Re: [Bioc-devel] singleCellTK

2024-04-23 Thread Joshua Campbell via Bioc-devel 
Thank you, much appreciated!

On Tue, Apr 23, 2024 at 1:08 PM Kern, Lori 
wrote:

> I see it is now building and checking cleanly.  We will un-deprecate the
> package.
>
> 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 Kern,
> Lori via Bioc-devel 
> *Sent:* Monday, April 22, 2024 9:08 AM
> *To:* bioc-devel@r-project.org ; Joshua
> Campbell 
> *Subject:* Re: [Bioc-devel] singleCellTK
>
> Please try to push the change to fix the gvsa issue.  We generally will
> only un-deprecate when we see a clean build/check report for at least the
> linux platform especially since the package has been failing for an
> extended period of time (since early December).
>
>
>
> 
> From: Bioc-devel  on behalf of Joshua
> Campbell via Bioc-devel 
> Sent: Monday, April 22, 2024 8:34 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] singleCellTK
>
> Hello,
> The package singleCellTK
> <
> https://secure-web.cisco.com/1wq8O1kSgJOUZsgHipzl-RZLqngGu3sumYdSdeICLNbaEfv7UgjYXQCq-KjeIeo2IQebPljENPurqCjIR52uece6VGfVOR-pnD8SRKU7TLNkof3-XXl98Suki3qq41FV9qTh0qMkw36ptlfnb5pMgdYmdhLXFrHQSI33LXovrzEMqTSDVL5de0eChB4wYWt3WCM4pyThcGUs8dT_vTluBqZAKWBrVmF1MLLCDZLuFLNpqplrox9UptS5DvdVoeo95UpfzRtKyVgJ8srififHUpyiaeEPGT7RAB5OqGqMaZkIyLzR0ZB1BWnV73JDTOuGO/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FsingleCellTK%2F>
> is
> currently slated for depreciation in Bioc devel (3.19). We have been
> actively fixing the dependency issues, mainly the underlying changes in
> Seurat update. We are fixing one last issue to be compatible with an update
> in the GSVA package which should allow the linux and macos builds to pass
> (should be done in the next day). The remaining windows build failing is
> due to other BioC packages not currently passing, but this is outside of
> our control.
>
> We have also changed the maintainer as the previous maintainer left the
> lab.
>
> We were hoping that the depreciation tag could be removed. We will
> continue to address any other issues that pop up going forward
> in release/devel.
>
> Thanks,
> Josh
>
> --
> Joshua D. Campbell, Ph.D.
> Section of Computational Biomedicine
> BU Chobanian & Avedisian School of Medicine
> 72 East Concord Street, E604B | Boston, MA 02118
> Phone: (617) 358-7260 | Email: c...@bu.edu
>
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>
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-- 
Joshua D. Campbell, Ph.D.

Re: [Bioc-devel] singleCellTK

2024-04-23 Thread Kern, Lori via Bioc-devel 
I see it is now building and checking cleanly.  We will un-deprecate the 
package.


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 Kern, Lori via 
Bioc-devel 
Sent: Monday, April 22, 2024 9:08 AM
To: bioc-devel@r-project.org ; Joshua Campbell 

Subject: Re: [Bioc-devel] singleCellTK

Please try to push the change to fix the gvsa issue.  We generally will only 
un-deprecate when we see a clean build/check report for at least the linux 
platform especially since the package has been failing for an extended period 
of time (since early December).




From: Bioc-devel  on behalf of Joshua 
Campbell via Bioc-devel 
Sent: Monday, April 22, 2024 8:34 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] singleCellTK

Hello,
The package singleCellTK
<https://secure-web.cisco.com/1wq8O1kSgJOUZsgHipzl-RZLqngGu3sumYdSdeICLNbaEfv7UgjYXQCq-KjeIeo2IQebPljENPurqCjIR52uece6VGfVOR-pnD8SRKU7TLNkof3-XXl98Suki3qq41FV9qTh0qMkw36ptlfnb5pMgdYmdhLXFrHQSI33LXovrzEMqTSDVL5de0eChB4wYWt3WCM4pyThcGUs8dT_vTluBqZAKWBrVmF1MLLCDZLuFLNpqplrox9UptS5DvdVoeo95UpfzRtKyVgJ8srififHUpyiaeEPGT7RAB5OqGqMaZkIyLzR0ZB1BWnV73JDTOuGO/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FsingleCellTK%2F>
 is
currently slated for depreciation in Bioc devel (3.19). We have been
actively fixing the dependency issues, mainly the underlying changes in
Seurat update. We are fixing one last issue to be compatible with an update
in the GSVA package which should allow the linux and macos builds to pass
(should be done in the next day). The remaining windows build failing is
due to other BioC packages not currently passing, but this is outside of
our control.

We have also changed the maintainer as the previous maintainer left the lab.

We were hoping that the depreciation tag could be removed. We will
continue to address any other issues that pop up going forward
in release/devel.

Thanks,
Josh

--
Joshua D. Campbell, Ph.D.
Section of Computational Biomedicine
BU Chobanian & Avedisian School of Medicine
72 East Concord Street, E604B | Boston, MA 02118
Phone: (617) 358-7260 | Email: c...@bu.edu

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this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
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Re: [Bioc-devel] singleCellTK

2024-04-22 Thread Kern, Lori via Bioc-devel 
Please try to push the change to fix the gvsa issue.  We generally will only 
un-deprecate when we see a clean build/check report for at least the linux 
platform especially since the package has been failing for an extended period 
of time (since early December).




From: Bioc-devel  on behalf of Joshua 
Campbell via Bioc-devel 
Sent: Monday, April 22, 2024 8:34 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] singleCellTK

Hello,
The package singleCellTK
<https://secure-web.cisco.com/1wq8O1kSgJOUZsgHipzl-RZLqngGu3sumYdSdeICLNbaEfv7UgjYXQCq-KjeIeo2IQebPljENPurqCjIR52uece6VGfVOR-pnD8SRKU7TLNkof3-XXl98Suki3qq41FV9qTh0qMkw36ptlfnb5pMgdYmdhLXFrHQSI33LXovrzEMqTSDVL5de0eChB4wYWt3WCM4pyThcGUs8dT_vTluBqZAKWBrVmF1MLLCDZLuFLNpqplrox9UptS5DvdVoeo95UpfzRtKyVgJ8srififHUpyiaeEPGT7RAB5OqGqMaZkIyLzR0ZB1BWnV73JDTOuGO/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FsingleCellTK%2F>
 is
currently slated for depreciation in Bioc devel (3.19). We have been
actively fixing the dependency issues, mainly the underlying changes in
Seurat update. We are fixing one last issue to be compatible with an update
in the GSVA package which should allow the linux and macos builds to pass
(should be done in the next day). The remaining windows build failing is
due to other BioC packages not currently passing, but this is outside of
our control.

We have also changed the maintainer as the previous maintainer left the lab.

We were hoping that the depreciation tag could be removed. We will
continue to address any other issues that pop up going forward
in release/devel.

Thanks,
Josh

--
Joshua D. Campbell, Ph.D.
Section of Computational Biomedicine
BU Chobanian & Avedisian School of Medicine
72 East Concord Street, E604B | Boston, MA 02118
Phone: (617) 358-7260 | Email: c...@bu.edu

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this message in error, please notify the sender immediately by e-mail and 
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[Bioc-devel] singleCellTK

2024-04-22 Thread Joshua Campbell via Bioc-devel 
Hello,
The package singleCellTK
 is
currently slated for depreciation in Bioc devel (3.19). We have been
actively fixing the dependency issues, mainly the underlying changes in
Seurat update. We are fixing one last issue to be compatible with an update
in the GSVA package which should allow the linux and macos builds to pass
(should be done in the next day). The remaining windows build failing is
due to other BioC packages not currently passing, but this is outside of
our control.

We have also changed the maintainer as the previous maintainer left the lab.

We were hoping that the depreciation tag could be removed. We will
continue to address any other issues that pop up going forward
in release/devel.

Thanks,
Josh

-- 
Joshua D. Campbell, Ph.D.
Section of Computational Biomedicine
BU Chobanian & Avedisian School of Medicine
72 East Concord Street, E604B | Boston, MA 02118
Phone: (617) 358-7260 | Email: c...@bu.edu

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