Re: [Bioc-devel] Including a submodule in the main package repository

[Kasper Daniel Hansen]

My opinion: maintain two repos and pull/push between them. You would want
the ability to have them out of sync anyway.

Best,
Kasper

On Thu, Jun 14, 2018 at 1:16 AM, Thomas Sherman  wrote:

> Hi all,
>
> I'm a developer for the CoGAPS package (https://github.com/FertigLab/
> CoGAPS). I'm looking into ways to build our core C++ code as a standalone
> application and I would like to be able to maintain a single repository for
> the C++ code and pull that into both repositories for the R package and
> standalone application. It seems the easiest way to do this would be to
> have a git submodule in the R package repository that refers to the C++
> code. However, based on this comment (https://github.com/
> Bioconductor/Contributions/issues/459#issuecomment-376671397) it seems
> that is not the desired configuration.
>
> The best alternative I can think of would be to provide a separate library
> for our core algorithm and then link against that in both the R package and
> standalone version. In this case, we would have to provide instructions for
> downloading and building the library - which seems like more work for the
> end user than if everything was included with a submodule.
>
> I'm wondering if the first approach using a submodule would be possible,
> and if not, has anyone ran into this issue before and found a nice solution.
>
> Thanks,
> Tom
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

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

Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

[Pijush Das]

 Dear Shepherd, Lori ,


The DESCRIPTION file is already edited before in github repository but that
time I unable to make the
same changes in Bioconductor repository.


After following your instruction what I have done is given below.


The SSH key is already set in github and Bioconductor repository before. I
hope it will helpful for other.
May be some step are not necessary for such kind of changes, I do not know.
It is just my experiment.


Firstly what I have done that I have downloaded the all content from github
repository by using the command below

$ git clone g...@github.com:pijush1285/sigFeature.git

After that I add the description file and commit by using the following
command. This downloading and committing is not
required for this case because I have done the changes in github repository
previously manually. Though I have done it

$ git add DESCRIPTION
$ git commit -m "commit DSCRIPTION"

After that I have puss the Description file in github repository. Some kind
of warning is showing.

$ git push origin master
Warning: Permanently added the RSA host key for IP address '192.30.253.112'
to the list of known hosts.
Everything up-to-date



After that I Configure the “remotes” of my local git repository by using
the command given below.

$ git remote add upstream g...@git.bioconductor.org:packages/sigFeature.git


After that I try to puss upstream master by using the command below.

$ git push upstream master
The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be
established.
ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
Counting objects: 3, done.
Delta compression using up to 2 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 721 bytes | 721.00 KiB/s, done.
Total 3 (delta 2), reused 1 (delta 0)
To git.bioconductor.org:packages/sigFeature.git
   727af94..8d24bbb  master -> master


But the change is not showing in Bioconductor repository. Will it take time
?


Please inform me if I have taken some wrong step in updating/editing  the
DESCRIPTION
file in Biocnductor repository.


Thank you

regards
Pijush






On Tue, Jun 12, 2018 at 7:38 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> Please continue to reply all so that the response thread remains on the
> mailing list and that others may help as well.
>
>
>
> Are you able to see the results of
>
>
> ssh -T g...@git.bioconductor.org
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Pijush Das 
> *Sent:* Tuesday, June 12, 2018 8:50:04 AM
> *To:* Shepherd, Lori
>
> *Subject:* Re: [Bioc-devel] BioC 2018 poster / talk / scholarship /
> workshop application deadline May 17
>
>
> Dear  Shepherd, Lori
>
>
> After running the script " git remote -v " the I have found the output
> given below.
>
> PC MINGW64 ~/Desktop/BioconductorEdit/New folder/sigFeature (master)
> $ git remote -v
> origin  https://github.com/pijush1285/sigFeature (fetch)
> origin  https://github.com/pijush1285/sigFeature (push)
> upstreamg...@git.bioconductor.org:packages/sigFeature.git (fetch)
> upstreamg...@git.bioconductor.org:packages/sigFeature.git (push)
>
>
>
> After that I have tried to solve the problem and get a new fatal problem
> given below.
>
> PC MINGW64 ~/Desktop/BioconductorEdit/New folder/sigFeature (master)
> $ git push upstream master
> ssh: connect to host git.bioconductor.org port 22: Connection timed out
> fatal: Could not read from remote repository.
>
> Please make sure you have the correct access rights
> and the repository exists.
>
>
>
> Please help to edit DESCRIPTION file present in Bioconductor repository.
>
>
> Thank you
>
> regards
> Pijush
>
>
>
>
> On Tue, Jun 12, 2018 at 5:09 PM, Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
> What is the results of
>
>
> git remote -v
>
>
> Did you add an upstream remote pointing to your package as described in
> the link Mike sent:
>
> https://bioconductor.org/developers/how-to/git/new-package-workflow/
>
>
>
>
>
>
> 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 Pijush
> Das 
> *Sent:* Tuesday, June 12, 2018 3:48:04 AM
> *To:* Mike Smith
> *Cc:* bioc-devel
> *Subject:* Re: [Bioc-devel] BioC 2018 poster / talk / scholarship /
> workshop application deadline May 17
>
> Hello Mike,
>
>
>
> There is a little mistake in the DESCRIPTION file in my package named
> "sigFeature".
> In the Description portion inside the DESCRIPTION file, there are
> words " Bayesian
> T sta

[Bioc-devel] Build time of submitted package

[Anamaria Elek]

I have opened an issue (#770) for the submission of my package to
Bioconductor. The prevuious package build resulted in warrning, which I
attempted to fix and commited the changes to GitHub, dumping the version
number and initiating the new build. This was yesterday, and I still
haven't got the build report, so I was wandering if there is a problem with
my package or the build system itself.

As this is my first time submitting to Bioconductor, it may be that I am
missing something obvious here, and I appreaciate any info or advice you
may provide.

Anamaria Elek

[[alternative HTML version deleted]]

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

[Bioc-devel] BiocStickers license

[Laurent Gatto]

For those that have BiocStickers, what are your toughts on license and
requiring attributions, as they seem to limit reuse possibilities.

See

 https://github.com/Bioconductor/BiocStickers/issues/54

for details.

Best wishes,

Laurent

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

Re: [Bioc-devel] BiocParallel on Windows Never Ends

[Martin Morgan]

yes it would be useful to post this to R-devel as a 'using 
parallel::makeCluster() question, removing BiocParallel from the 
equation, where some general insight might be had...


Martin

On 06/13/2018 05:00 PM, Dario Strbenac wrote:

Good day,

I couldn't get a working param object. It never completes the command

param = bpstart(SnowParam(2, manager.hostname = "144.130.152.1", manager.port = 
2559))

I obtained the IP address by typing "My IP address" into Google and it gave me 
the address shown. I used netstat -an and

   Proto  Local Address  Foreign AddressState
   TCP127.0.0.1:2559 0.0.0.0:0  LISTENING

was one of the results displayed. I have reproduced this problem on another 
computer with Windows 10. I also tried

param = bpstart(SnowParam(2, manager.hostname = "127.0.0.1", manager.port = 
2559)) but it doesn't complete.

I was able to identify the problem is with the line

bpbackend(x) <- do.call(parallel::makeCluster, cargs)

So, to summarise,


cargs

$`spec`
[1] 2

$type
[1] "SOCK"

$snowlib
[1] "C:/Program Files/R/R-3.5.0/library/BiocParallel"

$master
[1] "127.0.0.1"

$port
[1] 2559


do.call(parallel::makeCluster, cargs) # Freezes.


Should I ask the question on R-devel because it doesn't appear to be specific 
to Bioconductor ?

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel




This email message may contain legally privileged and/or...{{dropped:2}}

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

Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

[Shepherd, Lori]

It can take up to 24 hours to appear on the landing page for the package. We do 
a daily build and depending on when you pushed changes to the package will 
determine if the change is picked up in todays build or tomorrows build.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Pijush Das 
Sent: Thursday, June 14, 2018 3:43:49 AM
To: Shepherd, Lori
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop 
application deadline May 17

Dear Shepherd, Lori ,


The DESCRIPTION file is already edited before in github repository but that 
time I unable to make the
same changes in Bioconductor repository.


After following your instruction what I have done is given below.


The SSH key is already set in github and Bioconductor repository before. I hope 
it will helpful for other.
May be some step are not necessary for such kind of changes, I do not know.
It is just my experiment.


Firstly what I have done that I have downloaded the all content from github 
repository by using the command below

$ git clone g...@github.com:pijush1285/sigFeature.git

After that I add the description file and commit by using the following 
command. This downloading and committing is not
required for this case because I have done the changes in github repository 
previously manually. Though I have done it

$ git add DESCRIPTION
$ git commit -m "commit DSCRIPTION"

After that I have puss the Description file in github repository. Some kind of 
warning is showing.

$ git push origin master
Warning: Permanently added the RSA host key for IP address '192.30.253.112' to 
the list of known hosts.
Everything up-to-date



After that I Configure the �remotes� of my local git repository by using the 
command given below.

$ git remote add upstream g...@git.bioconductor.org:packages/sigFeature.git


After that I try to puss upstream master by using the command below.

$ git push upstream master
The authenticity of host 'git.bioconductor.org 
(34.192.48.227)' can't be established.
ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 
'git.bioconductor.org,34.192.48.227' (ECDSA) to 
the list of known hosts.
Counting objects: 3, done.
Delta compression using up to 2 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 721 bytes | 721.00 KiB/s, done.
Total 3 (delta 2), reused 1 (delta 0)
To git.bioconductor.org:packages/sigFeature.git
   727af94..8d24bbb  master -> master


But the change is not showing in Bioconductor repository. Will it take time ?


Please inform me if I have taken some wrong step in updating/editing  the 
DESCRIPTION
file in Biocnductor repository.


Thank you

regards
Pijush






On Tue, Jun 12, 2018 at 7:38 PM, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

Please continue to reply all so that the response thread remains on the mailing 
list and that others may help as well.



Are you able to see the results of


ssh -T g...@git.bioconductor.org




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Pijush Das mailto:topij...@gmail.com>>
Sent: Tuesday, June 12, 2018 8:50:04 AM
To: Shepherd, Lori

Subject: Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop 
application deadline May 17


Dear  Shepherd, Lori


After running the script " git remote -v " the I have found the output given 
below.

PC MINGW64 ~/Desktop/BioconductorEdit/New folder/sigFeature (master)
$ git remote -v
origin  https://github.com/pijush1285/sigFeature (fetch)
origin  https://github.com/pijush1285/sigFeature (push)
upstreamg...@git.bioconductor.org:packages/sigFeature.git (fetch)
upstreamg...@git.bioconductor.org:packages/sigFeature.git (push)



After that I have tried to solve the problem and get a new fatal problem given 
below.

PC MINGW64 ~/Desktop/BioconductorEdit/New folder/sigFeature (master)
$ git push upstream master
ssh: connect to host git.bioconductor.org port 22: 
Connection timed out
fatal: Could not read from remote repository.

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



Please help to edit DESCRIPTION file present in Bioconductor repository.


Thank you

regards
Pijush




On Tue, Jun 12, 2018 at 5:09 PM, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

What is the results of


git remote -v


Did you add an upstream remote pointing to your package as described in the 
link Mike sent:

https://bioconductor.org/developers/how-to/git/new-p

Re: [Bioc-devel] Build time of submitted package

[Shepherd, Lori]

My apologies.  We made an update to the system and I think it happen to be when 
you tried to push changes.  I will manually kick off a build for your package 
and you should have the report shortly.   In the future you can also ask 
questions on the github issue for your package as the reviewer should respond.


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 Anamaria Elek 

Sent: Thursday, June 14, 2018 7:00:40 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Build time of submitted package

I have opened an issue (#770) for the submission of my package to
Bioconductor. The prevuious package build resulted in warrning, which I
attempted to fix and commited the changes to GitHub, dumping the version
number and initiating the new build. This was yesterday, and I still
haven't got the build report, so I was wandering if there is a problem with
my package or the build system itself.

As this is my first time submitting to Bioconductor, it may be that I am
missing something obvious here, and I appreaciate any info or advice you
may provide.

Anamaria Elek

[[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] New Package Submission Tracker

[Shepherd, Lori]

The Single Package Builder for new package submissions is experience some 
intermittent connectivity issues.  We are working on the issue and hope to have 
it resolved soon.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

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

[Bioc-devel] undo decrease of package version

[Matthias Lienhard]

Hi all,

I accidentally decreased the version of my package qsea in the master 
branch from 1.7.0 to 1.5.2, which I cannot undo now, because of checks 
of the pre-receive hook:


git push upstream master
X11 forwarding request failed on channel 0
Counting objects: 6, done.
Delta compression using up to 64 threads.
Compressing objects: 100% (6/6), done.
Writing objects: 100% (6/6), 642 bytes | 642.00 KiB/s, done.
Total 6 (delta 4), reused 0 (delta 0)
remote: Error: Illegal version bump from '1.5.2' to '1.7.1'. Check
remote: http://bioconductor.org/developers/how-to/version-numbering/
remote: for details
To git.bioconductor.org:packages/qsea.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 
'g...@git.bioconductor.org:packages/qsea.git'


What can I do to correct my mistake?

Best regards, Matthias

--
Matthias Lienhard
Max Planck Institute for Molecular Genetics
Department of Computational Biology
Bioinformatics Group
Ihnestr. 63 - 73
14195 Berlin
phone: +49 (0)30 8413-1675

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

Re: [Bioc-devel] BiocStickers license

[Levi Waldron]

I see no need to require attribution, which doesn't seem practical anyways
if printing a sticker design.

On Thu, Jun 14, 2018 at 1:10 PM Laurent Gatto  wrote:

>
> For those that have BiocStickers, what are your toughts on license and
> requiring attributions, as they seem to limit reuse possibilities.
>
> See
>
>  https://github.com/Bioconductor/BiocStickers/issues/54
>
> for details.
>
> Best wishes,
>
> Laurent
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Levi Waldron
http://www.waldronlab.io
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

[[alternative HTML version deleted]]

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

Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

[Turaga, Nitesh]

Hi Pijush

You also might want to check the RSS feeds 
http://bioconductor.org/developers/gitlog/ to see if your package has been 
updated.

Best,

Nitesh 



> On Jun 14, 2018, at 3:43 AM, Pijush Das  wrote:
> 
> Dear Shepherd, Lori ,
> 
> 
> The DESCRIPTION file is already edited before in github repository but that
> time I unable to make the
> same changes in Bioconductor repository.
> 
> 
> After following your instruction what I have done is given below.
> 
> 
> The SSH key is already set in github and Bioconductor repository before. I
> hope it will helpful for other.
> May be some step are not necessary for such kind of changes, I do not know.
> It is just my experiment.
> 
> 
> Firstly what I have done that I have downloaded the all content from github
> repository by using the command below
> 
> $ git clone g...@github.com:pijush1285/sigFeature.git
> 
> After that I add the description file and commit by using the following
> command. This downloading and committing is not
> required for this case because I have done the changes in github repository
> previously manually. Though I have done it
> 
> $ git add DESCRIPTION
> $ git commit -m "commit DSCRIPTION"
> 
> After that I have puss the Description file in github repository. Some kind
> of warning is showing.
> 
> $ git push origin master
> Warning: Permanently added the RSA host key for IP address '192.30.253.112'
> to the list of known hosts.
> Everything up-to-date
> 
> 
> 
> After that I Configure the “remotes” of my local git repository by using
> the command given below.
> 
> $ git remote add upstream g...@git.bioconductor.org:packages/sigFeature.git
> 
> 
> After that I try to puss upstream master by using the command below.
> 
> $ git push upstream master
> The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be
> established.
> ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q.
> Are you sure you want to continue connecting (yes/no)? yes
> Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
> the list of known hosts.
> Counting objects: 3, done.
> Delta compression using up to 2 threads.
> Compressing objects: 100% (3/3), done.
> Writing objects: 100% (3/3), 721 bytes | 721.00 KiB/s, done.
> Total 3 (delta 2), reused 1 (delta 0)
> To git.bioconductor.org:packages/sigFeature.git
>   727af94..8d24bbb  master -> master
> 
> 
> But the change is not showing in Bioconductor repository. Will it take time
> ?
> 
> 
> Please inform me if I have taken some wrong step in updating/editing  the
> DESCRIPTION
> file in Biocnductor repository.
> 
> 
> Thank you
> 
> regards
> Pijush
> 
> 
> 
> 
> 
> 
> On Tue, Jun 12, 2018 at 7:38 PM, Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
> 
>> Please continue to reply all so that the response thread remains on the
>> mailing list and that others may help as well.
>> 
>> 
>> 
>> Are you able to see the results of
>> 
>> 
>> ssh -T g...@git.bioconductor.org
>> 
>> 
>> 
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Cancer Institute
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> --
>> *From:* Pijush Das 
>> *Sent:* Tuesday, June 12, 2018 8:50:04 AM
>> *To:* Shepherd, Lori
>> 
>> *Subject:* Re: [Bioc-devel] BioC 2018 poster / talk / scholarship /
>> workshop application deadline May 17
>> 
>> 
>> Dear  Shepherd, Lori
>> 
>> 
>> After running the script " git remote -v " the I have found the output
>> given below.
>> 
>> PC MINGW64 ~/Desktop/BioconductorEdit/New folder/sigFeature (master)
>> $ git remote -v
>> origin  https://github.com/pijush1285/sigFeature (fetch)
>> origin  https://github.com/pijush1285/sigFeature (push)
>> upstreamg...@git.bioconductor.org:packages/sigFeature.git (fetch)
>> upstreamg...@git.bioconductor.org:packages/sigFeature.git (push)
>> 
>> 
>> 
>> After that I have tried to solve the problem and get a new fatal problem
>> given below.
>> 
>> PC MINGW64 ~/Desktop/BioconductorEdit/New folder/sigFeature (master)
>> $ git push upstream master
>> ssh: connect to host git.bioconductor.org port 22: Connection timed out
>> fatal: Could not read from remote repository.
>> 
>> Please make sure you have the correct access rights
>> and the repository exists.
>> 
>> 
>> 
>> Please help to edit DESCRIPTION file present in Bioconductor repository.
>> 
>> 
>> Thank you
>> 
>> regards
>> Pijush
>> 
>> 
>> 
>> 
>> On Tue, Jun 12, 2018 at 5:09 PM, Shepherd, Lori <
>> lori.sheph...@roswellpark.org> wrote:
>> 
>> What is the results of
>> 
>> 
>> git remote -v
>> 
>> 
>> Did you add an upstream remote pointing to your package as described in
>> the link Mike sent:
>> 
>> https://bioconductor.org/developers/how-to/git/new-package-workflow/
>> 
>> 
>> 
>> 
>> 
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Cancer Institute
>> 
>> Department of Biostatistics & Bioinformatics
>

Re: [Bioc-devel] undo decrease of package version

[Turaga, Nitesh]

Hi Matthais,

You can change your commit locally. Your version hasn’t been updated because 
the pre-receive hook has caught it. Just to further explain, “pre-receive” is 
before the the commit is received by the bioconductor server, so the version on 
the server is still correct and unchanged.

You would need to edit your version on your local repository. Simply change the 
version number to a correct one and you should be able to push. If you are 
particular about your version numbers, and don’t want any bad versions along 
the way then you may try to amend your commit

`git commit —amend` 

This works ONLY if the version bump was in most recent commit on your local 
branch.

Let me know if this helps. If you have any further questions reply to this 
thread.

Best,

Nitesh 

> On Jun 14, 2018, at 9:14 AM, Matthias Lienhard  wrote:
> 
> Hi all,
> 
> I accidentally decreased the version of my package qsea in the master branch 
> from 1.7.0 to 1.5.2, which I cannot undo now, because of checks of the 
> pre-receive hook:
> 
> git push upstream master
> X11 forwarding request failed on channel 0
> Counting objects: 6, done.
> Delta compression using up to 64 threads.
> Compressing objects: 100% (6/6), done.
> Writing objects: 100% (6/6), 642 bytes | 642.00 KiB/s, done.
> Total 6 (delta 4), reused 0 (delta 0)
> remote: Error: Illegal version bump from '1.5.2' to '1.7.1'. Check
> remote: http://bioconductor.org/developers/how-to/version-numbering/
> remote: for details
> To git.bioconductor.org:packages/qsea.git
>  ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/qsea.git'
> 
> What can I do to correct my mistake?
> 
> Best regards, Matthias
> 
> -- 
> Matthias Lienhard
> Max Planck Institute for Molecular Genetics
> Department of Computational Biology
> Bioinformatics Group
> Ihnestr. 63 - 73
> 14195 Berlin
> phone: +49 (0)30 8413-1675
> 
> ___
> 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

Re: [Bioc-devel] BiocStickers license

[Lorena Pantano]

I am ok to drop that part as well.

> On Jun 14, 2018, at 9:32 AM, Levi Waldron  wrote:
> 
> I see no need to require attribution, which doesn't seem practical anyways
> if printing a sticker design.
> 
> On Thu, Jun 14, 2018 at 1:10 PM Laurent Gatto  wrote:
> 
>> 
>> For those that have BiocStickers, what are your toughts on license and
>> requiring attributions, as they seem to limit reuse possibilities.
>> 
>> See
>> 
>> https://github.com/Bioconductor/BiocStickers/issues/54
>> 
>> for details.
>> 
>> Best wishes,
>> 
>> Laurent
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
> 
> -- 
> Levi Waldron
> http://www.waldronlab.io
> Assistant Professor of Biostatistics CUNY School of Public Health
> US: +1 646-364-9616   Skype:
> levi.waldron
> 
>   [[alternative HTML version deleted]]
> 
> ___
> 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] undo decrease of package version

[Turaga, Nitesh]

Hi Matthais,

You DESCRIPTION file is malformed which is why the pre-receive hook did not 
catch the version number. 


<<< HEAD
Version: 1.5.2
Date: 2018-06-12
===
Version: 1.7.0
Date: 2018-03-22
>>> 90a1811ecfe3bbc3d9594f32d54b006afb2d2ac5


This is from a “merge” and has to be corrected. Please check, 
http://bioconductor.org/developers/how-to/git/resolve-conflicts/.

Best,

Nitesh 

> On Jun 14, 2018, at 10:41 AM, Matthias Lienhard  
> wrote:
> 
> Hi Nitesh,
> 
> unfortunately the pre-receive hook did not caught the accidental decrease 
> from 1.7.0 to 1.5.2, but now prevents me from correcting it back to 1.7.1.
> I did more local commits trying to resolve the issue already in the mean 
> time, so I cannot try your suggestion.
> 
> Best, Matthias
> 
> On 06/14/18 15:29, Turaga, Nitesh wrote:
>> Hi Matthais,
>> 
>> You can change your commit locally. Your version hasn’t been updated because 
>> the pre-receive hook has caught it. Just to further explain, “pre-receive” 
>> is before the the commit is received by the bioconductor server, so the 
>> version on the server is still correct and unchanged.
>> 
>> You would need to edit your version on your local repository. Simply change 
>> the version number to a correct one and you should be able to push. If you 
>> are particular about your version numbers, and don’t want any bad versions 
>> along the way then you may try to amend your commit
>> 
>>  `git commit —amend`
>> 
>> This works ONLY if the version bump was in most recent commit on your local 
>> branch.
>> 
>> Let me know if this helps. If you have any further questions reply to this 
>> thread.
>> 
>> Best,
>> 
>> Nitesh
>> 
>>> On Jun 14, 2018, at 9:14 AM, Matthias Lienhard  
>>> wrote:
>>> 
>>> Hi all,
>>> 
>>> I accidentally decreased the version of my package qsea in the master 
>>> branch from 1.7.0 to 1.5.2, which I cannot undo now, because of checks of 
>>> the pre-receive hook:
>>> 
>>> git push upstream master
>>> X11 forwarding request failed on channel 0
>>> Counting objects: 6, done.
>>> Delta compression using up to 64 threads.
>>> Compressing objects: 100% (6/6), done.
>>> Writing objects: 100% (6/6), 642 bytes | 642.00 KiB/s, done.
>>> Total 6 (delta 4), reused 0 (delta 0)
>>> remote: Error: Illegal version bump from '1.5.2' to '1.7.1'. Check
>>> remote: http://bioconductor.org/developers/how-to/version-numbering/
>>> remote: for details
>>> To git.bioconductor.org:packages/qsea.git
>>>  ! [remote rejected] master -> master (pre-receive hook declined)
>>> error: failed to push some refs to 
>>> 'g...@git.bioconductor.org:packages/qsea.git'
>>> 
>>> What can I do to correct my mistake?
>>> 
>>> Best regards, Matthias
>>> 
>>> -- 
>>> Matthias Lienhard
>>> Max Planck Institute for Molecular Genetics
>>> Department of Computational Biology
>>> Bioinformatics Group
>>> Ihnestr. 63 - 73
>>> 14195 Berlin
>>> phone: +49 (0)30 8413-1675
>>> 
>>> ___
>>> 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.
> 
> 
> -- 
> Matthias Lienhard
> Max Planck Institute for Molecular Genetics
> Department of Computational Biology
> Bioinformatics Group
> Ihnestr. 63 - 73
> 14195 Berlin
> phone: +49 (0)30 8413-1675



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] mygene package - fixing build error

[Chunlei Wu]

Hello group,


  We recently pushed some changes to mygene package to fix the build 
error:


https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/mygene/malbec2-buildsrc.html


  The changes were pushed to the master, do we need to merge the 
changes to RELEASE_3_7 branch? Is this something will be done automatically or 
maybe manually by the BioC core team? We did not have to create all these 
RELEASE branches in the past, so I suspect that was created automatically. 
Please advise. Thanks.


Best,


Chunlei


P.S. this is the output from our local dev folder:

$ git remote -v
origin  g...@github.com:biothings/mygene.R.git (fetch)
origin  g...@github.com:biothings/mygene.R.git (push)
upstreamg...@git.bioconductor.org:packages/mygene.git (fetch)
upstreamg...@git.bioconductor.org:packages/mygene.git (push)






[[alternative HTML version deleted]]

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

Re: [Bioc-devel] mygene package - fixing build error

[Turaga, Nitesh]

Hi Chunlei,

You have to merge the changes into RELEASE_3_7 yourself and push. Please check 
the documentation on the website about how to push a fix to RELEASE_3_7 branch.


http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

We create the branch automatically during the release process every 6 months. 
But we don’t merge changes to them, that’s up to the maintainers.

You also need to bump the version on your RELEASE branch, check 
http://bioconductor.org/developers/how-to/version-numbering/.

Best,

Nitesh 


> On Jun 14, 2018, at 1:58 PM, Chunlei Wu  wrote:
> 
> Hello group,
> 
> 
>  We recently pushed some changes to mygene package to fix the build 
> error:
> 
> 
> https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/mygene/malbec2-buildsrc.html
> 
> 
>  The changes were pushed to the master, do we need to merge the 
> changes to RELEASE_3_7 branch? Is this something will be done automatically 
> or maybe manually by the BioC core team? We did not have to create all these 
> RELEASE branches in the past, so I suspect that was created automatically. 
> Please advise. Thanks.
> 
> 
> Best,
> 
> 
> Chunlei
> 
> 
> P.S. this is the output from our local dev folder:
> 
> $ git remote -v
> origin  g...@github.com:biothings/mygene.R.git (fetch)
> origin  g...@github.com:biothings/mygene.R.git (push)
> upstreamg...@git.bioconductor.org:packages/mygene.git (fetch)
> upstreamg...@git.bioconductor.org:packages/mygene.git (push)
> 
> 
> 
> 
> 
> 
>   [[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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] mygene package - fixing build error

[Chunlei Wu]

Thanks for the posted instructions. We have now "cherry-pick"ed bugfix from the 
master to the RELEASE_3_7 branch, also bumped the version from 1.16.0 to 
1.16.1. Hope the build server will soon pick it up and pass the build.


Chunlei



From: Turaga, Nitesh 
Sent: Thursday, June 14, 2018 11:49 AM
To: Chunlei Wu
Cc: bioc-devel@r-project.org; Cyrus Afrasiabi
Subject: Re: [Bioc-devel] mygene package - fixing build error

Hi Chunlei,

You have to merge the changes into RELEASE_3_7 yourself and push. Please check 
the documentation on the website about how to push a fix to RELEASE_3_7 branch.


http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

We create the branch automatically during the release process every 6 months. 
But we don�t merge changes to them, that�s up to the maintainers.

You also need to bump the version on your RELEASE branch, check 
http://bioconductor.org/developers/how-to/version-numbering/.

Best,

Nitesh


> On Jun 14, 2018, at 1:58 PM, Chunlei Wu  wrote:
>
> Hello group,
>
>
>  We recently pushed some changes to mygene package to fix the build 
> error:
>
>
> https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/mygene/malbec2-buildsrc.html
>
>
>  The changes were pushed to the master, do we need to merge the 
> changes to RELEASE_3_7 branch? Is this something will be done automatically 
> or maybe manually by the BioC core team? We did not have to create all these 
> RELEASE branches in the past, so I suspect that was created automatically. 
> Please advise. Thanks.
>
>
> Best,
>
>
> Chunlei
>
>
> P.S. this is the output from our local dev folder:
>
> $ git remote -v
> origin  g...@github.com:biothings/mygene.R.git (fetch)
> origin  g...@github.com:biothings/mygene.R.git (push)
> upstreamg...@git.bioconductor.org:packages/mygene.git (fetch)
> upstreamg...@git.bioconductor.org:packages/mygene.git (push)
>
>
>
>
>
>
>[[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