Re: [Rd] survival bug?

[Ben Bolker]

  Microsoft offers fully-provisioned but time-limited developer images
for Windows 10 (I think they last for 3 months) for most major VM
platforms (including VirtualBox, which is the one I currently use).
There would certainly be a start-up cost in effort, but probably not any
financial cost.

   cheers
Ben Bolker

On 2020-03-03 4:02 p.m., Gabriel Becker wrote:
> Hi Terry,
> 
> http://win-builder.r-project.org/ and the rhub build service (which can be
> invoked by the rhub package) allow on demand checks in windows
> environments, though for active debugging the iteration time can be quite
> painful.
> 
> If you have access, e.g., through your employer, to a windows license you
> should also be able to do use VMWare or VirtualBox (I can never remember
> which one I like more) to run windows and test that way. This will have
> some start up cost in effort but allows active testing and iteration.
> 
> Hope that helps,
> ~G
> 
> On Tue, Mar 3, 2020 at 7:00 AM Therneau, Terry M., Ph.D. via R-devel <
> r-devel@r-project.org> wrote:
> 
>> My latest submission of survival3.1-10 to CRAN fails  a check, but only on
>> windows, which
>> I don't use.
>> How do I track this down?
>> The test in question works fine on my Linux box.
>>
>> Terry
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Bioc-devel] Change citation reference

[Shepherd, Lori]

The citation should have been updated now:
http://bioconductor.org/packages/3.11/bioc/html/vulcan.html

Thanks for notification of the issue.

Cheers,


Lori Shepherd

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 Federico 
Giorgi 
Sent: Thursday, February 27, 2020 3:24 PM
To: Stian L�gstad 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Change citation reference

Dear Stan: tahnks but yes, the version was updated a while ago, after the
change in inst/CITATION was done
Dear Lori: thanks a lot for looking into this!

Federico

On Thu, 27 Feb 2020 at 15:30, Stian L�gstad  wrote:

> Hi Federico,
>
> I believe you need to update the package version (in the DESCRIPTION file)
> to trigger a new build for those changes to be visible. If you update the
> version and push that change then a new build will be triggered.
>
> I see from http://bioconductor.org/checkResults/3.10/bioc-LATEST/ (search
> for "vulcan" there) that your package was last built:
> > Last Commit: b5638d5
> > Last Changed Date: 2019-10-29 13:10:48 -0500
>
> On Thu, Feb 27, 2020 at 3:19 PM Federico Giorgi 
> wrote:
>
>> Dear all,
>>
>> I would like to change the citation in the vulcan package.
>>
>> https://bioconductor.org/packages/release/bioc/html/vulcan.html
>>
>> I have changed the reference in the inst/CITATION file within the package
>> a
>> few weeks ago, but the old citation remains, even in the development
>> version:
>> https://bioconductor.org/packages/devel/bioc/html/vulcan.html
>>
>> Should I wait or is there another way to update the citation reference?
>>
>> Thanks,
>>
>> Federico
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> --
> Stian L�gstad
> +47 41 80 80 25
>

[[alternative HTML version deleted]]

___
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.
[[alternative HTML version deleted]]

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

Re: [Rd] survival bug?

[Gabriel Becker]

Hi Terry,

http://win-builder.r-project.org/ and the rhub build service (which can be
invoked by the rhub package) allow on demand checks in windows
environments, though for active debugging the iteration time can be quite
painful.

If you have access, e.g., through your employer, to a windows license you
should also be able to do use VMWare or VirtualBox (I can never remember
which one I like more) to run windows and test that way. This will have
some start up cost in effort but allows active testing and iteration.

Hope that helps,
~G

On Tue, Mar 3, 2020 at 7:00 AM Therneau, Terry M., Ph.D. via R-devel <
r-devel@r-project.org> wrote:

> My latest submission of survival3.1-10 to CRAN fails  a check, but only on
> windows, which
> I don't use.
> How do I track this down?
> The test in question works fine on my Linux box.
>
> Terry
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

[[alternative HTML version deleted]]

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Bioc-devel] Reverting on the 'master' branch

[Roel Janssen]

Except that it's impossible to have version 1.99.0 installed because the build
fails.

I will try to work on the bugs that I introduced to get the features in shape
before the next Bioconductor release.

Thanks all for your replies!

Kind regards,
Roel Janssen


On Tue, 2020-03-03 at 15:42 +, Martin Morgan wrote:
> Once a version has been made 'public', it's not possible to go backward -- R
> will say 'hey, you've got version 1.99.0 installed, so that's more recent than
> 1.13.0, so I won't update it'. So you're stuck with the version going forward.
> 
> Martin
> 
> On 3/3/20, 10:14 AM, "Bioc-devel on behalf of Turaga, Nitesh" <
> bioc-devel-boun...@r-project.org on behalf of nitesh.tur...@roswellpark.org>
> wrote:
> 
> Hi Roel,
> 
> I think at this point it makes sense to move forward. It is more trouble
> than it's worth to do "hard resets" and then edit version numbers manually. 
> 
> Or another thing you could do is, roll out some big changes before the
> next release ;) 
> 
> Best,
> 
> Nitesh 
> 
> > On Mar 2, 2020, at 5:09 PM, Roel Janssen  wrote:
> > 
> > Dear Nitesh,
> > 
> > Thanks for the quick replies.  And sorry for mixing your first and last
> name up.
> > :)
> > 
> > Well, we'd like to reserve 2.0.0 of our package for a "big feature
> update".  But
> > after some local testing we found a few bugs we cannot easily
> resolve.  I
> > already pushed those changes to the Bioconductor repository to check out
> whether
> > it would go smoothly through the continuous integration system of
> Bioconductor.
> > 
> > I think reverting makes sense, but if that's not an option I'll
> reconsider our
> > options.
> > 
> > Kind regards,
> > Roel Janssen
> > 
> > 
> > On Mon, 2020-03-02 at 19:13 +, Turaga, Nitesh wrote:
> >> I suggest you go forward with the version numbering. 
> >> 
> >> 1.99.0 --> 1.99.1 
> >> 
> >> At the next release your package will have 2.0.0. Take a look at the
> version
> >> numbering document  
> >> http://bioconductor.org/developers/how-to/version-numbering/.
> >> 
> >> Make the changes you need to and go to version number 1.99.1. This is
> the most
> >> straightforward way to deal with the problem at hand.
> >> 
> >> Best,
> >> 
> >> Nitesh 
> >> 
> >>> On Mar 2, 2020, at 2:08 PM, Roel Janssen  wrote:
> >>> 
> >>> Dear Turaga,
> >>> 
> >>> How do you suggest I do the equivalent of reverting a commit?
> >>> My package name is MutationalPatterns.
> >>> 
> >>> Kind regards,
> >>> Roel Janssen
> >>> 
> >>> 
> >>> On Mon, 2020-03-02 at 17:40 +, Turaga, Nitesh wrote:
>  Hi Roel,
>  
>  You cannot revert on the Git Bioconductor repo.
>  
>  What is your package name? 
>  
> > On Mar 2, 2020, at 10:51 AM, Roel Janssen  wrote:
> > 
> > Dear Bioconductor developers,
> > 
> > I'd like to revert the changes I made on the development branch
> > ("master" in Git), but a pre-receive hook that checks version
> numbers
> > prevents me from reverting the change:
> > 
> > remote: Error: Illegal version bump from '1.99.0' to '1.13.0'
> > 
> > The commit I am trying to revert bumps the version number from
> '1.13.0'
> > to '1.99.0'.  What should I do now?
> > 
> > Kind regards,
> > Roel Janssen
> >> 
> >> 
> >> 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.
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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

Re: [Bioc-devel] Reverting on the 'master' branch

[Martin Morgan]

Once a version has been made 'public', it's not possible to go backward -- R 
will say 'hey, you've got version 1.99.0 installed, so that's more recent than 
1.13.0, so I won't update it'. So you're stuck with the version going forward.

Martin

On 3/3/20, 10:14 AM, "Bioc-devel on behalf of Turaga, Nitesh" 
 
wrote:

Hi Roel,

I think at this point it makes sense to move forward. It is more trouble 
than it's worth to do "hard resets" and then edit version numbers manually. 

Or another thing you could do is, roll out some big changes before the next 
release ;) 

Best,

Nitesh 

> On Mar 2, 2020, at 5:09 PM, Roel Janssen  wrote:
> 
> Dear Nitesh,
> 
> Thanks for the quick replies.  And sorry for mixing your first and last 
name up.
> :)
> 
> Well, we'd like to reserve 2.0.0 of our package for a "big feature 
update".  But
> after some local testing we found a few bugs we cannot easily resolve.  I
> already pushed those changes to the Bioconductor repository to check out 
whether
> it would go smoothly through the continuous integration system of 
Bioconductor.
> 
> I think reverting makes sense, but if that's not an option I'll 
reconsider our
> options.
> 
> Kind regards,
> Roel Janssen
> 
> 
> On Mon, 2020-03-02 at 19:13 +, Turaga, Nitesh wrote:
>> I suggest you go forward with the version numbering. 
>> 
>> 1.99.0 --> 1.99.1 
>> 
>> At the next release your package will have 2.0.0. Take a look at the 
version
>> numbering document  
>> http://bioconductor.org/developers/how-to/version-numbering/.
>> 
>> Make the changes you need to and go to version number 1.99.1. This is 
the most
>> straightforward way to deal with the problem at hand.
>> 
>> Best,
>> 
>> Nitesh 
>> 
>>> On Mar 2, 2020, at 2:08 PM, Roel Janssen  wrote:
>>> 
>>> Dear Turaga,
>>> 
>>> How do you suggest I do the equivalent of reverting a commit?
>>> My package name is MutationalPatterns.
>>> 
>>> Kind regards,
>>> Roel Janssen
>>> 
>>> 
>>> On Mon, 2020-03-02 at 17:40 +, Turaga, Nitesh wrote:
 Hi Roel,
 
 You cannot revert on the Git Bioconductor repo.
 
 What is your package name? 
 
> On Mar 2, 2020, at 10:51 AM, Roel Janssen  wrote:
> 
> Dear Bioconductor developers,
> 
> I'd like to revert the changes I made on the development branch
> ("master" in Git), but a pre-receive hook that checks version numbers
> prevents me from reverting the change:
> 
> remote: Error: Illegal version bump from '1.99.0' to '1.13.0'
> 
> The commit I am trying to revert bumps the version number from 
'1.13.0'
> to '1.99.0'.  What should I do now?
> 
> Kind regards,
> Roel Janssen
>> 
>> 
>> 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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

Re: [Bioc-devel] Reverting on the 'master' branch

[Turaga, Nitesh]

Hi Roel,

I think at this point it makes sense to move forward. It is more trouble than 
it's worth to do "hard resets" and then edit version numbers manually. 

Or another thing you could do is, roll out some big changes before the next 
release ;) 

Best,

Nitesh 

> On Mar 2, 2020, at 5:09 PM, Roel Janssen  wrote:
> 
> Dear Nitesh,
> 
> Thanks for the quick replies.  And sorry for mixing your first and last name 
> up.
> :)
> 
> Well, we'd like to reserve 2.0.0 of our package for a "big feature update".  
> But
> after some local testing we found a few bugs we cannot easily resolve.  I
> already pushed those changes to the Bioconductor repository to check out 
> whether
> it would go smoothly through the continuous integration system of 
> Bioconductor.
> 
> I think reverting makes sense, but if that's not an option I'll reconsider our
> options.
> 
> Kind regards,
> Roel Janssen
> 
> 
> On Mon, 2020-03-02 at 19:13 +, Turaga, Nitesh wrote:
>> I suggest you go forward with the version numbering. 
>> 
>> 1.99.0 --> 1.99.1 
>> 
>> At the next release your package will have 2.0.0. Take a look at the version
>> numbering document  
>> http://bioconductor.org/developers/how-to/version-numbering/.
>> 
>> Make the changes you need to and go to version number 1.99.1. This is the 
>> most
>> straightforward way to deal with the problem at hand.
>> 
>> Best,
>> 
>> Nitesh 
>> 
>>> On Mar 2, 2020, at 2:08 PM, Roel Janssen  wrote:
>>> 
>>> Dear Turaga,
>>> 
>>> How do you suggest I do the equivalent of reverting a commit?
>>> My package name is MutationalPatterns.
>>> 
>>> Kind regards,
>>> Roel Janssen
>>> 
>>> 
>>> On Mon, 2020-03-02 at 17:40 +, Turaga, Nitesh wrote:
 Hi Roel,
 
 You cannot revert on the Git Bioconductor repo.
 
 What is your package name? 
 
> On Mar 2, 2020, at 10:51 AM, Roel Janssen  wrote:
> 
> Dear Bioconductor developers,
> 
> I'd like to revert the changes I made on the development branch
> ("master" in Git), but a pre-receive hook that checks version numbers
> prevents me from reverting the change:
> 
> remote: Error: Illegal version bump from '1.99.0' to '1.13.0'
> 
> The commit I am trying to revert bumps the version number from '1.13.0'
> to '1.99.0'.  What should I do now?
> 
> Kind regards,
> Roel Janssen
>> 
>> 
>> 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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Rd] survival bug?

[Therneau, Terry M., Ph.D. via R-devel]

My latest submission of survival3.1-10 to CRAN fails  a check, but only on 
windows, which 
I don't use.
How do I track this down?
The test in question works fine on my Linux box.

Terry



[[alternative HTML version deleted]]

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

[Bioc-devel] Bioc2020: TODAY March 3rd is the last day to submit proposals for workshops/talks/posters

[Shepherd, Lori]

Reminder: TODAY March 3rd is the last day to submit proposals for Bioc2020 
workshops/talks/posters! http://bioc2020.bioconductor.org/call-for-abstracts



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

Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

[Shepherd, Lori]

It can take up to 24 from a push to be reflected on the build report.

For release 3.10 (RELEASE_3_10  branch)  we see a version number of 1.2.0
http://bioconductor.org/checkResults/release/bioc-LATEST/bigPint/
and
For devel 3.11 (master branch)  we see a version number of 1.3.1  as well
http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/

The landing page http://bioconductor.org/packages/3.11/bioc/html/bigPint.html  
will only be updated on a successful build/check of the package so we don't 
propagate broken packages to users. If the fixes did not allow for a clean 
build and check it would not be reflected.

Also remember that in order for a change to propagate you need a valid version 
bump.  So your release version 1.2.0  in order to take effect would have needed 
to be 1.2.1.  And for devel master branch you would need a version of 1.3.2.

Never apologize for asking questions.  We are here to help.  And we appreciate 
that you are taking the time to fix the package and learn how to push the 
changes up correct.


I'll answer your specific questions below:

Firstly make sure your   git remotes are set up correctly  where origin is your 
github repository and upstream is pointing to the bioconductor repositories 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

origin  (your github)
origin  (your github)
upstream g...@git.bioconductor.org:packages/bigPint.git (fetch)
upstream g...@git.bioconductor.org:packages/bigPint.git (push)

1) Is it acceptable for me to push what is on my GitHub master branch (1.3.1) 
to the development branch of Bioconductor?
Yes. however you will want to bump the version number in the DESCRIPTION to 
1.3.2 because we have version 1.3.1 on our builders as indicated  
http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/.  This page 
reflects 1.3.0 because 1.3.1 has not built without ERROR and we would not 
propagate broken packages to users  
http://bioconductor.org/packages/3.11/bioc/html/bigPint.html.

2) Is it acceptable for me to likewise push what is on my GitHub master branch 
(1.3.1) to the release branch of Bioconductor? I am assuming I am only supposed 
to push the "cherry-pick" commits that resolve what had been causing an error 
originally? This may be difficult for me as I have since added many more 
changes to the master branch on GitHub after resolving that release error.
Yes although not recommended but we would rather have a working package than 
one ERRORing so if you don't think you can cherry-pick than yes.  The best 
option for that would be to checkout the RELEASE_3_10 branch and do a  git 
merge master.  You will have to change the version number in the DESCRIPTION to 
be consistent with release version numbers.  (1.2.1) AFTER the merge.

3) Is it possible to ask if there is anything else identifiably "out of line" 
with my setup (on my GitHub master, development branch, or release branch)? I 
am sure that once I complete this process successfully I will have be better 
positioned to critically think of what is happening - but right now I worry 
that due to my earlier mistakes, something may be "off" with my setup that will 
make it difficult for me to successfully follow any set of instructions.
I think you were on the right track so no further comments.
Some helpful hints :

  1.  git fetch --all will fetch all branches from your origin github and the 
upstream bioconductor location (this will be important to do after the next 
release in april to get the next RELEASE_3_11 branch)
  2.  it is always a good idea to do a   git pull upstream (branch name)  to 
pull any changes we have made. occasionally if we made an infrastructure change 
bioconductor will apply patches.  We also do the version bump changes at 
release time. So for your master devel branch   git pull upstream master  (git 
pull upstream RELEASE_3_10  for the current release)
  3.  If you do git merge  read the out message carefully and make sure there 
are no conflicts.  Conflicts means there is code that was changes in both files 
(locally and on the branch you want to merge)  so you will have to check the 
file to make sure you don't include merge conflicts -   The code conflicts are 
indicated with  >  and  <.  you delete those and keep the changes 
you want to commit.  Then add and commit like normal and git should give you 
messages about resolving conflicts.

Hope this helps.  Let me know if you run into any further trouble.

Cheers



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: L Rutter 
Sent: Tuesday, March 3, 2020 5:55 AM
To: Shepherd, Lori 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

Dear Lori:

Thank you for this helpful advice. I did successfully now manage to change my 
keys and name on the 

Re: [Bioc-devel] help: Adding a new branch with latest R version to package repository

[Shepherd, Lori]

 Additional branches are not allowed on our git.bioconductor.org  version (only 
master and the next RELEASE_X_Y)  and you will not be able to push up to 
Bioconductor upstream.  You can however add any additional branches you would 
like to your github repository.

Cheers,


Lori Shepherd

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 Selcen Ar� 

Sent: Tuesday, March 3, 2020 6:18 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] help: Adding a new branch with latest R version to 
package repository

Hi,

We try to publish a paper that based on ceRNAnetsim

package
(i am also developer of it) in development version of Bioconductor. But
actually reviewers want to test our result via this package. Unfortunately,
they could't because of version inconsistency between package and latest R
version.


Is it possible adding new branch to github repository for testing our
results via package? I mean, If we add a new branch to repository that
depends latest R version (3.6.2), will it cause a problem for Bioconductor
community?



Best,

Selcen

[[alternative HTML version deleted]]

___
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.
[[alternative HTML version deleted]]

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

[Bioc-devel] help: Adding a new branch with latest R version to package repository

[Selcen Arı]

Hi,

We try to publish a paper that based on ceRNAnetsim

package
(i am also developer of it) in development version of Bioconductor. But
actually reviewers want to test our result via this package. Unfortunately,
they could't because of version inconsistency between package and latest R
version.


Is it possible adding new branch to github repository for testing our
results via package? I mean, If we add a new branch to repository that
depends latest R version (3.6.2), will it cause a problem for Bioconductor
community?



Best,

Selcen

[[alternative HTML version deleted]]

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

Re: [Rd] dput()

[Martin Maechler]

> Martin Maechler 
> on Mon, 2 Mar 2020 15:36:51 +0100 writes:

> Duncan Murdoch 
> on Mon, 2 Mar 2020 04:43:53 -0500 writes:

>> On 02/03/2020 3:24 a.m., Martin Maechler wrote:
 robin hankin
 on Sun, 1 Mar 2020 09:26:24 +1300 writes:
>>> 
>>> >  Thanks guys, I guess I should have referred to FAQ 7.31
>>> > (which I am indeed very familiar with) to avoid
>>> > misunderstanding.  I have always used dput() to clarify
>>> > 7.31-type issues.
>>> 
>>> > The description in ?dput implies [to me at any rate] that
>>> > there will be no floating-point roundoff in its output.  I
>>> > hadn't realised that 'deparsing' as discussed in dput.Rd
>>> > includes precision roundoff issues.
>>> 
>>> > I guess the question I should have asked is close to
>>> > Ben's: "How to force dput() to return an exact
>>> > representation of a floating point number?".  Duncan's
>>> > reply is the insight I was missing: exact decimal
>>> > representation of a double might not be possible (this had
>>> > not occurred to me).  Also, Duncan's suggestion of control
>>> > = c("all", "hexNumeric") looks good and I will experiment
>>> > with this.
>>> 
>>> This was not Duncan's suggestion but rather  Duncan's *citation* :
>>> Note that he used  "  " !
>>> 
>>> The citation is from  ?deparseOpts  (to which one is pointed when 
reading ?dput),
>>> 
>>> but unfortunately many people nowadays have stopped reading texts
>>> that are longer than a tweet... ;-)
>>> 
>>> ... and indeed,  ?dput  and  ?deparse  use'control = "all"'
>>> instead of   c("all", "hexNumeric")  when talking about getting
>>> close to an inverse of parse()
>>> 
>>> As a matter of fact,  within R Core we had discussed this, many
>>> moons ago and actually had more or less decided to make "all"
>>> to *include* "digits17".
>>> 
>>> "digits17" is  "almost always" (I'm sorry I cannot quantify the
>>> 'almost' here) sufficient ... and is obviously conflicting with
>>> using hexadecimals instead of digits.
>>> 
>>> For R 4.0.0, I think we should finally consider doing something
>>> here :
>>> 
>>> 1) define "all" to include "digits17"
>>> so new "all" is current  c("all", "digits17")
>>> {in a way such that c("all", "hexNumeric") implicitly removes
>>> "digits17" (as it's in contradiction with "hexNumeric").
>>> 
>>> 2) add a new option  "AllHex" := c("all", "hexNumeric"),
>>> (Note the capital "A":  such that  match.arg()-like abbreviation
>>> of .deparseOpts() arguments remain possible and notably "all"
>>> does not suddenly become ambiguous)
>>> 
>>> Of course, '1)' is well possible without '2)',
>>> but '2)'  would allow to use  dput(*, control = "All")
>>> which is somewhat easier to readers & writers.

>> I think 1) is a good idea, and adding something with the meaning of 
>> AllHex seems useful:  but that's not a name I'd choose, since it's not 
>> consistent with the other names (which are almost all camelCase).  I'd 
>> choose something like "exact" (even though it isn't :-).

> Thank you -- you are right;
> all "AllHex" is too non-orthodox and hence a pain for people to
> get right, remember, etc.

> In light of  Steven Dirkse's reply (and other much older e-mails
> by others I remember only vaguely), it seems we still need to
> find an example (with numbers) where it is not exact  ...
> which makes  "exact" even more appropriate.

> Martin

I've now committed these two proposals, using "exact" -- to
R-devel (i.e., for R 4.0.0).

(wanted in one svn commit, but accidentally needed 2: svn r77891 + ...2).

Martin


>>> > On Sun, Mar 1, 2020 at 6:22 AM Duncan Murdoch
>>> >  wrote:
>>> >>
>>> >> On 29/02/2020 4:19 a.m., Ben Bolker wrote:
>>> >> >
>>> >> > I think Robin knows about FAQ 7.31/floating point
>>> >> (author of > 'Brobdingnag', among other numerical
>>> >> packages).  I agree that this is > surprising (to me).
>>> >> >
>>> >> > To reframe this question: is there way to get an
>>> >> *exact* ASCII > representation of a numeric value (i.e.,
>>> >> guaranteeing the restored value > is identical() to the
>>> >> original) ?
>>> >> >
>>> >> > .deparseOpts has
>>> >> >
>>> >> > ‘"digits17"’: Real and finite complex numbers are
>>> >> output using > format ‘"%.17g"’ which may give more
>>> >> precision than the > default (but the output will depend
>>> >> on the platform and there > may be loss of precision when
>>> >> read back).
>>> >> >
>>> >> > ... but this still doesn't guarantee that all precision
>>> >> is kept.
>>> >>
>>> >> "Using control = c("all", "hexNumeric") comes closest to
>>> >> making deparse() an inverse of parse(), as 

Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

[L Rutter]

Dear Lori:

Thank you for this helpful advice. I did successfully now manage to change
my keys and name on the git.credentials app you suggested on February 25.

At that time, my development version was building but my release version
was failing. So, I followed the instructions in the link you provided on
February 3 (
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/)
to update my release version. I was able to also follow the "Sync existing
repositories" tab at the beginning of the guideline.

After waiting for the updates, when I checked into my package (bigPint), I
noticed now both the development (
https://bioconductor.org/packages/devel/bioc/html/bigPint.html) and release
(https://bioconductor.org/packages/release/bioc/html/bigPint.html) version
are not building. I was surprised because I did not think I was making any
changes to the development version through these instructions. I also
notice my development version is 1.3.0, my release version is 1.2.0, and my
GitHub master branch (
https://github.com/lindsayrutter/bigPint/blob/master/DESCRIPTION) is
version 1.3.1. It also seems that the version on my local computer reversed
to 1.2.0.

I tentatively plan to:

1) Clone my GitHub master branch (version 1.3.1) back to my local computer
(to make sure I do not lose many recent changes I have made to my package).
2) Try to push my most current version (1.3.1) to the development branch of
Bioconductor.
3) Try to push changes to the release branch of Bioconductor.

I am pretty stuck even to the point where it is hard for me to formulate
questions but below are a few questions that might help me identify the
point of confusion:
1) Is it acceptable for me to push what is on my GitHub master branch
(1.3.1) to the development branch of Bioconductor?
2) Is it acceptable for me to likewise push what is on my GitHub master
branch (1.3.1) to the release branch of Bioconductor? I am assuming I am
only supposed to push the "cherry-pick" commits that resolve what had been
causing an error originally? This may be difficult for me as I have since
added many more changes to the master branch on GitHub after resolving that
release error.
3) Is it possible to ask if there is anything else identifiably "out of
line" with my setup (on my GitHub master, development branch, or release
branch)? I am sure that once I complete this process successfully I will
have be better positioned to critically think of what is happening - but
right now I worry that due to my earlier mistakes, something may be "off"
with my setup that will make it difficult for me to successfully follow any
set of instructions.

I apologize for reaching out about this headache of an issue now. I am just
concerned I may not be able to resolve this in a timely manner with my
current scope of knowledge.

Sincerely,
Lindsay


2020年2月25日(火) 21:14 Shepherd, Lori :

> Thank you for reaching out.   Have you tried checking your keys and
> changing your name on the git.credentials app?
>
> https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* L Rutter 
> *Sent:* Tuesday, February 25, 2020 1:55 AM
> *To:* Shepherd, Lori 
> *Cc:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
>
> Dear Lori:
>
> Thanks for the suggestions. I tried to follow the linked instructions on
> February 4 and February 9, but was unsuccessful both times (i.e. did not
> see the changes pushed to the release branch). I tried following the
> instructions again today. I notice that when I issue the command:
>
> git merge upstream/master
>
> I receive the message:
>
> merge: upstream/master - not something we can merge
>
> So, I clicked on the "Sync existing repositories" tab and checked that the
> instructions there were working. After adding the upstream branch as
> follows:
>
> git remote add upstream g...@git.bioconductor.org:packages/bigPint.git
>
> When I then try to fetch all (git fetch --all), I receive the following
> error:
>
> Fetching origin
> Fetching upstream
> FATAL: R any packages/bigpint lrutter DENIED by fallthru
> (or you mis-spelled the reponame)
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
> error: Could not fetch upstream
>
> I changed my GitHub userName about one year ago from "lrutter" to
> "lindsayrutter". By doing "git remote -v", I can see that my origin
> branches are correctly at "lindsayrutter", but I am unable to see about my
> upstream branches on git.bioconductor. This is my output from "git remote
> -v":
>
> origin https://github.com/lindsayrutter/bigPint (fetch)
> origin https://github.com/lindsayrutter/bigPint (push)
> upstream