Re: [Bioc-devel] Debugging not updated for coexnet package

[Juan David Henao Sanchez]

Hi.

Thanks for your help solving this issue. Could you please let me know how I
can fix the bug in the specific BioC version (3.11). How could I push my
current updated code into this specific version?

Thanks in advance.

I am looking forward to hearing from you soon.

Kind regards,

Juan

El mié., 13 may. 2020 a las 0:44, Hervé Pagès ()
escribió:

> Hi Juan,
>
> On 5/12/20 13:37, Juan David Henao Sanchez wrote:
> > Dear all.
> >
> > I received an error regarding my package coexnet when it is checking for
> > multiple platforms. I already fix the problem a couple of days ago and I
> > push the solution like:
> >
> > git push origin master
>
> Indeed the package is now green in Bioc devel (the master branch of your
> package):
>
>https://bioconductor.org/checkResults/3.12/bioc-LATEST/
>
> However, as I mentioned in the email I sent you off list, the package is
> still broken in BioC 3.11 (the current release):
>
>https://bioconductor.org/checkResults/3.11/bioc-LATEST/
>
> So you also need to fix the RELEASE_3_11 branch of your package.
>
> Best,
> H.
>
> >
> > However, I continue receiving the same error message and it is the same
> > previous version of my package.
> >
> > There is something additional I have to do to update my package?
> >
> > Thanks on advance,
> >
> > I look forward to hearing from you soon.
> >
> > Juan
> >
>
> --
> 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
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>


-- 
Juan David Henao
Magister in Bioinformatics
Universidad Nacional de Colombia

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Re: [Bioc-devel] Bad SSH key submissions

[Juan David Henao Sanchez]

Dear Nitesh

The command is:

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

and the message of error is:

Clonar en «coexnet»...
Permission denied (publickey).
fatal: Could not read from remote repository.

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

But I already have a public key as "j.henao". The result of git remote -v
is:

fatal: Not a git repository (or any of the parent directories): .git

Regards.


2017-10-09 16:13 GMT-05:00 Turaga, Nitesh <nitesh.tur...@roswellpark.org>:

> Please send a list of commands you are trying along with response.
>
>
> Also send the output of
>
> `git remote -v`
>
> Best,
>
> Nitesh
>
> > On Oct 6, 2017, at 6:45 PM, Juan David Henao Sanchez <
> judhena...@unal.edu.co> wrote:
> >
> > Hi.
> >
> > Thanks for taking the time to resolve my problems with the ssh
> connection.
> >
> > I'm writing to you because in the past days my ssh public key was
> recognized and I could clone my package from the git repository. But now I
> can't-do that, What is the possible reason? Should I do something else with
> the public key?
> >
> > Regards.
> >
> > 2017-10-05 11:12 GMT-05:00 Turaga, Nitesh <nitesh.tur...@roswellpark.org
> >:
> > Hi Maintainer,
> >
> > Your SVN ID is j.henao. If you want to submit SSH keys to access your
> package, you may ONLY submit with that SVN ID in the form. Please do not
> resubmit multiple times with the wrong key.
> >
> > You already have a key under “j.henao"
> >
> > Best,
> >
> > Nitesh
> >
> > 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.
> >
> >
> >
> > --
> > Juan David Henao
> > Maestría en Bioinformática
> > Universidad Nacional de Colombia
>
>
>
> 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.
>



-- 
Juan David Henao
Maestría en Bioinformática
Universidad Nacional de Colombia

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[Bioc-devel] BioC 3.6: CHECK report

[Juan David Henao Sanchez]

Hi.

I recently received an e-mail about a check error in the RUnit test in my
package "coexnet".

https://bioconductor.org/checkResults/3.6/bioc-LATEST/coexnet/malbec1-checksrc.html

I want to ask if my package was already in Bioconductor repository as
"development version", Why do I have this error whether in the past
Bioconductor check system didn't find any error?

Best regards.

-- 
Juan David Henao
Maestría en Bioinformática
Universidad Nacional de Colombia

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[Bioc-devel] git clone failed from git.bioconductor.org

[Juan David Henao Sanchez]

Hi,

I'm trying to clone my package from git.bioconductor.org as:

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

But, I recive the next message:

==
Clonar en «coexnet»...
Permission denied (publickey).
fatal: Could not read from remote repository.

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

I created a public key stored in /.ssh/id_rsa.pub and the private key in
the file id_rsa. Even, I created a config file with the next information:


host git-bioc
user juancholkovich
hostname git.bioconductor.org
port 22
identityfile ~/.ssh/id_rsa
=

But, the error persists.

How can I fix this problem?

Regards.


-- 
Juan David Henao
Maestría en Bioinformática
Universidad Nacional de Colombia

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Re: [Bioc-devel] How can I fix a vignette error in tokay1

[Juan David Henao Sanchez]

Hi.

The name of my package is coexnet.

2017-05-24 8:39 GMT-05:00 Obenchain, Valerie <
valerie.obench...@roswellpark.org>:

> What is the name of your package?
>
> Valerie
>
>
> On 05/23/2017 10:50 AM, Juan David Henao Sanchez wrote:
> > Hi,
> >
> > I get the next error when tokay1 runs my vignette.rmd file:
> >
> > LaTeX Error: File `framed.sty 'not found.
> >
> > How can I fix this error?
> >
> > Regards.
> >
>
>
>
> 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.
>



-- 
Juan David Henao
Maestría en Bioinformática
Universidad Nacional de Colombia

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[Bioc-devel] How can I fix a vignette error in tokay1

[Juan David Henao Sanchez]

Hi,

I get the next error when tokay1 runs my vignette.rmd file:

LaTeX Error: File `framed.sty 'not found.

How can I fix this error?

Regards.

-- 
Juan David Henao
Maestría en Bioinformática
Universidad Nacional de Colombia

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Re: [Bioc-devel] Question about R functions

[Juan David Henao Sanchez]

Hi Wang

You can create internal functions calling them as ".function", the point is
necessary to declare an internal function. Additionally, you can put all
your internal functions in the same R file and is not necessary create the
documentation for this functions.

Best regards.

Juan D. Henao

2017-03-30 15:02 GMT-05:00 Jing Wang :

> Hi,
>
>
>
> I have three functions (FA,FB,FC) in the package and all these functions
> need to call another function (FD). But I do not want other users to use
> the function FD and thus I do not want to create the document for FD in the
> R package.
>
>
>
> Could you please give me some suggestion how to do that?
>
>
>
> Thanks,
>
>
>
>
>
>
>
>
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-- 
Juan David Henao
Maestría en Bioinformática
Universidad Nacional de Colombia

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