[Bioc-devel] Bioconductor failing package MEAL
Carlos Ruiz
carlos.ruiz at isglobal.org
Thu Sep 14 19:30:43 CEST 2017
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.Turaga at 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.ruiz at 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 git at git.bioconductor.org:packages/MEAL.git (fetch)
> > upstream git at 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)
> >> upstream git at git.bioconductor.org:packages/MEAL (fetch)
> >> upstream git at 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.ruiz at 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. 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.ruiz at isglobal.org <javascript:;>>
> >>>> 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 sooner but I have just finished my
> holidays today. I have finished the vignettes today and I only need to
> update the tests to have a fully working version again. Therefore, I expect
> to push my changes during this week.
> >>>>
> >>>> MEAL contains wrappers to other methods to ease performing
> methylation and gene expression analyses. I previously created a data
> package to show MEAL functionalities and I used it in my vignettes. We have
> created a new data package (BRGEdata) in our group that could be used by
> different packages. My colleague uploaded it in the submission of
> omicRexpsome but he is experiencing some problems that are trying to solve
> with Martin.
> >>>>
> >>>> Until this package is not working, the new version of MEAL will fail
> to build the vignettes. Should I wait until BRGEdata issue is solved or can
> I update the package without including the vignettes?
> >>>>
> >>>> Bests,
> >>>>
> >>>> 2017-09-01 14:21 GMT+02:00 Shepherd, Lori <
> Lori.Shepherd at roswellpark.org <javascript:;>>:
> >>>> Dear MEAL maintainer,
> >>>>
> >>>> The MEAL package continues to fail to pass 'R CMD build' on all
> platforms in the devel version of Bioconductor (i.e. BioC 3.6):
> >>>>
> >>>> http://bioconductor.org/checkResults/3.6/bioc-LATEST/
> MEAL/malbec1-buildsrc.html
> >>>>
> >>>> If no action is taken we will begin the deprecation process for your
> package. Thank you for your time and effort.
> >>>>
> >>>> I understand that you reached out indicating there were big changes
> to MEAL; As it is getting closer to our next release (end Oct), these
> changes should be pushed as soon as possible to allow for others who depend
> on your package to update there packages accordingly
> >>>>
> >>>> Thanks for your contribution to Bioconductor.
> >>>>
> >>>>
> >>>> Lori Shepherd
> >>>> Bioconductor Core Team
> >>>> Roswell Park Cancer Institute
> >>>> Department of Biostatistics & Bioinformatics
> >>>> Elm & Carlton Streets
> >>>> Buffalo, New York 14263
> >>>> From: Carlos Ruiz <carlos.ruiz at isglobal.org <javascript:;>>
> >>>> Sent: Friday, July 21, 2017 9:24:41 AM
> >>>> To: Shepherd, Lori
> >>>> Subject: Re: Bioconductor failing package MEAL
> >>>>
> >>>> Hi Lori,
> >>>>
> >>>> I apology for not answering to you before. I am doing big changes to
> MEAL package. Currently, I have a working version but I have to redo the
> vignette and the tests. Once I finish them, I will make a new bump to my
> package.
> >>>>
> >>>> Bests,
> >>>> Carlos Ruiz
> >>>>
> >>>>
> >>>> 2017-07-21 15:17 GMT+02:00 Shepherd, Lori <
> Lori.Shepherd at roswellpark.org <javascript:;>>:
> >>>> Dear MEAL maintainer,
> >>>>
> >>>> The MEAL package continues to fail to pass 'R CMD build' on all
> platforms in the devel version of Bioconductor (i.e. BioC 3.6):
> >>>>
> >>>> http://bioconductor.org/checkResults/3.6/bioc-LATEST/
> MEAL/malbec1-buildsrc.html
> >>>>
> >>>> Don't hesitate to ask questions on the support site if you are having
> trouble.
> >>>>
> >>>> If no action is taken over the next several weeks we will begin the
> deprecation process for your package. Thank you for your time and effort.
> >>>>
> >>>>
> >>>> Thanks for your contribution to Bioconductor.
> >>>>
> >>>>
> >>>>
> >>>> Lori Shepherd
> >>>> Bioconductor Core Team
> >>>> Roswell Park Cancer Institute
> >>>> Department of Biostatistics & Bioinformatics
> >>>> Elm & Carlton Streets
> >>>> Buffalo, New York 14263
> >>>> From: Shepherd, Lori
> >>>> Sent: Wednesday, July 12, 2017 7:12:35 AM
> >>>> To: carles.hernandez at isglobal.org <javascript:;>;
> juanr.gonzalez at isglobal.org <javascript:;>; carlos.ruiz at isglobal.org
> <javascript:;>
> >>>> Subject: Bioconductor failing package MEAL
> >>>>
> >>>> Dear MEAL maintainer,
> >>>>
> >>>> I'd like to bring to your attention that the MAIT package is failing
> to pass 'R CMD build' on all platforms in the devel version of Bioconductor
> (i.e. BioC 3.6):
> >>>>
> >>>> http://bioconductor.org/checkResults/3.6/bioc-LATEST/
> MEAL/malbec1-buildsrc.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.
> >>>>
> >>>> If no action is taken over the next several weeks we will begin the
> deprecation process for your package. Thank you for your time and effort.
> >>>>
> >>>>
> >>>> Thanks for your contribution to Bioconductor.
> >>>>
> >>>>
> >>>> 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
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> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
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> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Carlos Ruiz
> >>>> PhD Student
> >>>> ISGlobal
> >>>> Instituto de Salud Global de Barcelona - Campus MAR
> >>>> Barcelona Biomedical Research Park (PRBB) (office 183.01 C)
> >>>> Doctor Aiguader, 88
> >>>> 08003 Barcelona, Spain
> >>>> Tel. +34 93 214 73 09
> >>>> carlos.ruiz at isglobal.org <javascript:;>
> >>>> 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
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> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Carlos Ruiz
> >>>> PhD Student
> >>>> ISGlobal
> >>>> Instituto de Salud Global de Barcelona - Campus MAR
> >>>> Barcelona Biomedical Research Park (PRBB) (office 183.01 C)
> >>>> Doctor Aiguader, 88
> >>>> 08003 Barcelona, Spain
> >>>> Tel. +34 93 214 73 09
> >>>> carlos.ruiz at isglobal.org <javascript:;>
> >>>> 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
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> >>>> ------------------------------------------------------------
> -----------------------------------------------------------------
> >>>> CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente
> a su destinatario y puede contener información confidencial, por lo que la
> utilización, divulgación y/o copia sin autorización está prohibida por la
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> comunique inmediatamente por esta misma vía y proceda a su destrucción.
> >>>> PROTECCIÓN DE DATOS. Sus datos de carácter personal utilizados en
> este envío, incluida su dirección de e-mail, forman parte de ficheros de
> titularidad de la Fundación ISGlobal para cualquier finalidades de
> contacto, relación institucional y/o envío de información sobre sus
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> >>>>
> >>>> This email message may contain legally privileged and/or confidential
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> >>>
> >>> --
> >>> 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.ruiz at isglobal.org <javascript:;>
> >>> www.isglobal.org
> >>>
> >>>
> >>> We are pleased to tell you that after three years of a strategic
> alliance between ISGlobal and CREAL, both institutions have merged. The
> resulting institution, which retains the ISGlobal name, will build upon the
> existing areas of excellence to become a world-class player in research,
> education and innovation in Global Health. More info at:
> >>> http://ow.ly/krQd301Nj3w
> >>>
> >>>
> >>>
> >>>
> >>> 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
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> cancellation and opposition by contacting the following address:
> >>> lopd at isglobal.org <javascript:;>. 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
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> cancellation and opposition by contacting the following address:
> lopd at isglobal.org <javascript:;>. ISGlobal Privacy Policy at
> www.isglobal.org.
> >>> ------------------------------------------------------------
> -----------------------------------------------------------------
> >>> CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente
> a su destinatario y puede contener información confidencial, por lo que la
> utilización, divulgación y/o copia sin autorización está prohibida por la
> legislación vigente. Si ha recibido este mensaje por error, le rogamos lo
> comunique inmediatamente por esta misma vía y proceda a su destrucción.
> >>> PROTECCIÓN DE DATOS. Sus datos de carácter personal utilizados en este
> envío, incluida su dirección de e-mail, forman parte de ficheros de
> titularidad de la Fundación ISGlobal para cualquier finalidades de
> contacto, relación institucional y/o envío de información sobre sus
> actividades. Los datos que usted nos pueda facilitar contestando este
> correo quedarán incorporados en los correspondientes ficheros, autorizando
> el uso de su dirección de e-mail para las finalidades citadas. Puede
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> dirigiéndose a lopd at isglobal.org <javascript:;> . Política de privacidad
> en www.isglobal.org.
> >>>
> >>> 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
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> >>
> >> --
> >> 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.ruiz at isglobal.org <javascript:;>
> >> www.isglobal.org
> >>
> >>
> >> We are pleased to tell you that after three years of a strategic
> alliance between ISGlobal and CREAL, both institutions have merged. The
> resulting institution, which retains the ISGlobal name, will build upon the
> existing areas of excellence to become a world-class player in research,
> education and innovation in Global Health. More info at:
> >> http://ow.ly/krQd301Nj3w
> >>
> >>
> >>
> >>
> >> 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:
> >> lopd at isglobal.org <javascript:;>. ISGlobal Privacy Policy at
> www.isglobal.org
> >> .
> >>
> >>
> >>
> >
> > --
> > 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.ruiz at isglobal.org <javascript:;>
> > www.isglobal.org
> >
> >
> > We are pleased to tell you that after three years of a strategic
> alliance between ISGlobal and CREAL, both institutions have merged. The
> resulting institution, which retains the ISGlobal name, will build upon the
> existing areas of excellence to become a world-class player in research,
> education and innovation in Global Health. More info at:
> > http://ow.ly/krQd301Nj3w
> >
> >
> >
> >
> > 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:
> > lopd at isglobal.org <javascript:;>. 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:
> lopd at isglobal.org <javascript:;>. ISGlobal Privacy Policy at
> www.isglobal.org.
> > ------------------------------------------------------------
> -----------------------------------------------------------------
> > CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente a
> su destinatario y puede contener información confidencial, por lo que la
> utilización, divulgación y/o copia sin autorización está prohibida por la
> legislación vigente. Si ha recibido este mensaje por error, le rogamos lo
> comunique inmediatamente por esta misma vía y proceda a su destrucción.
> > PROTECCIÓN DE DATOS. Sus datos de carácter personal utilizados en este
> envío, incluida su dirección de e-mail, forman parte de ficheros de
> titularidad de la Fundación ISGlobal para cualquier finalidades de
> contacto, relación institucional y/o envío de información sobre sus
> actividades. Los datos que usted nos pueda facilitar contestando este
> correo quedarán incorporados en los correspondientes ficheros, autorizando
> el uso de su dirección de e-mail para las finalidades citadas. Puede
> ejercer los derechos de acceso, rectificación, cancelación y oposición
> dirigiéndose a lopd at isglobal.org <javascript:;> . Política de privacidad
> en www.isglobal.org.
>
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
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> recipient(s), you are hereby notified that any disclosure, copying,
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--
Carlos Ruiz
PhD Student
*IS*
*Global*Instituto de Salud Global de Barcelona - Campus MAR
Barcelona Biomedical Research Park (PRBB) (office 183.01 C)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 73 09
*carlos.ruiz at isglobal.org <xxx at isglobal.org>*
www.isglobal.org
--
This message is intended exclusively for its addressee and may contain
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dissemination, copy or disclosure of this communication is strictly
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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:
lopd at isglobal.org. ISGlobal Privacy Policy at www.isglobal.org.
-----------------------------------------------------------------------------------------------------------------------------
CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente a su
destinatario y puede contener información confidencial, por lo que la
utilización, divulgación y/o copia sin autorización está prohibida por la
legislación vigente. Si ha recibido este mensaje por error, le rogamos lo
comunique inmediatamente por esta misma vía y proceda a su destrucción.
PROTECCIÓN DE DATOS. Sus datos de carácter personal utilizados en este
envío, incluida su dirección de e-mail, forman parte de ficheros de
titularidad de la Fundación ISGlobal para cualquier finalidades de
contacto, relación institucional y/o envío de información sobre sus
actividades. Los datos que usted nos pueda facilitar contestando este
correo quedarán incorporados en los correspondientes ficheros, autorizando
el uso de su dirección de e-mail para las finalidades citadas. Puede
ejercer los derechos de acceso, rectificación, cancelación y oposición
dirigiéndose a lopd at isglobal.org . Política de privacidad en
www.isglobal.org.
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