On Linux you can use 'ltrace' to get a list of all the environment
variables that R looks up. E.g., do the following in 'script' so all the
output is stored in a file ('typescript') and later look around in it for
the getenv calls.
$ R-devel --debugger=ltrace --debugger-args="-f -e getenv"
...
[pid 25055] libR.so->getenv("R_HOME")
= "/home/R/R-devel/lib/R"
[pid 25055] libR.so->getenv("R_TRANSLATIONS")
= nil
[pid 25055] libR.so->getenv("R_PLATFORM")
= nil
...
> tools:::.check_packages(c("testFixup_0.1.tar.gz", "--as-cran"))[pid
25055] libR.so->getenv("_R_NS_LOAD_") =
nil
[pid 25055] libR.so->getenv("_R_CHECK_ELAPSED_TIMEOUT_")
= nil
[pid 25055] libR.so->getenv("R_CHECK_ENVIRON")
= nil
[pid 25055] libreadline.so.6->getenv("HOME")
= "/homes/bill"
[pid 25055] libR.so->getenv("_R_CHECK_TIMINGS_")
= nil
[pid 25055] libR.so->getenv("R_ENABLE_JIT")
= nil
[pid 25055] libR.so->getenv("R_HOME")
= "/home/R/R-devel/lib/R"
[pid 25055] libR.so->getenv("_R_CHECK_USE_INSTALL_LOG_")
= nil
[pid 25055] libR.so->getenv("_R_CHECK_SUBDIRS_NOCASE_")
= nil
[pid 25055] libR.so->getenv("_R_CHECK_ALL_NON_ISO_C_")
= nil
... hundreds more lines ...
> q("no")
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Thu, Jul 2, 2020 at 7:24 AM Jan Gorecki <j.gore...@wit.edu.pl> wrote:
> Thank you Gabor
>
> On Thu, Jul 2, 2020 at 10:20 AM Gábor Csárdi <csardi.ga...@gmail.com>
> wrote:
> >
> > You can set the _R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_=true env var and
> > use R-devel.
> >
> > Alternatively, and you don't need R-devel for this, you can run R CMD
> > --html INSTALL on your package, and then look for messages that
> > contain "treated as a topic", e.g.
> >
> > curl_fds html
> > Rd warning: /Users/gaborcsardi/works/processx/man/curl_fds.Rd:11: file
> > link ‘multi_fdset’ in package ‘curl’ does not exist and so has been
> > treated as a topic
> >
> > Gabor
> >
> >
> > On Thu, Jul 2, 2020 at 10:06 AM Jan Gorecki <j.gore...@wit.edu.pl>
> wrote:
> > >
> > > Hi,
> > > What is the recommended way to test for those issues locally?
> > > If it is tested during cran submission, then seems reasonable to be
> enabled just by --as-cran switch. Is it?
> > > Thanks
> > >
> > > On Wed 17 Jun, 2020, 12:32 AM Wayne Oldford, <rwoldf...@uwaterloo.ca>
> wrote:
> > >>
> > >> Thank you!
> > >>
> > >> -----Original Message-----
> > >> From: Gábor Csárdi <csardi.ga...@gmail.com>
> > >> Date: Tuesday, June 16, 2020 at 4:32 PM
> > >> To: Wayne Oldford <rwoldf...@uwaterloo.ca>
> > >> Cc: List r-package-devel <r-package-devel@r-project.org>
> > >> Subject: Re: [R-pkg-devel] check cross-references error: Non-file
> package-anchored link(s)
> > >>
> > >> This is how to look up the filename. The first "sp" is the topic
> name,
> > >> the second is the package name.
> > >>
> > >> > help("sp", "sp")[[1]]
> > >> [1] "C:/Users/csard/R/win-library/4.0/sp/help/00sp"
> > >>
> > >> So you need to link to the "00sp.Rd" file: \link[sp:00sp]{sp}
> > >>
> > >> Gabor
> > >>
> > >> On Tue, Jun 16, 2020 at 9:09 PM Wayne Oldford <
> rwoldf...@uwaterloo.ca> wrote:
> > >> >
> > >> > Hi
> > >> >
> > >> > I got caught by this new test this week in trying to push an
> updated release of the loon package to CRAN.
> > >> >
> > >> > By following this thread, I corrected my cross-references to
> external packages but I got stymied by
> > >> > the one I hoped to give to the "sp" package for Spatial data
> > >> >
> > >> > _________
> > >> >
> > >> > Here is the history:
> > >> >
> > >> > I tried
> > >> > \link[sp:sp]{sp}
> > >> > which failed here:
> > >> > Debian: <
> https://win-builder.r-project.org/incoming_pretest/loon_1.3.1_20200616_162128/Debian/00check.log
> >
> > >> > Status: 1 WARNING
> > >> >
> > >> >
> > >> > That was meant to correct an earlier attempt (it did for other
> links to "scales" for example) where I had tried
> > >> > \link[sp]{sp}
> > >> > and failed here:
> > >> > Debian: <
> https://win-builder.r-project.org/incoming_pretest/loon_1.3.1_20200615_213749/Debian/00check.log
> >
> > >> > Status: 1 WARNING
> > >> >
> > >> >
> > >> > So to complete the possibilities as I understand them, I just
> now tried
> > >> > \link{sp}
> > >> > which, as might be expected, failed here:
> > >> > Debian: <
> https://win-builder.r-project.org/incoming_pretest/loon_1.3.1_20200616_213921/Debian/00check.log
> >
> > >> > Status: 1 WARNING
> > >> > As expected, error here was different: "Missing link" as
> opposed to "Non-file package-anchored link"
> > >> >
> > >> > _________
> > >> >
> > >> >
> > >> > I am not sure whether I have missed a subtlety in WRE or that
> the peculiar circumstance
> > >> > where the package, the topic, and the file name are all
> identical (sp) is some weird boundary case.
> > >> >
> > >> > Without further advice, I think I am just going to remove the
> link to "sp".
> > >> > It really is just a courtesy link to the package description
> for "sp".
> > >> >
> > >> > Thanks in advance for your thoughts.
> > >> >
> > >> > Wayne
> > >> >
> > >> >
> > >> >
> > >> >
> > >> > -----Original Message-----
> > >> > From: R-package-devel <r-package-devel-boun...@r-project.org>
> on behalf of Georgi Boshnakov <georgi.boshna...@manchester.ac.uk>
> > >> > Date: Tuesday, June 16, 2020 at 9:27 AM
> > >> > To: Gábor Csárdi <csardi.ga...@gmail.com>, Duncan Murdoch <
> murdoch.dun...@gmail.com>
> > >> > Cc: List r-package-devel <r-package-devel@r-project.org>
> > >> > Subject: Re: [R-pkg-devel] check cross-references error:
> Non-file package-anchored link(s)
> > >> >
> > >> > I think that the current behaviour is documented in WRE:
> > >> >
> > >> > "...There are two other forms of optional argument
> specified as \link[pkg]{foo} and
> > >> > \link[pkg:bar]{foo} to link to the package pkg, to files
> foo.html and bar.html respectively.
> > >> > These are rarely needed, perhaps to refer to
> not-yet-installed packages (but there the HTML
> > >> > help system will resolve the link at run time) or in the
> normally undesirable event that more
> > >> > than one package offers help on a topic7 (in which case the
> present package has precedence so
> > >> > this is only needed to refer to other packages). They are
> currently only used in HTML help
> > >> > (and ignored for hyperlinks in LATEX conversions of help
> pages), and link to the file rather
> > >> > than the topic (since there is no way to know which topics
> are in which files in an uninstalled
> > >> > package) ... Because they have been frequently misused,
> the HTML help system looks for topic foo in package pkg
> > >> > if it does not find file foo.html."
> > >> >
> > >> > Unless I am missing something, it seems that it would be
> relatively painless to reverse the logic of the current behaviour of the
> help system,
> > >> > i.e. to start looking first for the topic and then for a
> file.
> > >> >
> > >> > Georgi Boshnakov
> > >> >
> > >> > -----Original Message-----
> > >> > From: R-package-devel <
> r-package-devel-boun...@r-project.org> On Behalf Of Gábor Csárdi
> > >> > Sent: 16 June 2020 13:44
> > >> > To: Duncan Murdoch <murdoch.dun...@gmail.com>
> > >> > Cc: List r-package-devel <r-package-devel@r-project.org>
> > >> > Subject: Re: [R-pkg-devel] check cross-references error:
> Non-file package-anchored link(s)
> > >> >
> > >> > On Mon, Jun 15, 2020 at 5:30 PM Duncan Murdoch <
> murdoch.dun...@gmail.com> wrote:
> > >> > >
> > >> > > On 15/06/2020 12:05 p.m., Martin Maechler wrote:
> > >> > > >>>>>> Duncan Murdoch on Sun, 14 Jun 2020 07:28:03
> -0400 writes:
> > >> > > >
> > >> > > > > I agree with almost everything you wrote, except
> one thing: this isn't
> > >> > > > > newly enforced, it has been enforced since the
> help system began. What
> > >> > > > > I think is new is that there are now tests for
> it. Previously those
> > >> > > > > links just wouldn't work.
> > >> > > >
> > >> > > > > Duncan Murdoch
> > >> > > >
> > >> > > > Yes, to all... including Duncan's agreement with Gábor.
> > >> > > >
> > >> > > > Also, Duncan M earlier did mention that he had wanted to
> > >> > > > *change* the link-to-file behavior for these cases
> (when he wrote
> > >> > > > most of the Rd2html source code) but somehow did not
> get it.
> > >> > >
> > >> > > Actually, I don't think I pushed for this change at the
> time (or at
> > >> > > least I didn't push much). I just wish now that I had,
> because I
> > >> > > think it will be harder to do it now than it would have
> been then.
> > >> > >
> > >> > > Duncan
> > >> >
> > >> > I am not entirely sure, but maybe just documenting the
> current behaviour and undoing 78674 could work. With some tweaks? E.g.
> > >> >
> > >> > * updating R-exts to say that \link[pkg:topic]{text} will
> link to `topic.html` in `pkg` first (for historical reasons), and falls
> back to searching for `topic` in `pkg` at render time.
> > >> > * updating Rd2HTML to look for the topic and use it in the
> link, instead of throwing a warning, in it cannot find `topic.html`
> > >> > * removing the `R CMD check` warning for non-file links,
> that was added in 78674 :)
> > >> >
> > >> > Is there anything else?
> > >> >
> > >> > Gabor
> > >> >
> > >> > [...]
> > >> >
> > >> > ______________________________________________
> > >> > R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> > >> > ______________________________________________
> > >> > R-package-devel@r-project.org mailing list
> > >> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> > >> >
> > >> >
> > >> > ______________________________________________
> > >> > R-package-devel@r-project.org mailing list
> > >> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> > >>
> > >>
> > >> ______________________________________________
> > >> R-package-devel@r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> ______________________________________________
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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