[Bioc-devel] Bioconductor 3.5 release: NEWS files

[Obenchain, Valerie]

Hi all,

One last plug to update your NEWS files. We branch on Monday so please
commit changes before then.

Valerie



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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Bioconductor 3.5 release: April 7 deadlines

[Valerie Obenchain]

Yes, that's what the API freeze means. The goal is to prevent last 
minute changes in chimeraviz from breaking downstream packages that 
depend on chimeraviz. By the way, the API freeze was Friday, April 7.


Valerie


On 04/21/2017 03:21 AM, Stian Lågstad wrote:
I've added a new function to my package chimeraviz (so far it's in a 
separate branch and not commited to Bioconductor). Does the API freeze 
mean that I have to wait until the Bioconductor release before I 
commit it to the devel branch?


On Fri, Apr 7, 2017 at 2:38 AM, Valerie Obenchain > wrote:


Hi,

Some recent activity has caused some (red) ripples across the
builds and the El Capitan Mac builds are still unsettled. To
accommodate, we're extending the deadline to pass R CMD build and
check with no errors to next Friday
(http://www.bioconductor.org/developers/release-schedule/
).
Thanks to everyone for cleaning up their packages and
communicating problems (and solutions!) on the lists.

Key deadlines for April 7 are

- No new packages added to the 3.5 roster

- No more API changes

- Current release 3.4 builds will stop

- Annotation packages (both internal and contributed) posted to
the 3.5 repo

Valerie

___
Bioc-devel@r-project.org  mailing
list
https://stat.ethz.ch/mailman/listinfo/bioc-devel





--
Stian Lågstad
+47 41 80 80 25


___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Bioconductor 3.5 release: April 7 deadlines

[Stian Lågstad]

I've added a new function to my package chimeraviz (so far it's in a
separate branch and not commited to Bioconductor). Does the API freeze mean
that I have to wait until the Bioconductor release before I commit it to
the devel branch?

On Fri, Apr 7, 2017 at 2:38 AM, Valerie Obenchain 
wrote:

> Hi,
>
> Some recent activity has caused some (red) ripples across the builds and
> the El Capitan Mac builds are still unsettled. To accommodate, we're
> extending the deadline to pass R CMD build and check with no errors to next
> Friday (http://www.bioconductor.org/developers/release-schedule/). Thanks
> to everyone for cleaning up their packages and communicating problems (and
> solutions!) on the lists.
>
> Key deadlines for April 7 are
>
> - No new packages added to the 3.5 roster
>
> - No more API changes
>
> - Current release 3.4 builds will stop
>
> - Annotation packages (both internal and contributed) posted to the 3.5
> repo
>
> Valerie
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Stian Lågstad
+47 41 80 80 25

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Bioconductor 3.5 release: potential deprecations

[Obenchain, Valerie]

Hi Roel,

Thank you for working on the package.

The builds start at 5pm EST daily. If it's helpful, you can see which R
version, compilers and compiler flags are used for each build machine by
clicking the name at the top left of the report:

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

Valerie



On 04/20/2017 12:38 AM, Janssen-10, R.R.E. wrote:
> Dear Valerie,
>
> We're working on MutationalPatterns as you can see (we've had our last 
> changes pushed into the SVN repository just two days ago).
> Due to the timezone differences between Europe and the US, we seem to be 
> missing out the starting point of a new build round.
>
> So, at which time do you start a new build round?  We have the fixes in place 
> to address the build issues.
> There seems to be a difference between the R setup on your build machines and 
> ours, which leads to differences in the tests.  They all pass on our 
> machines, so it's hard for us to debug this in a timely manner.
>
> Thanks!
>
> Kind regards,
> Roel Janssen
>
> 
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Obenchain, 
> Valerie [valerie.obench...@roswellpark.org]
> Sent: Wednesday, April 19, 2017 9:19 PM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] Bioconductor 3.5 release: potential deprecations
>
> Hi,
>
> Due to errors / unresponsive maintainers this new group of packages has
> been identified for potential deprecation in Biocondcutor 3.5.
>
> anamiR
> FunChiP
> MutationalPatterns
> seqplots
> snm
> ssviz
> stepwiseCM
> ToPASeq
>
> If anyone is interested in taking over as maintainer please let us know.
> If not fixed by Friday, April 21, these will be deprecated in 3.5.
>
> Valerie
>
>
>
> 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.
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
>
> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
> te informeren door het bericht te retourneren. Het Universitair Medisch
> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de 
> W.H.W.
> (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
> de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
>
> Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
>
> --
>
> This message may contain confidential information and ...{{dropped:23}}

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Bioconductor 3.5 release: potential deprecations

[Janssen-10, R.R.E.]

Dear Valerie,

We're working on MutationalPatterns as you can see (we've had our last changes 
pushed into the SVN repository just two days ago).
Due to the timezone differences between Europe and the US, we seem to be 
missing out the starting point of a new build round.

So, at which time do you start a new build round?  We have the fixes in place 
to address the build issues.
There seems to be a difference between the R setup on your build machines and 
ours, which leads to differences in the tests.  They all pass on our machines, 
so it's hard for us to debug this in a timely manner.

Thanks!

Kind regards,
Roel Janssen


From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Obenchain, 
Valerie [valerie.obench...@roswellpark.org]
Sent: Wednesday, April 19, 2017 9:19 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Bioconductor 3.5 release: potential deprecations

Hi,

Due to errors / unresponsive maintainers this new group of packages has
been identified for potential deprecation in Biocondcutor 3.5.

anamiR
FunChiP
MutationalPatterns
seqplots
snm
ssviz
stepwiseCM
ToPASeq

If anyone is interested in taking over as maintainer please let us know.
If not fixed by Friday, April 21, these will be deprecated in 3.5.

Valerie



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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

--

De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
te informeren door het bericht te retourneren. Het Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.

Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

--

This message may contain confidential information and is...{{dropped:11}}

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.5 release: potential deprecations

[Obenchain, Valerie]

Hi,

Due to errors / unresponsive maintainers this new group of packages has
been identified for potential deprecation in Biocondcutor 3.5.

anamiR
FunChiP
MutationalPatterns
seqplots
snm
ssviz
stepwiseCM
ToPASeq

If anyone is interested in taking over as maintainer please let us know.
If not fixed by Friday, April 21, these will be deprecated in 3.5.

Valerie



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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.5 release: update NEWS

[Obenchain, Valerie]

Reminder to please update your NEWS files. These files are collated and
included in the release announcement so it's worth polishing them up.

Thanks.

Valerie



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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.5 release: stop commits to 3.4 release branch

[Obenchain, Valerie]

Today we'll stop commits to the 3.4 release branch at COB EST. Please
commit any last changes before that time. We'll wait one more day to get
a final build report and then stop the release builds all together.

Thanks.

Valerie



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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.5 release: April 7 deadlines

[Valerie Obenchain]

Hi,

Some recent activity has caused some (red) ripples across the builds and 
the El Capitan Mac builds are still unsettled. To accommodate, we're 
extending the deadline to pass R CMD build and check with no errors to 
next Friday (http://www.bioconductor.org/developers/release-schedule/). 
Thanks to everyone for cleaning up their packages and communicating 
problems (and solutions!) on the lists.


Key deadlines for April 7 are

- No new packages added to the 3.5 roster

- No more API changes

- Current release 3.4 builds will stop

- Annotation packages (both internal and contributed) posted to the 3.5 repo

Valerie

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.5 release: db0, OrgDb and TxDb packages

[Obenchain, Valerie]

Hi,

The new db0, OrgDb and TxDb packages are now available in the devel branch.

# db0:

Updated all 19:

anopheles.db0_3.4.2.tar.gz
chicken.db0_3.4.2.tar.gz
fly.db0_3.4.2.tar.gz
pig.db0_3.4.2.tar.gz
xenopus.db0_3.4.2.tar.gz
arabidopsis.db0_3.4.2.tar.gz
chimp.db0_3.4.2.tar.gz
human.db0_3.4.2.tar.gz
rat.db0_3.4.2.tar.gz
yeast.db0_3.4.2.tar.gz
bovine.db0_3.4.2.tar.gz
ecoliK12.db0_3.4.2.tar.gz
malaria.db0_3.4.2.tar.gz
rhesus.db0_3.4.2.tar.gz
zebrafish.db0_3.4.2.tar.gz
canine.db0_3.4.2.tar.gz
ecoliSakai.db0_3.4.2.tar.gz
mouse.db0_3.4.2.tar.gz
worm.db0_3.4.2.tar.gz


# OrgDb:

Updated all 19:

org.Ce.eg.db_3.4.1.tar.gz
org.EcK12.eg.db_3.4.1.tar.gz
org.Mm.eg.db_3.4.1.tar.gz
org.Rn.eg.db_3.4.1.tar.gz
org.Ag.eg.db_3.4.1.tar.gz
org.Cf.eg.db_3.4.1.tar.gz
org.EcSakai.eg.db_3.4.1.tar.gz
org.Mmu.eg.db_3.4.1.tar.gz
org.Sc.sgd.db_3.4.1.tar.gz
org.At.tair.db_3.4.1.tar.gz
org.Dm.eg.db_3.4.1.tar.gz
org.Gg.eg.db_3.4.1.tar.gz
org.Pf.plasmo.db_3.4.1.tar.gz
org.Ss.eg.db_3.4.1.tar.gz
org.Bt.eg.db_3.4.1.tar.gz
org.Dr.eg.db_3.4.1.tar.gz
org.Hs.eg.db_3.4.1.tar.gz
org.Pt.eg.db_3.4.1.tar.gz
org.Xl.eg.db_3.4.1.tar.gz


# TxDb:

Added 1 new package:

TxDb.Ggallus.UCSC.galGal5.refGene_3.4.0.tar.gz

Updated 4 active tracks:

TxDb.Celegans.UCSC.ce11.refGene_3.4.1.tar.gz
TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.1.tar.gz
TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1.tar.gz 
TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1.tar.gz


# Updated PFAM and GO:

PFAM.db_3.4.1.tar.gz
GO.db_3.4.1.tar.gz


I found what appear to be 2 abandoned OrgDb packages,
org.Tgondii.eg.db_1.0.tar.gz and org.Sco.eg.db_2.4.2.tar.gz. It looks
like these were last updated in October 2015. I've emailed the authors
but one bounced the other hasn't responded. Given that the OrgDb data
are a snapshot in time vs tied to a genome build it's important to
regenerate these every 6 months. If I don't hear back from the authors
I'll remove these from the repo.

Valerie


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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.5 Release: db0 packages

[Obenchain, Valerie]

The new db0 packages (all version 3.4.2) are now available in the devel
repo. Let me know if you notice any problems.

Thanks.

Valerie



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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.5 release: March 31 deadlines

[Obenchain, Valerie]

Hi all,

Reminder that today (March 31) is the last day for new package
submissions. I've run into a few problems generating the db0 annotation
packages so unfortunately they won't be ready today - I'm hoping Monday
at the latest.

  http://www.bioconductor.org/developers/release-schedule/

Valerie



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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.5 release: contributed annotation packages

[Obenchain, Valerie]

Dear annotation contributors,

Just a reminder the deadline to update annotation packages is Friday
April 7. Please make updated packages available via dropbox or another
location that allows wget. Indicate if the old version should be
included in the upcoming release or if the new package should replace it.

Thanks.

Valerie



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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Bioconductor 3.5 release: deprecated packages

[Obenchain, Valerie]

Sorry, xcms was a mistake on my part. This package is not deprecated.

Valerie


On 03/23/2017 10:06 AM, Obenchain, Valerie wrote:
> Just a heads up about deprecated packages.
>
> These have been 'deprecated' in Biocondcutor 3.4 and will be 'defunct'
> in Bioconductor 3.5. The 'defunct' status means they are removed from
> the nightly builds, don't have a landing page and aren't available via
> biocLite().
>
> Software:
> betr
>
> Experimental Data:
> encoDnasel
> ggtut
>
> These have been 'deprecated' in devel at some point over the past 6
> months and will appear 'deprecated' the 3.5 release. They will be
> 'defunct' in the new devel, Bioconductor 3.6.
>
> Software:
> coRNAi
> networkBMA
> xcms
> AtlasRDF
> GEOsearch
> saps
> mmnet
> CopyNumber450k
> MeSHSim
> GENE.E
>
> Experimental Data:
> CopyNumber450kData
>
> Feel free to contact me with any questions.
>
> Valerie
>
>
> 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.
> ___
> Bioc-devel@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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.5 release

[Obenchain, Valerie]

Hi all,

The release of Bioconductor 3.5 will be Tuesday, April 25. Please see
the schedule for details:

  http://www.bioconductor.org/developers/release-schedule/

Over the next month we'll announce the key deadlines on bioc-devel. Lori
sent the first one last week and it's important for anyone planning to
submit a new package:

  https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010594.html

As you know, part of preparing for the release is cleaning up the
software and experimental data build reports. It would be greatly
appreciated if you could proactively look at your packages and help us
get them "in the green" with a clean build and check.

  http://www.bioconductor.org/checkResults/


Thanks.

Valerie




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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel