXSGOGVe3Ee8qt1XYN4fraNRyxTAewqnC9SkVz0R1nQdaUPBhbBNAJo5E-R9em72gaphy1VOuwNul219-EPQug_O_SL0CFbt7Twf2Xgmt2U8Y0Zml2cIDGiSRYkPfiQxbJMohb-19idtd9WZ813UCm9Twqayf_KuxiqzTKEcPRDqbpKVcTT/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FDSS.html

We need the source code to update the Debian package.

Kind regards
   Andreas.

Am Tue, Dec 12, 2023 at 03:09:29PM +0100 schrieb Andreas Tille:
> Hi,
>
> could someone please have a look at the source download?
>
> Thank you
>    Andreas.
>
> Am Fri, Dec 08, 2023 at 04:04:27PM +0100 schrieb Andreas Tille:
> > Hi,
> >
> > when looking at
> >
> >     https://secure-web.cisco.com/1IXs1DXRx2Y9dsRzzvLX84yK4Ym9eNeMVhLE8Z1rSs1XEmkvc9TlBtwJTB7DOPYrI0g0KgeG9hBwAaYvDvLqRK1ebqhCu939zH8_Ck55gAkqlcowiWK7FEtyGnoy96fpqFd5u8Kq4cTsmPqXSGOGVe3Ee8qt1XYN4fraNRyxTAewqnC9SkVz0R1nQdaUPBhbBNAJo5E-R9em72gaphy1VOuwNul219-EPQug_O_SL0CFbt7Twf2Xgmt2U8Y0Zml2cIDGiSRYkPfiQxbJMohb-19idtd9WZ813UCm9Twqayf_KuxiqzTKEcPRDqbpKVcTT/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FDSS.html
> >
> > and following the link "Source Archive" at bottom of the page linking
> > to
> >     https://secure-web.cisco.com/15BklqjFB-NkLwrDhwI3-Chm5lIsfsZx3HGG4qR9PglFPGp8MDxMcMhd53rhclhE1eG5z0mpDqljZ8aI2luxCjYaJRC5FmDMfUoyjm_D_a1Y8WRQ3aLjtPntuNWsRSuvmnS-UMkwWWHSzG6ngdm5sMDHLC_xudenk0l3XKkHs8-NVh47VDo-25g67Oham6vEDGZhTAbePruF86hxZG2Gi_Gp8ozOtWHVxTIhkx0AbGXQUCcnK-VqaVSr0Hccm4ihUo-Nd4x3ZeSe7uwT0gJcnU-3IJPz4S7eH0bawwmQLxYdOuJPQUXaev51clpMOkXyT/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.18%2Fbioc%2Fsrc%2Fcontrib%2FArchive%2FDSS%2F
> >
> > I can only see
> >
> >    Page Not Found
> >    The page you were looking for was not found.
> >
> > I'm trying to upgrade the Debian package of DSS to its latest version
> > and would need the source tarball which can be usually downloaded from
> > the "Source Archive" link.
> >
> > Kind regards
> >     Andreas.
> >
> > --
> > http://secure-web.cisco.com/1Y3FjQ3OXq4yJhUvLN0ecxalWPMsbdxBN0HymctCBHh1bnToxtrtowlogQtON_22uKVOTc9pavLt0rb0ByGDyVDsoLkxqCPFWhTWCXlKWTD8TxQdHXMUmwZJPCRQNKU0ZsT-cpAnDDZSBxu5NvHH95o0sX0kLdbDho808f7jP7DV1pyCo6ja1UwB-M6ThjD4LsGhzd2Szqxr51cRJ_M159zxRh3o_7tYS7EegGzTkKSqFefWg2RNv2f31tfktcgx-gx6EoLZjJhl7lsZvPFlRt_8yNpODPX7iehx2QrdSs7ZKPNIbbHWE-iEtxeqpBnQV/http%3A%2F%2Ffam-tille.de
>
> --
> http://secure-web.cisco.com/1Y3FjQ3OXq4yJhUvLN0ecxalWPMsbdxBN0HymctCBHh1bnToxtrtowlogQtON_22uKVOTc9pavLt0rb0ByGDyVDsoLkxqCPFWhTWCXlKWTD8TxQdHXMUmwZJPCRQNKU0ZsT-cpAnDDZSBxu5NvHH95o0sX0kLdbDho808f7jP7DV1pyCo6ja1UwB-M6ThjD4LsGhzd2Szqxr51cRJ_M159zxRh3o_7tYS7EegGzTkKSqFefWg2RNv2f31tfktcgx-gx6EoLZjJhl7lsZvPFlRt_8yNpODPX7iehx2QrdSs7ZKPNIbbHWE-iEtxeqpBnQV/http%3A%2F%2Ffam-tille.de
>
>

--
http://secure-web.cisco.com/1Y3FjQ3OXq4yJhUvLN0ecxalWPMsbdxBN0HymctCBHh1bnToxtrtowlogQtON_22uKVOTc9pavLt0rb0ByGDyVDsoLkxqCPFWhTWCXlKWTD8TxQdHXMUmwZJPCRQNKU0ZsT-cpAnDDZSBxu5NvHH95o0sX0kLdbDho808f7jP7DV1pyCo6ja1UwB-M6ThjD4LsGhzd2Szqxr51cRJ_M159zxRh3o_7tYS7EegGzTkKSqFefWg2RNv2f31tfktcgx-gx6EoLZjJhl7lsZvPFlRt_8yNpODPX7iehx2QrdSs7ZKPNIbbHWE-iEtxeqpBnQV/http%3A%2F%2Ffam-tille.de

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