Re: [Bioc-devel] BiocGenerics request

2017-10-13 Thread Stephanie M. Gogarten 



On 10/13/17 3:32 PM, Hervé Pagès wrote:

Hi Stephanie,

Can you provide a little bit more context? Have you observed
conflicts between VariantAnnotation:::asVCF() and other asVCF()
functions defined elsewhere? Any reason why you can't use/import
VariantAnnotation:::asVCF() in your package?


I would prefer to leave VariantAnnotation in "Suggests" rather than 
"Imports" for performance reasons - it adds substantially to package 
load time, but will be used only rarely.




Alternatively, have you considered using/defining a coercion method
to VCF instead? That should work (and would be preferred) if you
don't need the extra arguments that an "asVCF" method would allow
you to support.


I will look into coercion methods; thanks for the suggestion! Can one 
define a coercion method where the "to" class is in a package that's not 
attached until the method is called (with requireNamespace)?


thanks,
Stephanie



The VCF class is defined in the VariantAnnotation package so it
would be weird to have the asVCF() generic in BiocGenerics.

Cheers,
H.


On 10/13/2017 01:55 PM, Stephanie M. Gogarten wrote:

Can we move the "asVCF" generic to BiocGenerics?

thanks,
Stephanie

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Re: [Bioc-devel] BiocGenerics request

2017-10-13 Thread Hervé Pagès 

Hi Stephanie,

Can you provide a little bit more context? Have you observed
conflicts between VariantAnnotation:::asVCF() and other asVCF()
functions defined elsewhere? Any reason why you can't use/import
VariantAnnotation:::asVCF() in your package?

Alternatively, have you considered using/defining a coercion method
to VCF instead? That should work (and would be preferred) if you
don't need the extra arguments that an "asVCF" method would allow
you to support.

The VCF class is defined in the VariantAnnotation package so it
would be weird to have the asVCF() generic in BiocGenerics.

Cheers,
H.


On 10/13/2017 01:55 PM, Stephanie M. Gogarten wrote:

Can we move the "asVCF" generic to BiocGenerics?

thanks,
Stephanie

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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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[Bioc-devel] BiocGenerics request

2017-10-13 Thread Stephanie M. Gogarten 

Can we move the "asVCF" generic to BiocGenerics?

thanks,
Stephanie

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Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

2017-10-13 Thread Matthew Myint 
Hi,

Thanks for the explanation! To clarify, the proper step after the
first time you helped restore my repository was to change the Github
branch (with duplicates) to master_deprecated, and switch in the
restored one as master?


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Regards
Matthew Myint
Life Science Undergraduate, Year 4
NUS


On Sat, Oct 14, 2017 at 2:49 AM, Turaga, Nitesh
 wrote:
> Hi Matthew,
>
> After closer inspection of “cytofkit”, it was this commit which caused the 
> duplicates.
>
> commit 4050c245d04af30705245f48931e677a6b4ae159
> Merge: 467f659 e6cef6c
> Author: Hervé Pagès 
> Date:   Wed Sep 20 13:19:45 2017 -0700
>
> Merge branch 'master' of git.bioconductor.org:packages/cytofkit
>
>
> It was a fetch and merge. So, it means that the GitHub repository hosted 
> (https://github.com/JinmiaoChenLab/cytofkit) did not deprecate the “master” 
> with duplicate commits by Sept 20th. This was not done till Sept 27th, based 
> on your GitHub 
> logs(https://github.com/JinmiaoChenLab/cytofkit/commits/master_deprecated).
>
>
> Best,
>
> Nitesh
>
>
>> On Oct 13, 2017, at 2:18 PM, Turaga, Nitesh  
>> wrote:
>>
>> Hi Matthew,
>>
>> I’ll have to fix your branch again, for this I need some time. Do not push 
>> any more changes.
>>
>> *When you pull from the upstream (g...@git.bioconductor.org), you are not 
>> supposed to get any duplicate commits.*
>>
>> If a merge is giving you duplicate commits, it means that you didn’t switch 
>> your master branch out. Or forgot to checkout the non-duplicate master.
>>
>> Best,
>>
>> Nitesh
>>
>>
>>
>>> On Oct 13, 2017, at 2:13 PM, Matthew Myint  
>>> wrote:
>>>
>>> Hi,
>>>
>>> After you helped me fix my repository, whenever I had updates I would use 
>>> the steps from 
>>> https://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/
>>>
>>> 1) note down what files needed to be updated in the repository
>>>
>>> 2) pull from upstream and merge to local branch 
>>> https://master.bioconductor.org/developers/how-to/git/pull-upstream-changes/
>>>
>>> 3) update the needed files in the repository and commit
>>>
>>> 4) push to both origin and upstream
>>>
>>> Also, just to clarify, the branch pushing I was referring to was the 
>>> “switcheroo” in the link 
>>> https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-6-abandon-changes.md
>>>
>>> Thanks and regards
>>> Matthew
>>> Sent from my iPhone
>>>
>>> On 13 Oct 2017, at 22:35, Turaga, Nitesh  
>>> wrote:
>>>
 Hi Matthew,

 I remember fixing this repository for you a few weeks ago.

 You cannot push branches to the Bioconductor repository, that is in the 
 FAQ, and documentation.

 Can you tell me what exactly are the steps you are trying that, you are 
 getting duplicate commits again?

 Best,

 Nitesh

> On Oct 13, 2017, at 3:39 AM, Matthew Myint  
> wrote:
>
> Hi,
>
> Recently I noticed in hindsight that my repository had duplicate
> commits, but I missed this during my normal package updating
> procedures.
>
> It was odd that the hook didn't reject these, so I made a clean branch
> from a commit before the problem occurred and cherry-picking commits
> to the present state. However, trying to push this to bioconductor git
> returned an error
>
>> remote: FATAL: + refs/heads/master packages/cytofkit c.hao DENIED by 
>> fallthru
>> remote: error: hook declined to update refs/heads/master
>> To git.bioconductor.org:packages/cytofkit.git
>> ! [remote rejected] master -> master (hook declined)
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org:packages/cytofkit.git'
>
> I've kept the original backed up, and here is the clean branch and
> back up branch for reference.
>
> Here is the link to my repo for additional reference
> https://github.com/JinmiaoChenLab/cytofkit
> https://github.com/JinmiaoChenLab/cytofkit/network (network display
> for easy visualisation)
>
> Sorry for the hassle
>
> Regards
> Matthew Myint
> Life Science Undergraduate, Year 4
> NUS
>
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 This email message

Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

2017-10-13 Thread Turaga, Nitesh 
Hi Matthew,

After closer inspection of “cytofkit”, it was this commit which caused the 
duplicates. 

commit 4050c245d04af30705245f48931e677a6b4ae159
Merge: 467f659 e6cef6c
Author: Hervé Pagès 
Date:   Wed Sep 20 13:19:45 2017 -0700

Merge branch 'master' of git.bioconductor.org:packages/cytofkit


It was a fetch and merge. So, it means that the GitHub repository hosted 
(https://github.com/JinmiaoChenLab/cytofkit) did not deprecate the “master” 
with duplicate commits by Sept 20th. This was not done till Sept 27th, based on 
your GitHub 
logs(https://github.com/JinmiaoChenLab/cytofkit/commits/master_deprecated). 


Best,

Nitesh 


> On Oct 13, 2017, at 2:18 PM, Turaga, Nitesh  
> wrote:
> 
> Hi Matthew,
> 
> I’ll have to fix your branch again, for this I need some time. Do not push 
> any more changes. 
> 
> *When you pull from the upstream (g...@git.bioconductor.org), you are not 
> supposed to get any duplicate commits.* 
> 
> If a merge is giving you duplicate commits, it means that you didn’t switch 
> your master branch out. Or forgot to checkout the non-duplicate master.
> 
> Best,
> 
> Nitesh 
> 
> 
> 
>> On Oct 13, 2017, at 2:13 PM, Matthew Myint  
>> wrote:
>> 
>> Hi,
>> 
>> After you helped me fix my repository, whenever I had updates I would use 
>> the steps from 
>> https://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/
>> 
>> 1) note down what files needed to be updated in the repository
>> 
>> 2) pull from upstream and merge to local branch 
>> https://master.bioconductor.org/developers/how-to/git/pull-upstream-changes/
>> 
>> 3) update the needed files in the repository and commit
>> 
>> 4) push to both origin and upstream
>> 
>> Also, just to clarify, the branch pushing I was referring to was the 
>> “switcheroo” in the link 
>> https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-6-abandon-changes.md
>> 
>> Thanks and regards
>> Matthew 
>> Sent from my iPhone
>> 
>> On 13 Oct 2017, at 22:35, Turaga, Nitesh  
>> wrote:
>> 
>>> Hi Matthew,
>>> 
>>> I remember fixing this repository for you a few weeks ago. 
>>> 
>>> You cannot push branches to the Bioconductor repository, that is in the 
>>> FAQ, and documentation.
>>> 
>>> Can you tell me what exactly are the steps you are trying that, you are 
>>> getting duplicate commits again?
>>> 
>>> Best,
>>> 
>>> Nitesh 
>>> 
 On Oct 13, 2017, at 3:39 AM, Matthew Myint  
 wrote:
 
 Hi,
 
 Recently I noticed in hindsight that my repository had duplicate
 commits, but I missed this during my normal package updating
 procedures.
 
 It was odd that the hook didn't reject these, so I made a clean branch
 from a commit before the problem occurred and cherry-picking commits
 to the present state. However, trying to push this to bioconductor git
 returned an error
 
> remote: FATAL: + refs/heads/master packages/cytofkit c.hao DENIED by 
> fallthru
> remote: error: hook declined to update refs/heads/master
> To git.bioconductor.org:packages/cytofkit.git
> ! [remote rejected] master -> master (hook declined)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/cytofkit.git'
 
 I've kept the original backed up, and here is the clean branch and
 back up branch for reference.
 
 Here is the link to my repo for additional reference
 https://github.com/JinmiaoChenLab/cytofkit
 https://github.com/JinmiaoChenLab/cytofkit/network (network display
 for easy visualisation)
 
 Sorry for the hassle
 
 Regards
 Matthew Myint
 Life Science Undergraduate, Year 4
 NUS
 
 ___
 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.
> 
> 
> 
> 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] EXTERNAL: Re: Cannot move 'xps' to GIT

2017-10-13 Thread cstrato 

Dear Martin,

Following your advice

   https://bioconductor.org/developers/how-to/git/maintain-github-bioc/

I did the following:

$ cd xps
$ git remote add upstream g...@git.bioconductor.org:packages/xps.git
$ git fetch upstream
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
From git.bioconductor.org:packages/xps
 * [new branch]  RELEASE_2_10 -> upstream/RELEASE_2_10
 * [new branch]  RELEASE_2_11 -> upstream/RELEASE_2_11
 * [new branch]  RELEASE_2_12 -> upstream/RELEASE_2_12
 * [new branch]  RELEASE_2_13 -> upstream/RELEASE_2_13
 * [new branch]  RELEASE_2_14 -> upstream/RELEASE_2_14
 * [new branch]  RELEASE_2_2 -> upstream/RELEASE_2_2
 * [new branch]  RELEASE_2_3 -> upstream/RELEASE_2_3
 * [new branch]  RELEASE_2_4 -> upstream/RELEASE_2_4
 * [new branch]  RELEASE_2_5 -> upstream/RELEASE_2_5
 * [new branch]  RELEASE_2_6 -> upstream/RELEASE_2_6
 * [new branch]  RELEASE_2_7 -> upstream/RELEASE_2_7
 * [new branch]  RELEASE_2_8 -> upstream/RELEASE_2_8
 * [new branch]  RELEASE_2_9 -> upstream/RELEASE_2_9
 * [new branch]  RELEASE_3_0 -> upstream/RELEASE_3_0
 * [new branch]  RELEASE_3_1 -> upstream/RELEASE_3_1
 * [new branch]  RELEASE_3_2 -> upstream/RELEASE_3_2
 * [new branch]  RELEASE_3_3 -> upstream/RELEASE_3_3
 * [new branch]  RELEASE_3_4 -> upstream/RELEASE_3_4
 * [new branch]  RELEASE_3_5 -> upstream/RELEASE_3_5
 * [new branch]  master -> upstream/master
$ git fetch upstream
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
$ git merge upstream/master
Already up-to-date.
$ git push origin master
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
Everything up-to-date
$ git remote -v
origin  g...@git.bioconductor.org:packages/xps (fetch)
origin  g...@git.bioconductor.org:packages/xps (push)
upstreamg...@git.bioconductor.org:packages/xps.git (fetch)
upstreamg...@git.bioconductor.org:packages/xps.git (push)
$ git checkout master
M   DESCRIPTION
M   NEWS
M   configure.in
Already on 'master'
Your branch is up-to-date with 'origin/master'.
$ git add -v DESCRIPTION
add 'DESCRIPTION'
$ git add -v NEWS
add 'NEWS'
$ git add -v configure.in
add 'configure.in'
$ git push origin master
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
Everything up-to-date
$ git push upstream master
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
Everything up-to-date


I hope that I could commit my changes and my development version on

   https://github.com/cstrato/xps

will be updated to 'xps_1.37.2'


(PS: my repository https://github.com/cstrato/xps is still empty)

Thank you very much for your help.
Best regards,
Christian


On 10/12/17 23:21, Martin Morgan wrote:

On 10/12/2017 04:13 PM, cstrato wrote:

Dear Martin,

Thank you for your informative reply.

1, My SSH public key that you mentioned is the correct one.



2, After following your advice and running

   ssh -v g...@git.bioconductor.org

I got:

OpenSSH_7.4p1, LibreSSL 2.5.0
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: Connecting to git.bioconductor.org [34.192.48.227] port 22.
debug1: Connection established.
debug1: identity file /Users/rabbitus/.ssh/id_rsa type 1
debug1: key_load_public: No such file or directory
...
debug1: Remote: PTY allocation disabled.
PTY allocation request failed on channel 0
hello c.stratowa, this is git@ip-172-30-0-33 running gitolite3 
v3.6.6-6-g7c8f0ab on git 2.13.0

...
bash: debug1:: command not found



3, Nevertheless, I could run:

   git clone g...@git.bioconductor.org:packages/xps

I got:
Cloning into 'xps'...
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
remote: Counting objects: 2757, done.
remote: Compressing objects: 100% (2741/2741), done.
remote: Total 2757 (delta 2077), reused 0 (delta 0)
Receiving objects: 100% (2757/2757), 5.62 MiB | 945.00 KiB/s, done.
Resolving deltas: 100% (2077/2077), done.
Checking connectivity... done.


 From the Bioconductor perspective, I think you are 'good to go', and 
you could follow, e.g.,


     http://bioconductor.org/developers/how-to/git/maintain-bioc-only/

to commit and push changes to the Bioconductor git repository. These 
changes would be incorporated into the nightly builds, etc., as before.


4, In 'https://github.com/settings/keys' I deleted the old SSH key and 
tried to add a new SSH key, where in 'Key' I copied once again my 
public 'id_rsa'. However, once again I received an email with the 
wrong key 'df:2d:78:4f:**'


This is the 'fingerprint' of the SSH public key, rather than the public 
key itself.



I do not understand why my correct key is not accepted.

According to 'https://caius.github.io/github_id/' my user id is:
cstrato is github user #32616897

My public key at 'https://github.com/cstrato.keys' is still empty.



I don't know the answer to this github question; maybe public keys are 
not displayed by default? At any rate it 'does not matter'; github 
allows you to clone via https + password,

Re: [Bioc-devel] EXTERNAL: Permission denied for ImmuneSpaceR repo

2017-10-13 Thread Turaga, Nitesh 
Please send me a list of commands you have tried. I’d like to see the outputs 
as well.

e.henrich has associated keys to it coming from www.github.com/immunespace.keys 

Best,

Nitesh 

> On Oct 13, 2017, at 1:36 PM, Immune Space  wrote:
> 
> Hi Nitesh,
> 
> We resubmitted the git transition form again on Wednesday, but we still don't 
> have access to ImmuneSpaceR repository in BIoc yet. Could you look into this?
> 
> Best,
> ImmuneSpace Team



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[Bioc-devel] Bioconductor 3.6 release: OrgDb and TxDb annotations

2017-10-13 Thread Van Twisk, Daniel 
Hello everyone,

The new OrgDb and TxDb packages are now available on the devel branch, e.g.,
https://bioconductor.org/packages/devel/data/annotation/html/org.Rn.eg.db.html
https://bioconductor.org/packages/devel/data/annotation/html/TxDb.Rnorvegicus.UCSC.rn5.refGene.html

Updated OrgDb packages:

Package   Version
org.Ag.eg.db   3.4.2
org.At.tair.db  3.4.2
org.Bt.eg.db3.4.2
org.Ce.eg.db   3.4.2
org.Cf.eg.db3.4.2
org.Dm.eg.db 3.4.2
org.Dr.eg.db3.4.2
org.EcK12.eg.db 3.4.2
org.EcSakai.eg.db   3.4.2
org.Gg.eg.db   3.4.2
org.Hs.eg.db   3.4.2
org.Mm.eg.db3.4.2
org.Mmu.eg.db  3.4.2
org.Pf.plasmo.db   3.4.2
org.Pt.eg.db3.4.2
org.Rn.eg.db   3.4.2
org.Sc.sgd.db  3.4.2
org.Ss.eg.db3.4.2
org.Xl.eg.db3.4.2


Updated TxDb packages:

Package  Version
TxDb.Btaurus.UCSC.bosTau8.refGene   3.4.2
TxDb.Celegans.UCSC.ce11.refGene   3.4.2
TxDb.Cfamiliaris.UCSC.canFam3.refGene 3.4.2
TxDb.Drerio.UCSC.danRer10.refGene   3.4.2
TxDb.Ggallus.UCSC.galGal4.refGene 3.4.2
TxDb.Ggallus.UCSC.galGal5.refGene 3.4.2
TxDb.Mmulatta.UCSC.rheMac3.refGene  3.4.2
TxDb.Mmulatta.UCSC.rheMac8.refGene  3.4.2
TxDb.Ptroglodytes.UCSC.panTro4.refGene  3.4.2
TxDb.Rnorvegicus.UCSC.rn5.refGene3.4.2


Please contact me if you encounter any problems with the new packages.

Best,

Dan



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[Bioc-devel] Bioconductor 3.6 release: update NEWS

2017-10-13 Thread Obenchain, Valerie 
Package maintainers,

If you haven't already, please update the NEWS files in your packages. This 
information will be included in the release announcement. The deadline for 
updating NEWS files is Tuesday, October 24:

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

Thanks.

Valerie


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Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

2017-10-13 Thread Turaga, Nitesh 
Hi Matthew,

I remember fixing this repository for you a few weeks ago. 

You cannot push branches to the Bioconductor repository, that is in the FAQ, 
and documentation.

Can you tell me what exactly are the steps you are trying that, you are getting 
duplicate commits again?

Best,

Nitesh 

> On Oct 13, 2017, at 3:39 AM, Matthew Myint  wrote:
> 
> Hi,
> 
> Recently I noticed in hindsight that my repository had duplicate
> commits, but I missed this during my normal package updating
> procedures.
> 
> It was odd that the hook didn't reject these, so I made a clean branch
> from a commit before the problem occurred and cherry-picking commits
> to the present state. However, trying to push this to bioconductor git
> returned an error
> 
>> remote: FATAL: + refs/heads/master packages/cytofkit c.hao DENIED by fallthru
>> remote: error: hook declined to update refs/heads/master
>> To git.bioconductor.org:packages/cytofkit.git
>> ! [remote rejected] master -> master (hook declined)
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org:packages/cytofkit.git'
> 
> I've kept the original backed up, and here is the clean branch and
> back up branch for reference.
> 
> Here is the link to my repo for additional reference
> https://github.com/JinmiaoChenLab/cytofkit
> https://github.com/JinmiaoChenLab/cytofkit/network (network display
> for easy visualisation)
> 
> Sorry for the hassle
> 
> Regards
> Matthew Myint
> Life Science Undergraduate, Year 4
> NUS
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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Re: [Bioc-devel] EXTERNAL: BioC 3.6: timeouts on veracruz1 (OS X)

2017-10-13 Thread Ramon Diaz-Uriarte 
Dear Martin,


On Fri, 13-October-2017, at 12:27:31, Martin Morgan 
 wrote:
> On 10/12/2017 07:08 AM, Ramon Diaz-Uriarte wrote:
>> Dear All,
>>
>> I have noticed that on the latest build report, a package I maintain,
>> OncoSimulR
>> (http://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/veracruz1-buildsrc.html),
>
> I wonder if it is this issue
>
>https://github.com/Bioconductor/BiocParallel/issues/67
>
> which would occur if your vignette has parallel code (using 'fork'
> processed via parallel::mclapply or indirectly via
> BiocParallel::MulticoreParam() / doParallel etc.)
>

Yes! I have both explicit calls to mclapply and implicit ones (functions
that call functions that call mclapply) in the vignette.

> If so then the best strategy is to wait for an upstream fix.
>

OK. Thank you.

Best,


R.

> Martin
>
>
>> has status timeout on veracruz1. Package building stalls during
>> creation of the vignette (that is not happening in the malbec1 ---linux---
>> build). I have noticed that this same pattern (timeout with build stopped 
>> when
>> creating the vignette in veracruz1 but not in malbec1) seems to affect
>> other packages
>> (http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html#show=timeout).
>>
>> Is there anything we should do? Just looking at the log I do not know how
>> to proceed.
>>
>>
>> Thanks,
>>
>>
>> R.
>>
>>
>>
>> --
>> Ramon Diaz-Uriarte
>> Department of Biochemistry, Lab B-25
>> Facultad de Medicina
>> Universidad Autónoma de Madrid
>> Arzobispo Morcillo, 4
>> 28029 Madrid
>> Spain
>>
>> Phone: +34-91-497-2412
>>
>> Email: rdia...@gmail.com
>> ramon.d...@iib.uam.es
>>
>> http://ligarto.org/rdiaz
>>
>> ___
>> 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.


--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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Re: [Bioc-devel] EXTERNAL: BioC 3.6: timeouts on veracruz1 (OS X)

2017-10-13 Thread Martin Morgan 

On 10/12/2017 07:08 AM, Ramon Diaz-Uriarte wrote:

Dear All,

I have noticed that on the latest build report, a package I maintain,
OncoSimulR
(http://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/veracruz1-buildsrc.html),


I wonder if it is this issue

  https://github.com/Bioconductor/BiocParallel/issues/67

which would occur if your vignette has parallel code (using 'fork' 
processed via parallel::mclapply or indirectly via 
BiocParallel::MulticoreParam() / doParallel etc.)


If so then the best strategy is to wait for an upstream fix.

Martin



has status timeout on veracruz1. Package building stalls during
creation of the vignette (that is not happening in the malbec1 ---linux---
build). I have noticed that this same pattern (timeout with build stopped when
creating the vignette in veracruz1 but not in malbec1) seems to affect
other packages
(http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html#show=timeout).

Is there anything we should do? Just looking at the log I do not know how
to proceed.


Thanks,


R.



--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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

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Re: [Bioc-devel] EXTERNAL: git push problem to bioconductor

2017-10-13 Thread Riccardo Romoli 

Hi, Martin,
now all works great.

Thanks for all.

All the best
Riccardo

On 13/10/17 10:49, Martin Morgan wrote:

On 10/13/2017 04:35 AM, Riccardo Romoli wrote:

Hi bioc-devel,

I am unable to push to g...@git.bioconductor.org to may package called 
"flagme".


Please try again -- your public key was associated with the incorrect 
svn identifier.


Martin



###
$ git push upstream master
X11 forwarding request failed on channel 0
FATAL: W any packages/flagme rromoli 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.
###

I followed instructions in the developer section and I have submitted 
my public key through the google form (more than 48h ago) and tried to 
link my git account, which also has that key, but with no luck.


###
$ git remote -v
origin    g...@github.com:rromoli/flagme.git (fetch)
origin    g...@github.com:rromoli/flagme.git (push)
upstream    g...@git.bioconductor.org:packages/flagme.git (fetch)
upstream    g...@git.bioconductor.org:packages/flagme.git (push)

$ ssh -T g...@git.bioconductor.org
...
R  packages/flagme
...
###

As final consideration I am able to push to my github account.

Hope you can help me to fix this issue.

All the best
Riccardo





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.


--
Riccardo Romoli, PhD
Mass Spectrometry Centre - CISM
University of Florence
Via Ugo Schiff 6, 50019 Sesto Fiorentino (FI), Italy
Phone: +39 055 4573783/2
email: riccardo.rom...@unifi.it
web site: www.cism.unifi.it

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Re: [Bioc-devel] EXTERNAL: git push problem to bioconductor

2017-10-13 Thread Martin Morgan 

On 10/13/2017 04:35 AM, Riccardo Romoli wrote:

Hi bioc-devel,

I am unable to push to g...@git.bioconductor.org to may package called 
"flagme".


Please try again -- your public key was associated with the incorrect 
svn identifier.


Martin



###
$ git push upstream master
X11 forwarding request failed on channel 0
FATAL: W any packages/flagme rromoli 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.
###

I followed instructions in the developer section and I have submitted my 
public key through the google form (more than 48h ago) and tried to link 
my git account, which also has that key, but with no luck.


###
$ git remote -v
origin    g...@github.com:rromoli/flagme.git (fetch)
origin    g...@github.com:rromoli/flagme.git (push)
upstream    g...@git.bioconductor.org:packages/flagme.git (fetch)
upstream    g...@git.bioconductor.org:packages/flagme.git (push)

$ ssh -T g...@git.bioconductor.org
...
R  packages/flagme
...
###

As final consideration I am able to push to my github account.

Hope you can help me to fix this issue.

All the best
Riccardo





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[Bioc-devel] git push problem to bioconductor

2017-10-13 Thread Riccardo Romoli 

Hi bioc-devel,

I am unable to push to g...@git.bioconductor.org to may package called 
"flagme".


###
$ git push upstream master
X11 forwarding request failed on channel 0
FATAL: W any packages/flagme rromoli 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.
###

I followed instructions in the developer section and I have submitted my 
public key through the google form (more than 48h ago) and tried to link 
my git account, which also has that key, but with no luck.


###
$ git remote -v
origing...@github.com:rromoli/flagme.git (fetch)
origing...@github.com:rromoli/flagme.git (push)
upstreamg...@git.bioconductor.org:packages/flagme.git (fetch)
upstreamg...@git.bioconductor.org:packages/flagme.git (push)

$ ssh -T g...@git.bioconductor.org
...
R  packages/flagme
...
###

As final consideration I am able to push to my github account.

Hope you can help me to fix this issue.

All the best
Riccardo


--
Riccardo Romoli, PhD
Mass Spectrometry Centre - CISM
University of Florence
Via Ugo Schiff 6, 50019 Sesto Fiorentino (FI), Italy
Phone: +39 055 4573783/2
email: riccardo.rom...@unifi.it
web site: www.cism.unifi.it

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[Bioc-devel] Git push error and duplicate commits

2017-10-13 Thread Matthew Myint 
Hi,

Recently I noticed in hindsight that my repository had duplicate
commits, but I missed this during my normal package updating
procedures.

It was odd that the hook didn't reject these, so I made a clean branch
from a commit before the problem occurred and cherry-picking commits
to the present state. However, trying to push this to bioconductor git
returned an error

> remote: FATAL: + refs/heads/master packages/cytofkit c.hao DENIED by fallthru
> remote: error: hook declined to update refs/heads/master
> To git.bioconductor.org:packages/cytofkit.git
>  ! [remote rejected] master -> master (hook declined)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/cytofkit.git'

I've kept the original backed up, and here is the clean branch and
back up branch for reference.

Here is the link to my repo for additional reference
https://github.com/JinmiaoChenLab/cytofkit
https://github.com/JinmiaoChenLab/cytofkit/network (network display
for easy visualisation)

Sorry for the hassle

Regards
Matthew Myint
Life Science Undergraduate, Year 4
NUS

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