[Bioc-devel] Bioconductor 3.7 is released

[Obenchain, Valerie]

Thanks to all the developers for contributing to the project!

Full release announcement here:

  http://bioconductor.org/news/bioc_3_7_release/


The Bioconductor Team


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Re: [Bioc-devel] The following bioconductor packages have duplicate commits

[Justin Silverman]

actually I think I solved it...


> On May 1, 2018, at 12:47 PM, Justin Silverman  wrote:
> 
> Hi all, 
>   Trying to resolve duplicate commits. Sorry, I feel like I have ignored 
> a recent email with the same problem as I am about to mention (but I can't 
> find it)... I am having trouble synchronizing with bioconductor remote 
> server. I keep getting permission errorL
> 
> 
> g...@git.bioconductor.org: Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> 
> 
> What am I doing wrong?
> Thanks!
> Justin
> 
> 
> 
>> On Apr 30, 2018, at 1:34 PM, Turaga, Nitesh  
>> wrote:
>> 
>> Hi Maintainers,
>> 
>> We just concluded the bump in the RELEASE_3_7 branch and master. But, the 
>> following packages have a history of duplicate commits and we are leaving it 
>> up to the maintainers to fix these duplicate commits. 
>> 
>> There were 12 software packages that had duplicate commits. Please fix these 
>> packages, otherwise the duplicate commits will keep propagating. 
>> 
>> methylumi
>> sva
>> bumphunter
>> compcodeR
>> flowClean
>> similaRpeak
>> IONiseR
>> rnaseqcomp
>> iCOBRA
>> PanVizGenerator
>> nucleoSim
>> philr
>> 
>> 
>> We will set up a more detailed document on how to resolve duplicate commits, 
>> but there are many ways. I’m listing just one of them below.
>> 
>> How to resolve duplicate commits
>> ———
>> 
>> Sync your package to the existing version on Bioconductor now. 
>> (http://bioconductor.org/developers/how-to/git/pull-upstream-changes/)
>> 
>> 1. Make a backup of the branch with duplicate commits, call this 
>> “master_backup” or “RELEASE_3_7_backup”.
>> 
>> On master, (make sure you are on master by “ git checkout master”)
>> 
>>  git branch master_backup
>> 
>> 2. Identify the commit from which the duplicates have originated. These 
>> commits are more often than not, “merge” commits.
>> 
>> 3. Reset you branch to the commit *before* the merge commit.
>> 
>>  git reset —hard 
>> 
>> 4. Now cherry pick your commits from the master_backup branch. 
>> 
>>  git cherry-pick 
>> 
>>  4a. The commits you cherry-pick should be only 1 version of the 
>> duplicate commit, i.e don’t cherry-pick the same commit twice. 
>>  
>>  4b. Include the branching and version bump commits in your cherry-pick. 
>> Make the package history look as normal as possible.
>> 
>> 
>> These packages have duplicate commits which are just being discovered 
>> because there has been no update in the last development cycle. 
>> 
>> Best,
>> 
>> Nitesh Turaga
>> Bioconductor Core Team
>> 
>> 
>> 
>> 
>> 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.
> 

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Re: [Bioc-devel] The following bioconductor packages have duplicate commits

[Justin Silverman]

Hi all, 
Trying to resolve duplicate commits. Sorry, I feel like I have ignored 
a recent email with the same problem as I am about to mention (but I can't find 
it)... I am having trouble synchronizing with bioconductor remote server. I 
keep getting permission errorL


g...@git.bioconductor.org: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.


What am I doing wrong?
Thanks!
Justin



> On Apr 30, 2018, at 1:34 PM, Turaga, Nitesh  
> wrote:
> 
> Hi Maintainers,
> 
> We just concluded the bump in the RELEASE_3_7 branch and master. But, the 
> following packages have a history of duplicate commits and we are leaving it 
> up to the maintainers to fix these duplicate commits. 
> 
> There were 12 software packages that had duplicate commits. Please fix these 
> packages, otherwise the duplicate commits will keep propagating. 
> 
> methylumi
> sva
> bumphunter
> compcodeR
> flowClean
> similaRpeak
> IONiseR
> rnaseqcomp
> iCOBRA
> PanVizGenerator
> nucleoSim
> philr
> 
> 
> We will set up a more detailed document on how to resolve duplicate commits, 
> but there are many ways. I’m listing just one of them below.
> 
> How to resolve duplicate commits
> ———
> 
> Sync your package to the existing version on Bioconductor now. 
> (http://bioconductor.org/developers/how-to/git/pull-upstream-changes/)
> 
> 1. Make a backup of the branch with duplicate commits, call this 
> “master_backup” or “RELEASE_3_7_backup”.
> 
> On master, (make sure you are on master by “ git checkout master”)
> 
>   git branch master_backup
> 
> 2. Identify the commit from which the duplicates have originated. These 
> commits are more often than not, “merge” commits.
> 
> 3. Reset you branch to the commit *before* the merge commit.
> 
>   git reset —hard 
> 
> 4. Now cherry pick your commits from the master_backup branch. 
> 
>   git cherry-pick 
> 
>   4a. The commits you cherry-pick should be only 1 version of the 
> duplicate commit, i.e don’t cherry-pick the same commit twice. 
>   
>   4b. Include the branching and version bump commits in your cherry-pick. 
> Make the package history look as normal as possible.
> 
> 
> These packages have duplicate commits which are just being discovered because 
> there has been no update in the last development cycle. 
> 
> Best,
> 
> Nitesh Turaga
> Bioconductor Core Team
> 
> 
> 
> 
> 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.

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Re: [Bioc-devel] The following bioconductor packages have duplicate commits

[Turaga, Nitesh]

Hi,

Your package is not cleaned up. According to the link you sent me, it still has 
duplicate commits. 

https://github.com/cafletezbrant/flowClean/commits/master

Look at commits from oct 7,2016 and earlier. 

Please take a look at the instructions I sent out along with the initial email 
and try to follow that. If you have any questions regarding the process, please 
let me know and post back to the thread and I’ll be happy to answer. 

Best regards,

Nitesh 


> On May 1, 2018, at 11:11 AM, Kipper Fletez-Brant  
> wrote:
> 
> pkg name: flowClean
> GitHub: https://github.com/cafletezbrant/flowClean
> 
> On Tue, May 1, 2018 at 9:59 AM, Turaga, Nitesh 
>  wrote:
> Hello Maintainers,
> 
> Once you have resolved your package, please let me know both your package 
> name, and GitHub link where your package commit history has been cleaned. 
> 
> Best,
> 
> Nitesh 
> 
> > On May 1, 2018, at 9:55 AM, Kipper Fletez-Brant  
> > wrote:
> > 
> > Thanks Nitesh.
> > 
> > Following the manual [1] I believe I have resolved this issue.
> > 
> > [1] 
> > https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
> > 
> > On Mon, Apr 30, 2018 at 1:34 PM, Turaga, Nitesh 
> >  wrote:
> > Hi Maintainers,
> > 
> > We just concluded the bump in the RELEASE_3_7 branch and master. But, the 
> > following packages have a history of duplicate commits and we are leaving 
> > it up to the maintainers to fix these duplicate commits. 
> > 
> > There were 12 software packages that had duplicate commits. Please fix 
> > these packages, otherwise the duplicate commits will keep propagating. 
> > 
> > methylumi
> > sva
> > bumphunter
> > compcodeR
> > flowClean
> > similaRpeak
> > IONiseR
> > rnaseqcomp
> > iCOBRA
> > PanVizGenerator
> > nucleoSim
> > philr
> > 
> > 
> > We will set up a more detailed document on how to resolve duplicate 
> > commits, but there are many ways. I’m listing just one of them below.
> > 
> > How to resolve duplicate commits
> > ———
> > 
> > Sync your package to the existing version on Bioconductor now. 
> > (http://bioconductor.org/developers/how-to/git/pull-upstream-changes/)
> > 
> > 1. Make a backup of the branch with duplicate commits, call this 
> > “master_backup” or “RELEASE_3_7_backup”.
> > 
> > On master, (make sure you are on master by “ git checkout master”)
> > 
> > git branch master_backup
> > 
> > 2. Identify the commit from which the duplicates have originated. These 
> > commits are more often than not, “merge” commits.
> > 
> > 3. Reset you branch to the commit *before* the merge commit.
> > 
> > git reset —hard 
> > 
> > 4. Now cherry pick your commits from the master_backup branch. 
> > 
> > git cherry-pick 
> > 
> > 4a. The commits you cherry-pick should be only 1 version of the 
> > duplicate commit, i.e don’t cherry-pick the same commit twice. 
> > 
> > 4b. Include the branching and version bump commits in your 
> > cherry-pick. Make the package history look as normal as possible.
> > 
> > 
> > These packages have duplicate commits which are just being discovered 
> > because there has been no update in the last development cycle. 
> > 
> > Best,
> > 
> > Nitesh Turaga
> > Bioconductor Core Team
> > 
> > 
> > 
> > 
> > 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.
> 



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, 
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this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] The following bioconductor packages have duplicate commits

[Turaga, Nitesh]

Hello Maintainers,

Once you have resolved your package, please let me know both your package name, 
and GitHub link where your package commit history has been cleaned. 

Best,

Nitesh 

> On May 1, 2018, at 9:55 AM, Kipper Fletez-Brant  
> wrote:
> 
> Thanks Nitesh.
> 
> Following the manual [1] I believe I have resolved this issue.
> 
> [1] 
> https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
> 
> On Mon, Apr 30, 2018 at 1:34 PM, Turaga, Nitesh 
>  wrote:
> Hi Maintainers,
> 
> We just concluded the bump in the RELEASE_3_7 branch and master. But, the 
> following packages have a history of duplicate commits and we are leaving it 
> up to the maintainers to fix these duplicate commits. 
> 
> There were 12 software packages that had duplicate commits. Please fix these 
> packages, otherwise the duplicate commits will keep propagating. 
> 
> methylumi
> sva
> bumphunter
> compcodeR
> flowClean
> similaRpeak
> IONiseR
> rnaseqcomp
> iCOBRA
> PanVizGenerator
> nucleoSim
> philr
> 
> 
> We will set up a more detailed document on how to resolve duplicate commits, 
> but there are many ways. I’m listing just one of them below.
> 
> How to resolve duplicate commits
> ———
> 
> Sync your package to the existing version on Bioconductor now. 
> (http://bioconductor.org/developers/how-to/git/pull-upstream-changes/)
> 
> 1. Make a backup of the branch with duplicate commits, call this 
> “master_backup” or “RELEASE_3_7_backup”.
> 
> On master, (make sure you are on master by “ git checkout master”)
> 
> git branch master_backup
> 
> 2. Identify the commit from which the duplicates have originated. These 
> commits are more often than not, “merge” commits.
> 
> 3. Reset you branch to the commit *before* the merge commit.
> 
> git reset —hard 
> 
> 4. Now cherry pick your commits from the master_backup branch. 
> 
> git cherry-pick 
> 
> 4a. The commits you cherry-pick should be only 1 version of the 
> duplicate commit, i.e don’t cherry-pick the same commit twice. 
> 
> 4b. Include the branching and version bump commits in your 
> cherry-pick. Make the package history look as normal as possible.
> 
> 
> These packages have duplicate commits which are just being discovered because 
> there has been no update in the last development cycle. 
> 
> Best,
> 
> Nitesh Turaga
> Bioconductor Core Team
> 
> 
> 
> 
> 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, 
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Re: [Bioc-devel] push access to adaptest

[Nima Hejazi]

Great — thank you for helping us out with this.

Best,
Nima

On Tue, May 1, 2018 at 5:35 AM Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Nima has been added to adaptest.
>
> Valerie
>
>
> On 04/30/2018 02:05 PM, WILSON CAI wrote:
>
> i approve
>
> On Mon, Apr 30, 2018 at 11:13 AM Nima Hejazi  
>  wrote:
>
>
> Hello BioC team ---
>
> Wilson Cai (cc'd) and I are co-developers / co-authors of the adaptest
> package  
>  that has joined the
> Bioconductor ecosystem as of 3.7. I would like to request push access to
> this repository on the git server to ensure that we're able to effectively
> continue development on the package going forward. As Wilson is listed as
> the maintainer, he already has push access --- would it be possible to
> extend this to me as well? Thanks in advance for help with this.
>
> ​Best,
> Nima
>
> --
> Nima Hejazi
> Doctoral Student
> Group in Biostatistics  
> 
> University of California, Berkeleystat.berkeley.edu/~nhejazi 
>  
>  |nimahejazi.org
> van der Laan Group  
>  | Hubbard
> Group  
>
>
>
> 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.

-- 
Warm Regards,
— Nima Hejazi

--
Nima Hejazi
Doctoral Student
Group in Biostatistics 
University of California, Berkeley
stat.berkeley.edu/~nhejazi  |
nimahejazi.org
van der Laan Group  | Hubbard Group


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Re: [Bioc-devel] Web App for SSH keys

[Obenchain, Valerie]

On 04/19/2018 06:29 PM, Leonardo Collado Torres wrote:

Hi Valerie,

Thanks for the reply and the doc changes ^^. I added a few short replies below.

Best,
Leo

On Thu, Apr 19, 2018 at 4:49 PM, Obenchain, Valerie
 
wrote:


Hi Leo,

Great feedback, thanks.

On 04/19/2018 08:04 AM, Leonardo Collado Torres wrote:

This looks great Valerie, congrats to all of those involved in making
the web app! I hope that it leads to less questions/confusion.

Here are some minor comments, mostly about including some links/docs.

* Under the which packages we have access to, I noticed that it's not
showing the experimental data packages. I guess that's because they
are not in git yet (right?).


All software, data experiment and workflow packages are in git. You should
be able to see all associated with your account. One of the goals of the app
was to make package access more transparent which could help explain why a
`push` or `fetch` failed. We match your email to the username we have in the
gitolite packages.conf file. When I search packages.conf I see your username
on these packages:

~/git.bioconductor.org/admin/gitolite-admin >grep -B 1
'master.*collado-torres' conf/packages.conf
repo packages/sva
RW master = j.leek l.collado-torres
--
repo packages/derfinder
RW master = l.collado-torres
--
repo packages/derfinderHelper
RW master = l.collado-torres
--
repo packages/derfinderPlot
RW master = l.collado-torres
--
repo packages/regionReport
RW master = l.collado-torres
--
repo packages/recount
RW master = l.collado-torres
--
repo packages/recountWorkflow
RW master = l.collado-torres


If there is a package missing that you should have access to let us know.
Also let me know if this differs from the list you saw when you were logged
in.



This matches what I saw when I logged in. The only data package I've
contributed to Bioc is derfinderData. We haven't had to make any
changes to it in a long time as you can see at
https://github.com/leekgroup/derfinderData. I don't know if that
played a role in the package not showing up on m list. My email is
there on the DESCRIPTION file though
https://github.com/leekgroup/derfinderData/blob/master/DESCRIPTION#L7.

You're right, not all experimental data packages show up in this list because 
they aren't all in the packages.conf config file. The reason is historical. 
When we first started the experimental data packages we viewed them as static 
or at least changing very little. SVN write access wasn't given unless the 
maintainer explicitly requested it. When we transitioned from SVN to Git, only 
packages with write access by a specific maintainer were transferred to the 
config file.

After the next release we'll go through the data packages and make sure they're 
all in packages.conf with write access by the maintainer in DESCRIPTION.









* Under add an ssh key, the second option mentions "username.keys
files in your GitHub account". I hadn't heard about this before. Is
that file made automatically by editing
https://github.com/settings/keys? If there's a website that describes
this in more detail, I suggest including a link to it.


Yes, this is the standard keys file and is edited through github account
settings.

A link has been added to the github HOWTO page:

https://help.github.com/articles/adding-a-new-ssh-key-to-your-github-account/



I like the change, it's much clearer!




* I've seen several emails where Nitesh and others ask developers to
check their SSH key using ssh -T 
g...@git.bioconductor.org, so maybe
adding a reminder there would be good. Actually, maybe just include a
link to http://bioconductor.org/developers/how-to/git/faq/ from this
new site. By the way, that last link is not directly available from
http://bioconductor.org/developers/ (I think), I had to go to
http://bioconductor.org/developers/how-to/git/ then "See other
frequently asked questions."


I've added a link to the FAQ.



Nice! By the way, I just noticed a typo on
http://bioconductor.org/developers/how-to/git/faq/ bullet 17:

git clone 
g...@git.bioconductor.org:packagse/

packagse -> packages

Fixed (may take 20 minutes to propagate).








Since the FAQ is specific to version control it probably still belongs under
developers -> Git Source Control. Maybe we could change the title from 'See
other frequently asked questions' to just 'FAQ' or something more obvious.




Ok! To me it's really the "Git / ssh Bioc FAQ".

I'll pass that on, thanks.

Val








* Typo: "Which packages do I have acces to?" --> access


Fixed.


Valerie




Best,
Leo

On Wed, Apr 18, 2018 at 12:53 PM, Obenchain, Valerie
 
wrote:

My last email didn't make it through to the list - trying again ...


The Web App for managing SSH keys is now available at

 

Re: [Bioc-devel] push access to adaptest

[Obenchain, Valerie]

Nima has been added to adaptest.

Valerie

On 04/30/2018 02:05 PM, WILSON CAI wrote:

i approve

On Mon, Apr 30, 2018 at 11:13 AM Nima Hejazi 
 wrote:



Hello BioC team ---

Wilson Cai (cc'd) and I are co-developers / co-authors of the adaptest
package 

 that has joined the
Bioconductor ecosystem as of 3.7. I would like to request push access to
this repository on the git server to ensure that we're able to effectively
continue development on the package going forward. As Wilson is listed as
the maintainer, he already has push access --- would it be possible to
extend this to me as well? Thanks in advance for help with this.

​Best,
Nima

--
Nima Hejazi
Doctoral Student
Group in Biostatistics 

University of California, Berkeley
stat.berkeley.edu/~nhejazi 

 |
nimahejazi.org
van der Laan Group 

 | Hubbard
Group 









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 
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Re: [Bioc-devel] Need some help to submit a R package.

[Martin Morgan]

The status of your package is unchanged from before; wait for the 
reviewer to comment further on your package. Martin


On 05/01/2018 01:30 AM, Pijush Das wrote:

Dear Sir,



Please inform me the current status of the package named "sigFeature".
The package link is given below.
https://github.com/Bioconductor/Contributions/issues/713



Thank you



regards
Pijush





On Fri, Apr 27, 2018 at 7:00 PM, Pijush Das > wrote:



Now it is opening. It may be some kind of problem is there with the
internet connection.



On Fri, Apr 27, 2018 at 6:56 PM, Shepherd, Lori
> wrote:

I am still able to open the link:

https://github.com/Bioconductor/Contributions/issues/713



Perhaps there is some firewall or ani-virus program you are
running that is blocking access?


When you try to go to the link, what message is displayed?


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


*From:* Bioc-devel > on behalf of
Shepherd, Lori 
*Sent:* Friday, April 27, 2018 8:18:23 AM
*To:* Pijush Das; Morgan, Martin
*Cc:* bioc-devel@r-project.org 
*Subject:* Re: [Bioc-devel] Need some help to submit a R package.
I am able to open this link.  Perhaps it was an intermittent
internet connection issue?  Are you able to open the link now?


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Pijush Das >
Sent: Friday, April 27, 2018 7:06:07 AM
To: Morgan, Martin
Cc: Shepherd, Lori; bioc-devel@r-project.org

Subject: Re: [Bioc-devel] Need some help to submit a R package.

Dear Sir,


I have found some problem in github link given below:
https://github.com/Bioconductor/Contributions/issues/713

The link is not opening. Is there any problem in github repository?
Please check it.


Thank you


regards
Pijush







On Thu, Apr 26, 2018 at 2:32 PM, Martin Morgan
>> wrote:
Wait for the reviewer to comment further on your package.

On 04/26/2018 02:20 AM, Pijush Das wrote:
Dear Sir,


I have found that my package sigFeature had passed all the built
test without errors or warnings
on all platforms.
What should I do next ?





regards
Pijush












On Tue, Apr 24, 2018 at 10:56 PM, Shepherd, Lori
>



>

     After the webhook is set up you will need to do another
version bump
     to trigger the build -  Please post further correspondence
regarding
     your package submission on the open github issue


https://github.com/Bioconductor/Contributions/issues/713

     >


     Lori Shepherd

     Bioconductor 

Re: [Bioc-devel] Suggested edits to support site posting guide

[Hervé Pagès]

Thanks Leo for the link to April Wensel's blog.

I wonder if she is 100% serious with her rant about the Grandma
thing but I found it pretty funny!

H.


On 04/30/2018 01:16 PM, Michael Love wrote:

hi Leo,

We currently have "Rudeness and ad hominem comments are not
acceptable" in the section on replying. This is nice and simple.

I think most of the people reading the guide will be first time
question-askers, but I'm glad we have the above bulletpoint so we can
say someone was breaking the site guidelines if they were rude.

I don't think we need to link to the anti-RTFM piece, because I don't
think I've ever seen that phrase used on Bioc support (or if I saw it,
it was a while ago and I forgot about it). If you want to incorporate
any of the positive suggestions from there to the section on replying
go for it.

Anyone should feel free to keep editing the Gdoc. I'll wait a week or
so and then do a PR to the site.

best,
Mike


On Mon, Apr 30, 2018 at 3:30 PM, Tim Triche, Jr.  wrote:

well, Hadley usually walks people through the steps required to 1) file a
bug reproducibly or 2) learn how to do the thing in question organically,
and his universe is doing OK, so N=1 in favor of that approach.  Also a lot
of people helped me learning Perl (!) on Usenet (!!!) so yeah I'm old but
it seems like civility was once a little more common.  Bioc-devel and
support.bioconductor.com are healthy communities, I would hope that nobody
minds this being spelled out explicitly.

I love Prof Ripley and he's never been anything but nice to me, still,
r-help's reputation took a beating from his insistence on self-reliance.
Several times when I thought I understood a library or process, I'd write
up an example and discover that what I believed to be true was not, in
fact, true -- perhaps an example was cordoned off with \{dontrun} or some
such, perhaps an upstream package broke unwritten assumptions, whatever.
My point is that it can be beneficial for the answerer as for the asker,
and perhaps if one does not have time to provide a working example in an
answer, then it might be better to let another person with sufficient time
go ahead and address that question.

JMHO, since you asked "everyone else".

Best,


--t

On Mon, Apr 30, 2018 at 2:58 PM, Leonardo Collado Torres 
wrote:


Hi Mike, Lori and everyone else,

I recently saw this tweet
https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_aprilwensel_status_989248246878035972=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=S5D7QD263pcF-j96zEV-sY0v_ulBJ_ZpI9JMXcbAEOI=-p8hKcFjc_9ArMb2xpIHzDt9ZrOm5Ojtf4XrEmnC5tw=
 that links
to 
https://urldefense.proofpoint.com/v2/url?u=https-3A__medium.com_compassionate-2Dcoding_its-2Dtime-2D=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=S5D7QD263pcF-j96zEV-sY0v_ulBJ_ZpI9JMXcbAEOI=tqcYe_NWBZlekYGeTonoXkxgnYpjk14j_DFWw0yVcRk=
to-retire-rtfm-31acdfef654f#---0-162

First, I'm curious if you've read it and if you like it. Second, maybe
we could include some of it (or link to it) in the suggested changes
to the posting guide that Mike is working on.

Best,
Leo



On Fri, Apr 20, 2018 at 10:10 AM, Shepherd, Lori
 wrote:

May I also suggested when you are satisfied with user feedback and

alterations to create a pull request for the website repository



https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_bioconductor.org=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=S5D7QD263pcF-j96zEV-sY0v_ulBJ_ZpI9JMXcbAEOI=lDZRqONtpk4hTnHzIpBY0FHTUu2Y8-fCZ9-kechwRKI=




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of

Michael Love 

Sent: Thursday, April 12, 2018 11:23:35 AM
To: bioc-devel
Subject: [Bioc-devel] Suggested edits to support site posting guide

dear all,

I've edited the text from the posting guide

 to update it a
bit.

For example, some of the text still referred to the mailing list
:
"Compose a new message with a new subject line".

Mostly, though, I wanted to emphasize posting all of their R code and
information about the experiment, which is often missing from support

site

posts. The self-contained example with data and code is rarely possible
because many Bioc users have large datasets that can't be shared.

Curious if this is useful or if others have suggestions. The following
link allows edits: