[Bioc-devel] Moving minfi classes definition to a lighter package

2021-03-01 Thread Carlos Ruiz
Dear Bioc developers,

I have been developing different packages to analyze DNA methylation. In
all of them, I have used minfi's class GenomicRatioSet to manage DNA
methylation data, in order to take profit of the features of
RangedSummarizedExperiment.

Although I am very happy with the potential of the class, importing its
definition from minfi, makes me add the package to imports. As minfi has a
high number of dependencies (129 in the current release), my packages end
up having hundreds of dependencies too. This is particularly problematic as
I do not use any of the other functions of minfi.

I am wondering whether it could be possible to move minfi's class (or at
least GenomicRatioSet) to a lighter package, so people developing packages
on DNA methylation could rely on this class without having to import the
whole minfi package and its dependencies.

Thank you very much,
-- 

Carlos Ruiz

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Re: [Bioc-devel] TIMEOUT on package MEAL

2018-04-20 Thread Carlos Ruiz
Hi Lori,

I made some changes to the MEAL vignettes and now MEAL successfully 
passes tests on Linux and Windows (build time: 1854 and 1613 seconds 
respectively). However, it still times out in OSX. Should I try to 
reduce the building time in merida2?

Thanks,
Carlos Ruiz

El 13/04/2018 a las 19:39, Shepherd, Lori escribió:
>
> It is by fluke that the windows did not time out... The 
> builders timeout occur at 2400 sec and you are right up against the 
> edge at 2145.4 seconds on windows.
>
>
> The build reports include an EllapsedTime  indication in the summary 
> section for each builder ...
>
>
> Your package does not meet the requirement (<2400 (40min!!)  and your 
> vignette needs to be altered to fit the time constraints of the builders.
>
>
> You should easily be able to test R CMD build on your system and log 
> the time to debug this issue. On linux there is the `time `  
> option.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ----
> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of 
> Carlos Ruiz <carlos.r...@isglobal.org>
> *Sent:* Friday, April 13, 2018 11:26:03 AM
> *To:* Turaga, Nitesh; Bioc-devel
> *Subject:* Re: [Bioc-devel] TIMEOUT on package MEAL
> Hi BiocDevel,
>
> Could you help me with this issue? The report is not very informative. I
> suspect that the vignettes are taking too long but I have two vignettes
> and I don't know which one is more problematic. I don't understand
> either why I have a timeout in OS and Linux but not in Windows.
>
> When I had to deal with warnings or errors, I was able to reproduce them
> in my computer and solve them. Is there any way to reproduce the timeouts?
>
> Thank you,
>
> Carlos Ruiz
>
>
> El 12/04/2018 a las 18:22, Turaga, Nitesh escribió:
> > Dear maintainer,
> >
> > I'd like to bring to your attention that the  your package is 
> getting a TIMEOUT 'R CMD build' on platforms in the devel version of 
> Bioconductor (i.e. BioC 3.7):
> >
> > 
> http://bioconductor.org/checkResults/devel/bioc-LATEST/MEAL/malbec2-install.html
> >
> > Would you mind taking a look at this? Don't hesitate to ask on the 
> bioc-devel mailing list if you have any question or need help.
> >
> > The package is failing on devel which is very problematic. If it is 
> not fixed in devel in a timely manner we would also consider this 
> package for potential deprecation in the next cycle.  The deadline for 
> passing R CMD build and check in devel is April 25.
> >
> > Thanks for your contribution to Bioconductor.
> >
> > Pleae be advised that Bioconductor has switched from svn to Git. 
> Some helpful
> > links can be found here:
> > https://bioconductor.org/developers/how-to/git/
> >
> > Best,
> >
> > Nitesh Turaga
> > Bioconductor Core Team
> >
> > This email message may contain legally privileged and/or 
> confidential information.  If you are not the intended recipient(s), 
> or the employee or agent responsible for the delivery of this message 
> to the intended recipient(s), you are hereby notified that any 
> disclosure, copying, distribution, or use of this email message is 
> prohibited.  If you have received this message in error, please notify 
> the sender immediately by e-mail and delete this email message from 
> your computer. Thank you.
>
> -- 
> Carlos Ruiz
> PhD Student
> ISGlobal
> Barcelona Institute for Global Health - Campus MAR
> Barcelona Biomedical Research Park (PRBB) (office 001)
> Doctor Aiguader, 88
> 08003 Barcelona, Spain
> Tel. +34 93 214 7309
> carlos.r...@isglobal.org
> www.isglobal.org <http://www.isglobal.org>
>
> This message is intended exclusively for its addressee and may contain
> information that is CONFIDENTIAL and protected by professional
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> that any dissemination, copy or disclosure of this communication is
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> please immediately notify us via e-mail and delete it.
>
> DATA PROTECTION. We inform you that your personal data, including your
> e-mail address and data included in your email correspondence, are
> included in the ISGlobal Foundation files. Your personal data will be
> used for the purpose of contacting you and sending information on the
> activities of the above foundations. You can exercise your rights of
>

Re: [Bioc-devel] TIMEOUT on package MEAL

2018-04-13 Thread Carlos Ruiz

Hi BiocDevel,

Could you help me with this issue? The report is not very informative. I 
suspect that the vignettes are taking too long but I have two vignettes 
and I don't know which one is more problematic. I don't understand 
either why I have a timeout in OS and Linux but not in Windows.


When I had to deal with warnings or errors, I was able to reproduce them 
in my computer and solve them. Is there any way to reproduce the timeouts?


Thank you,

Carlos Ruiz


El 12/04/2018 a las 18:22, Turaga, Nitesh escribió:

Dear maintainer,

I'd like to bring to your attention that the  your package is getting a TIMEOUT 
'R CMD build' on platforms in the devel version of Bioconductor (i.e. BioC 3.7):

http://bioconductor.org/checkResults/devel/bioc-LATEST/MEAL/malbec2-install.html

Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel 
mailing list if you have any question or need help.

The package is failing on devel which is very problematic. If it is not fixed 
in devel in a timely manner we would also consider this package for potential 
deprecation in the next cycle.  The deadline for passing R CMD build and check 
in devel is April 25.

Thanks for your contribution to Bioconductor.

Pleae be advised that Bioconductor has switched from svn to Git. Some helpful
links can be found here:
https://bioconductor.org/developers/how-to/git/

Best,

Nitesh Turaga
Bioconductor Core Team

This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.


--
Carlos Ruiz
PhD Student
ISGlobal
Barcelona Institute for Global Health - Campus MAR
Barcelona Biomedical Research Park (PRBB) (office 001)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 7309
carlos.r...@isglobal.org
www.isglobal.org

This message is intended exclusively for its addressee and may contain 
information that is CONFIDENTIAL and protected by professional 
privilege. If you are not the intended recipient you are hereby notified 
that any dissemination, copy or disclosure of this communication is 
strictly prohibited by law. If this message has been received in error, 
please immediately notify us via e-mail and delete it.


DATA PROTECTION. We inform you that your personal data, including your 
e-mail address and data included in your email correspondence, are 
included in the ISGlobal Foundation files. Your personal data will be 
used for the purpose of contacting you and sending information on the 
activities of the above foundations. You can exercise your rights of 
access, rectification, cancellation and opposition by contacting the 
following address: l...@isglobal.org. ISGlobal Privacy Policy at 
www.isglobal.org.




--


This message is intended exclusively for its addressee and may contain

information that is CONFIDENTIAL and protected by professional privilege. 
If

you are not the intended recipient you are hereby notified that any

dissemination, copy or disclosure of this communication is strictly 
prohibited
by law. If this message has been received in error, please 
immediately notify

us via e-mail and delete it.



DATA PROTECTION. We 
inform you that your personal data, including your
e-mail address and data 
included in your email correspondence, are included in
the ISGlobal 
Foundation files. Your personal data will be used for the purpose
of 
contacting you and sending information on the activities of the above


foundations. You can exercise your rights of access, rectification,

cancellation and opposition by contacting the following address: 
l...@isglobal.org <mailto:l...@isglobal.org>. ISGlobal
Privacy Policy at 
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CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente a
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vigente. Si ha recibido este mensaje por error, le rogamos lo 
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Re: [Bioc-devel] Bioconductor failing package MEAL

2017-09-18 Thread Carlos Ruiz

Hi,
It worked. Now I can make pushes.
Thanks,
Carlos

El 14/09/2017 a las 20:23, Turaga, Nitesh escribió:

Bioc-git server* (git.bioconductor.org).

Ignore the typo.


On Sep 14, 2017, at 2:20 PM, ni41435_ca <nitesh.tur...@roswellpark.org> wrote:

Hi Carlos

Your ID is standardized across all your packages now to “c.ruiz”. Your key is 
the one your submitted most recently

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQDEMdup9kYuv4KO5MO1lctLXl4Griu571wbbDZU+ueZHhtuEm2WBqWTC0Zp6V+rszWORQkDGcM2ym+pVMNapSbFFbCJPDG1kxXpJI+2
 …..

Please use that key to access all of your packages. You shouldn’t have to do 
anything more, please try to access the bioc-devel-git server, and let me know 
if you are able to successfully.

Best,

Nitesh



On Sep 14, 2017, at 1:30 PM, Carlos Ruiz <carlos.r...@isglobal.org> wrote:

Hi Nitesh,

I have checked my mail and I have 3 different SVN ids, one for each package I 
have submitted:

- r.carlos: MEAL
- c.ruiz-arenas: MultiDataSet
- c.ruiz: scoreInvHap

When I submitted MultiDataSet, I asked Bioc to consolidate my svn user. From 
then, I used c.ruiz-arenas for MEAL and MultiDataSet. Finally, for the next 
release, I got scoreInvHap accepted and I have now realized that I have another 
svn user. What can I do to solve it?

Thank you,

Carlos Ruiz




El jueves, 14 de septiembre de 2017, Turaga, Nitesh 
<nitesh.tur...@roswellpark.org> escribió:
Hi Carlos,

Do you by any chance have 2 separate SVN id’s?

1. c.ruiz
2. c.ruiz-arenas

Best,

Nitesh



On Sep 14, 2017, at 12:17 PM, Carlos Ruiz <carlos.r...@isglobal.org> wrote:

Hi,
Today I definitely was able to fetch from the Bioc git. However, I cannot push. 
Here, the commands and the error:


C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git push upstream master
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to the l
ist of known hosts.
FATAL: W any packages/MEAL c.ruiz 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.
C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git remote -v
origin  https://github.com/isglobal-brge/MEAL.git (fetch)
origin  https://github.com/isglobal-brge/MEAL.git (push)
upstreamg...@git.bioconductor.org:packages/MEAL.git (fetch)
upstreamg...@git.bioconductor.org:packages/MEAL.git (push)

Can you help me?

Thanks,

Carlos Ruiz


El 13/09/2017 a las 10:09, Carlos Ruiz escribió:

Hi to both,

These are the commands that I tried and the error:

$ git remote -v
origin  https://github.com/isglobal-brge/MEAL.git (fetch)
origin  https://github.com/isglobal-brge/MEAL.git (push)
upstreamg...@git.bioconductor.org:packages/MEAL (fetch)
upstreamg...@git.bioconductor.org:packages/MEAL (push)


$  git fetch --all
Fetching origin
Fetching upstream
Permission denied (publickey).
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 think that there was a similar error in the BiocDevel list that was solved 
after sending the ssh keys. I resent the form yesterday so I hope tomorrow I'll 
be able to push. Just in case, my svn user name was c.ruiz-arenas.

Bests,
Carlos Ruiz

El 12/09/2017 a las 18:12, Shepherd, Lori escribió:

Once you submit the key you should have access.  Please provide the calls you 
are using and also the results of git remote -v



Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Carlos Ruiz <carlos.r...@isglobal.org>
Sent: Tuesday, September 12, 2017 12:08:15 PM
To: Shepherd, Lori
Subject: Re: Bioconductor failing package MEAL

Hi,

I am experiencing some problems with the git system. I think that i have not 
properly configured the ssh keys. I have filled again the form with the ssh 
keys (user name: c.ruiz-arenas). Once you introduced my keys in the system, 
should I do anything else to update the repo? Should I change the configuration 
on git?

Thank you,
Carlos Ruiz

El 12/09/2017 a las 17:37, Shepherd, Lori escribió:

Please update. We have temporarily added your package to the deprecation list 
as we did not hear from you and there were no updates. If you package builds 
and checks cleanly we will remove it from the list of deprecated packages.

Please also be advised we have transitioned to git. There are some useful 
information here:
http://bioconductor.org/developers/how-to/git/


Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Carlos Ruiz <carlos.r...@isglobal.org>
Sent: Tuesday, September 12, 2017 11:28:33 AM
To: Shepherd, Lori
Subject: Re: Bioconductor failing package MEAL

Hi Lori,

I apologize for not replying you 

Re: [Bioc-devel] Bioconductor failing package MEAL

2017-09-15 Thread Carlos Ruiz
Hi Nitesh,

I have checked my mail and I have 3 different SVN ids, one for each package
I have submitted:

- r.carlos: MEAL
- c.ruiz-arenas: MultiDataSet
- c.ruiz: scoreInvHap

When I submitted MultiDataSet, I asked Bioc to consolidate my svn user.
From then, I used c.ruiz-arenas for MEAL and MultiDataSet. Finally, for the
next release, I got scoreInvHap accepted and I have now realized that I
have another svn user. What can I do to solve it?

Thank you,

Carlos Ruiz




El jueves, 14 de septiembre de 2017, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> escribió:

> Hi Carlos,
>
> Do you by any chance have 2 separate SVN id’s?
>
> 1. c.ruiz
> 2. c.ruiz-arenas
>
> Best,
>
> Nitesh
>
>
> > On Sep 14, 2017, at 12:17 PM, Carlos Ruiz <carlos.r...@isglobal.org
> <javascript:;>> wrote:
> >
> > Hi,
> > Today I definitely was able to fetch from the Bioc git. However, I
> cannot push. Here, the commands and the error:
> >
> >
> > C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git push upstream
> master
> > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA)
> to the l
> > ist of known hosts.
> > FATAL: W any packages/MEAL c.ruiz 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.
> > C:\Users\cruiz.ISGLOBAL\Documents\MEAL [master =]> git remote -v
> > origin  https://github.com/isglobal-brge/MEAL.git (fetch)
> > origin  https://github.com/isglobal-brge/MEAL.git (push)
> > upstream    g...@git.bioconductor.org:packages/MEAL.git (fetch)
> > upstreamg...@git.bioconductor.org:packages/MEAL.git (push)
> >
> > Can you help me?
> >
> > Thanks,
> >
> > Carlos Ruiz
> >
> >
> > El 13/09/2017 a las 10:09, Carlos Ruiz escribió:
> >> Hi to both,
> >>
> >> These are the commands that I tried and the error:
> >>
> >> $ git remote -v
> >> origin  https://github.com/isglobal-brge/MEAL.git (fetch)
> >> origin  https://github.com/isglobal-brge/MEAL.git (push)
> >> upstreamg...@git.bioconductor.org:packages/MEAL (fetch)
> >> upstreamg...@git.bioconductor.org:packages/MEAL (push)
> >>
> >>
> >> $  git fetch --all
> >> Fetching origin
> >> Fetching upstream
> >> Permission denied (publickey).
> >> 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 think that there was a similar error in the BiocDevel list that was
> solved after sending the ssh keys. I resent the form yesterday so I hope
> tomorrow I'll be able to push. Just in case, my svn user name was
> c.ruiz-arenas.
> >>
> >> Bests,
> >> Carlos Ruiz
> >>
> >> El 12/09/2017 a las 18:12, Shepherd, Lori escribió:
> >>> Once you submit the key you should have access.  Please provide the
> calls you are using and also the results of git remote -v
> >>>
> >>>
> >>>
> >>> Lori Shepherd
> >>> Bioconductor Core Team
> >>> Roswell Park Cancer Institute
> >>> Department of Biostatistics & Bioinformatics
> >>> Elm & Carlton Streets
> >>> Buffalo, New York 14263
> >>> From: Carlos Ruiz <carlos.r...@isglobal.org <javascript:;>>
> >>> Sent: Tuesday, September 12, 2017 12:08:15 PM
> >>> To: Shepherd, Lori
> >>> Subject: Re: Bioconductor failing package MEAL
> >>>
> >>> Hi,
> >>>
> >>> I am experiencing some problems with the git system. I think that i
> have not properly configured the ssh keys. I have filled again the form
> with the ssh keys (user name: c.ruiz-arenas). Once you introduced my keys
> in the system, should I do anything else to update the repo? Should I
> change the configuration on git?
> >>>
> >>> Thank you,
> >>> Carlos Ruiz
> >>>
> >>> El 12/09/2017 a las 17:37, Shepherd, Lori escribió:
> >>>> Please update. We have temporarily added your package to the
> deprecation list as we did not hear from you and there were no updates. If
> you package builds and checks cleanly we will remove it from the list of
> deprecated packages.
> >>>>
> >>>> Please also be advised we have transitioned to git. The

[Bioc-devel] Deprecating a class

2017-06-27 Thread Carlos Ruiz

Hi Bioc developers,

A year ago, we introduced a class in my package MEAL to manage 
methylation data. After some Bioc releases, we realised that we don't 
really need this class and that it is better to reuse other Bioc classes 
to facilitate package usability. Is there any protocol to deprecate a 
class? There is only a guide to deprecate functions and methods.


For the new release, I was thinking on deprecating the constructors of 
my class, while keeping the methods. Is that OK?


Bests,

--
Carlos Ruiz
PhD Student
ISGlobal
Barcelona Institute for Global Health - Campus MAR
Barcelona Biomedical Research Park (PRBB) (office 001)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 7309
carlos.r...@isglobal.org
www.isglobal.org

We are pleased to tell you that after three years of a strategic alliance 
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This message is intended exclusively for its addressee and may contain 
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foundations. You can exercise your rights of access, rectification, 
cancellation and opposition by contacting the following address: 
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in the ISGlobal Foundation files. Your personal data will be used for the 
purpose of contacting you and sending information on the activities of the 
above foundations. You can exercise your rights of access, rectification, 
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[Bioc-devel] Doubt with deprecating a function

2016-10-20 Thread Carlos Ruiz
Hi everyone,

I am the developer of MEAL package. In the previous release, I 
deprecated a function (multiCorrMethExprs). In this release, I marked 
this function as defuncted. I followed the instructions of 
Bioconductor's web page: I included the defunct function in the body of 
my function, I removed its manual page and I added a new manual page 
with the deprecated function name. I forgot to do these steps until the 
very last day and now my package has a warning in the release branch:

> * checking for missing documentation entries ... WARNING Undocumented 
> code objects: 'multiCorrMethExprs' All user-level objects in a package 
> should have documentation entries. See chapter 'Writing R 
> documentation files' in the 'Writing R

Do you know how I can solve this issue? I know that is not very 
important and I will be solved in the next release when I won't export 
this function. However, I would like to learn how to properly defunct a 
function.
Bests,

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