[R-pkg-devel] Why .Rbuildignore doesn't ignore?

Fri Mar 5 13:08:19 CET 2021

Dear Jeff,

I am aware I don't need to be worried about those two warnings but many
thanks anyway.

Jose Barrera
Statistician, Associate Lecturer

*IS**Global*
Barcelona Institute for Global Health - Campus MAR
Barcelona Biomedical Research Park (PRBB) (Room Hypatia)

Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 2147383
jose.barrera using isglobal.org
<https://www.linkedin.com/in/josebarrera>
Personal website: sites.google.com/view/josebarrera
www.isglobal.org

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El jue, 4 mar 2021 a las 21:23, Henrik Bengtsson (<
henrik.bengtsson using gmail.com>) escribió:

> FYI, and in case others wonder or search for this later, the warnings:
>
> Warning: invalid uid value replaced by that for user 'nobody'
> Warning: invalid gid value replaced by that for user 'nobody'
>
> are harmless and has nothing to do with your problem reported here.
> It happens because on the system you're running your user account has
> a user ID (UID) and a group ID (GID) that are > 32767, e.g.
>
> $ id
> uid=34002(alice) gid=34001(alicelab)
>
> Since 'R CMD build' aims at building a *.tar.gz file that works also
> only older systems with older tar software that only supports UID/GID
> <= 32767, it created the *.tar.gz file with mockup UID=32767,
> GID=32767 (called 'nobody') instead of your actual UID/GID.
>
> /Henrik
>
> On Thu, Mar 4, 2021 at 11:59 AM Duncan Murdoch <murdoch.duncan using gmail.com>
> wrote:
> >
> > I don't have any strong suggestions.  Things I'd look for:
> >
> > - is the .Rbuildignore filename spelled correctly?  It was in your
> > message, but maybe there's something different in the actual file on
> > disk.  Running file.exists(".Rbuildignore") should return TRUE if your
> > working directory is the main package directory.
> >
> > - is it encoded properly?  I don't know that this would cause trouble,
> > but it might.  Run tools::showNonASCIIfile(".Rbuildignore")  to see if
> > there are any non-ASCII chars in it.
> >
> > - are the filename patterns entered correctly?  Spaces or punctuation
> > before or after the patterns will be taken to be part of the pattern.
> > If your working directory is the top level package directory, this
> > emulates the test R CMD build uses:
> >
> >   files <- list.files()
> >   files[tools:::inRbuildignore(files, ".")]
> >
> > It should list all the files that you want to ignore.
> >
> > Duncan Murdoch
> >
> > On 04/03/2021 2:06 p.m., Jose Barrera wrote:
> > > Dear Duncan and Jeff,
> > >
> > > Yes, I see those files when tar xvf miclust_1.2.6.tar.gz.
> > >
> > > As usual, I am both building and checking in a terminal (outside
> RStudio):
> > >
> > > $ R CMD build miclust --resave-data
> > > * checking for file ‘miclust/DESCRIPTION’ ... OK
> > > * preparing ‘miclust’:
> > > * checking DESCRIPTION meta-information ... OK
> > > * checking for LF line-endings in source and make files and shell
> scripts
> > > * checking for empty or unneeded directories
> > > * building ‘miclust_1.2.6.tar.gz’
> > > Warning: invalid uid value replaced by that for user 'nobody'
> > > Warning: invalid gid value replaced by that for user 'nobody'
> > >
> > > Then
> > >
> > > $ R CMD check --as-cran miclust_1.2.6.tar.gz
> > >
> > > If I move miclust.Rproj and README.Rmd outside the development
> directory,
> > > then there is no problem, but I find that solution somewhat dirty. Any
> > > ideas?
> > >
> > > Thanks,
> > >
> > > Jose Barrera
> > > Statistician, Associate Lecturer
> > >
> > > *IS**Global*
> > > Barcelona Institute for Global Health - Campus MAR
> > > Barcelona Biomedical Research Park (PRBB) (Room Hypatia)
> > >
> > > Doctor Aiguader, 88
> > > 08003 Barcelona, Spain
> > > Tel. +34 93 2147383
> > > jose.barrera using isglobal.org
> > > <https://www.linkedin.com/in/josebarrera>
> > > Personal website: sites.google.com/view/josebarrera
> > > 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 filing system. Your personal data will be
> used
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> > > personal data, rectification, erasure, restriction of processing, data
> > > portability and object by contacting the following address: *
> lopd using isglobal.org
> > > <lopd using isglobal.org>*. ISGlobal Privacy Policy at *www.isglobal.org
> > > <http://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
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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
> > > 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, supresión, limitación
> del
> > > tratamiento, portabilidad y oposición dirigiéndose a *
> lopd using isglobal.org
> > > <lopd using isglobal.org>* . Política de privacidad en *www.isglobal.org
> > > <http://www.isglobal.org/>*.
> > >
> > >
> > > El jue, 4 mar 2021 a las 18:19, Jeff Newmiller (<
> jdnewmil using dcn.davis.ca.us>)
> > > escribió:
> > >
> > >> Don't run check against your development directory. Run it against the
> > >> tar.gz file.
> > >>
> > >> On March 4, 2021 5:09:07 AM PST, Jose Barrera <
> jose.barrera using isglobal.org>
> > >> wrote:
> > >>> Dear all,
> > >>>
> > >>> devtools::check() gives me the following NOTE:
> > >>>
> > >>> * Non-standard files/directories found at top level:
> > >>>      ‘README.Rmd’ ‘miclust.Rproj’
> > >>>
> > >>> I get the same result with R CMD check --as-cran and R CMD check in a
> > >>> terminal.
> > >>>
> > >>> My .Rbuildignore includes both ^.*\.Rproj$ and ^README\.Rmd$.
> > >>>
> > >>> I haven't had this issue when checking another package I recently and
> > >>> successfully sent to CRAN, so I have no idea why I get that NOTE now.
> > >>>
> > >>> I would appreciate any help to know why .Rbuildignore seems not to
> > >>> ignore
> > >>> those files.
> > >>>
> > >>> Thanks,
> > >>>
> > >>> Jose Barrera
> > >>> Statistician, Associate Lecturer
> > >>>
> > >>> *IS**Global*
> > >>> Barcelona Institute for Global Health - Campus MAR
> > >>> Barcelona Biomedical Research Park (PRBB) (Room Hypatia)
> > >>>
> > >>> Doctor Aiguader, 88
> > >>> 08003 Barcelona, Spain
> > >>> Tel. +34 93 2147383
> > >>> jose.barrera using isglobal.org
> > >>> <https://www.linkedin.com/in/josebarrera>
> > >>> Personal website: sites.google.com/view/josebarrera
> > >>> 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 filing system. 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 to  access to
> > >>> personal data, rectification, erasure, restriction of processing,
> data
> > >>> portability and object by contacting the following address:
> > >>> *lopd using isglobal.org
> > >>> <lopd using isglobal.org>*. ISGlobal Privacy Policy at *www.isglobal.org
> > >>> <http://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, supresión, limitación
> > >>> del
> > >>> tratamiento, portabilidad y oposición dirigiéndose a *
> lopd using isglobal.org
> > >>> <lopd using isglobal.org>* . Política de privacidad en *www.isglobal.org
> > >>> <http://www.isglobal.org/>*.
> > >>
> > >> --
> > >> Sent from my phone. Please excuse my brevity.
> > >>
> > >
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

-- 

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 using isglobal.org <mailto:lopd using isglobal.org>. ISGlobal
Privacy Policy at 
www.isglobal.org <http://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 using isglobal.org <mailto:lopd using isglobal.org>* *. Política de 
privacidad
en www.isglobal.org <http://www.isglobal.org/>.

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