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 at 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
$ 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
* 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
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 at 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 18:19, Jeff Newmiller (<
jdnewmil at dcn.davis.ca.us>)
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 at isglobal.org>
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 at isglobal.org
<https://www.linkedin.com/in/josebarrera>
Personal website: sites.google.com/view/josebarrera
www.isglobal.org
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included
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su
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la
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