[Bioc-devel] Final List of Deprecated Packages for Bioc3.10

Thanks Nitesh.

I ported the fix and the package builds fine - besides the deprecation warning:

http://bioconductor.org/checkResults/devel/bioc-LATEST/PathNet

Best,
Ludwig
Hi Ludwig,

Thank you for volunteering to take over as maintainer for PathNet and PathNetData.

You should now have access to both packages as the maintainer. They should show up on the build machine tomorrow.

You should port your fix(s) to the build machine for the PathNet package when you can and see if it is fixed on the devel builder.

Best regards,

 Nitesh

> On Dec 4, 2019, at 1:54 PM, Shepherd, Lori <Lori.Shepherd at RoswellPark.org> wrote:
>
> We will start the process and be in touch off the bioc mailing list.
>
> We would require you officially take over as maintainer as all bioconductor packages require an active maintainer.  PathNet was failing and we reached out (several times) and deemed the package orphaned as we never heard back from the currently listed maintainer.
>
> Cheers,
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>
> Sent: Wednesday, December 4, 2019 1:32 PM
> To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; bioc-devel at r-project.org <bioc-devel at r-project.org>
> Subject: Re: Final List of Deprecated Packages for Bioc3.10
>
>
> Yes, I could do that if needed.
>
> ________________________________
> From: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
> Sent: Wednesday, December 4, 2019 1:28 PM
> To: Ludwig Geistlinger; bioc-devel at r-project.org
> Subject: Re: Final List of Deprecated Packages for Bioc3.10
>
> ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.***
>
> Are you volunteering to permanently take over as maintainer of this package?
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>
> Sent: Wednesday, December 4, 2019 1:22 PM
> To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; bioc-devel at r-project.org <bioc-devel at r-project.org>
> Subject: Re: Final List of Deprecated Packages for Bioc3.10
>
> Hi Lori,
>
> Is it possible to undeprecate the "PathNet" package?
> I just checked, the problem is a failing unit test, causing the otherwise well working package to fail R CMD check.
>
> I fixed this here on a local clone of https://git.bioconductor.org/packages/PathNet<https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bioconductor.org_packages_PathNet&d=DwMFAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE&m=hXVVPnvQ8N1q2LgQkQOS5W7zBluTCo4kY2Gmj4i4RXY&s=q1rBhXn6bs7NDTSKvbP9xKPMjQ4tUSuSwBvC-YYzWSI&e=> and could push these minor changes if granted access.
>
> The PathNet package implements a solid network-based enrichment method and the corresponding paper has some 50 citations - it would thus be unfortunate to see it gone.
>
> Thanks,
> Ludwig
>
>
> ________________________________________
> From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
> Sent: Monday, October 7, 2019 9:41 AM
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10
>
> The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly.
>
> The final list for the 3.10 release is as follows:
>
> Maintainer requested deprecation:
>
> Software:
>
> SNPchip
> GenomeGraphs
> HTSanalyzeR
> Rchemcpp
> charm
> Pbase
>
>
> Experiment Data Package:
>
> charmData
>
>
>
> Unresponsive/not-maintained packages:
>
> Software:
>
> dSimer
> flipflop
> exomePeak
> CNPBayes
> brainImageR
> plateCore
> rHVDM
> SEPA
> condcomp
> PathNet
> scone
> birte
> mlm4omics
> RnaSeqSampleSize
>
>
> Experiment Data Package:
>
> facopy.annot
> allenpvc
>
>
> Renaming The package CAMTHC is marked for deprecation. This package has been renamed to debCAM
>
>
>
> The following Annotation Packages have been user requested deprecated:
>
> MafDb.gnomADex.r2.0.1.GRCh38
> MafDb.gnomAD.r2.0.1.GRCh38
> MafDb.gnomADex.r2.0.1.hs37d5
> MafDb.gnomAD.r2.0.1.hs37d5
> They are replaced with
>
> MafDb.gnomADex.r2.1.GRCh38
> MafDb.gnomAD.r2.1.GRCh38
> MafDb.gnomADex.r2.1.hs37d5
> MafDb.gnomAD.r2.1.hs37d5
>
>
> The Bioconductor team will continue to send emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion. Packages that are ERRORing and not fixed before the October 30th 3.10 release will immediately be marked as deprecated in devel 3.11.
>
> Thank you
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department 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), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE&m=hXVVPnvQ8N1q2LgQkQOS5W7zBluTCo4kY2Gmj4i4RXY&s=npv0ZxWtaD0vGTxwpMw-hYI6BMzlx-YhCp1dtAugg6U&e=>
>
> 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), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
>
>
> 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), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
>       [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
I'll take care of the undeprecation.   Thank you for taking this responsibility on.

Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Thanks Nitesh.

I ported the fix and the package builds fine - besides the deprecation warning:

http://bioconductor.org/checkResults/devel/bioc-LATEST/PathNet

Best,
Ludwig

________________________________________
From: Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org>
Sent: Thursday, December 19, 2019 2:12 PM
To: Shepherd, Lori
Cc: Ludwig Geistlinger; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

Hi Ludwig,

Thank you for volunteering to take over as maintainer for PathNet and PathNetData.

You should now have access to both packages as the maintainer. They should show up on the build machine tomorrow.

You should port your fix(s) to the build machine for the PathNet package when you can and see if it is fixed on the devel builder.

Best regards,

 Nitesh

> On Dec 4, 2019, at 1:54 PM, Shepherd, Lori <Lori.Shepherd at RoswellPark.org> wrote:
>
> We will start the process and be in touch off the bioc mailing list.
>
> We would require you officially take over as maintainer as all bioconductor packages require an active maintainer.  PathNet was failing and we reached out (several times) and deemed the package orphaned as we never heard back from the currently listed maintainer.
>
> Cheers,
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>
> Sent: Wednesday, December 4, 2019 1:32 PM
> To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; bioc-devel at r-project.org <bioc-devel at r-project.org>
> Subject: Re: Final List of Deprecated Packages for Bioc3.10
>
>
> Yes, I could do that if needed.
>
> ________________________________
> From: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
> Sent: Wednesday, December 4, 2019 1:28 PM
> To: Ludwig Geistlinger; bioc-devel at r-project.org
> Subject: Re: Final List of Deprecated Packages for Bioc3.10
>
> ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.***
>
> Are you volunteering to permanently take over as maintainer of this package?
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>
> Sent: Wednesday, December 4, 2019 1:22 PM
> To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; bioc-devel at r-project.org <bioc-devel at r-project.org>
> Subject: Re: Final List of Deprecated Packages for Bioc3.10
>
> Hi Lori,
>
> Is it possible to undeprecate the "PathNet" package?
> I just checked, the problem is a failing unit test, causing the otherwise well working package to fail R CMD check.
>
> I fixed this here on a local clone of https://git.bioconductor.org/packages/PathNet<https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bioconductor.org_packages_PathNet&d=DwMFAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE&m=hXVVPnvQ8N1q2LgQkQOS5W7zBluTCo4kY2Gmj4i4RXY&s=q1rBhXn6bs7NDTSKvbP9xKPMjQ4tUSuSwBvC-YYzWSI&e=> and could push these minor changes if granted access.
>
> The PathNet package implements a solid network-based enrichment method and the corresponding paper has some 50 citations - it would thus be unfortunate to see it gone.
>
> Thanks,
> Ludwig
>
>
> ________________________________________
> From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
> Sent: Monday, October 7, 2019 9:41 AM
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10
>
> The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly.
>
> The final list for the 3.10 release is as follows:
>
> Maintainer requested deprecation:
>
> Software:
>
> SNPchip
> GenomeGraphs
> HTSanalyzeR
> Rchemcpp
> charm
> Pbase
>
>
> Experiment Data Package:
>
> charmData
>
>
>
> Unresponsive/not-maintained packages:
>
> Software:
>
> dSimer
> flipflop
> exomePeak
> CNPBayes
> brainImageR
> plateCore
> rHVDM
> SEPA
> condcomp
> PathNet
> scone
> birte
> mlm4omics
> RnaSeqSampleSize
>
>
> Experiment Data Package:
>
> facopy.annot
> allenpvc
>
>
> Renaming The package CAMTHC is marked for deprecation. This package has been renamed to debCAM
>
>
>
> The following Annotation Packages have been user requested deprecated:
>
> MafDb.gnomADex.r2.0.1.GRCh38
> MafDb.gnomAD.r2.0.1.GRCh38
> MafDb.gnomADex.r2.0.1.hs37d5
> MafDb.gnomAD.r2.0.1.hs37d5
> They are replaced with
>
> MafDb.gnomADex.r2.1.GRCh38
> MafDb.gnomAD.r2.1.GRCh38
> MafDb.gnomADex.r2.1.hs37d5
> MafDb.gnomAD.r2.1.hs37d5
>
>
> The Bioconductor team will continue to send emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion. Packages that are ERRORing and not fixed before the October 30th 3.10 release will immediately be marked as deprecated in devel 3.11.
>
> Thank you
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department 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), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=OdfcI7SrMMnS3DAUJULIgzR9ZFOeXSyzUMNqMKXj4yE&m=hXVVPnvQ8N1q2LgQkQOS5W7zBluTCo4kY2Gmj4i4RXY&s=npv0ZxWtaD0vGTxwpMw-hYI6BMzlx-YhCp1dtAugg6U&e=>
>
> 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), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
>
>
> 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), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
>       [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.