[R-pkg-devel] CRAN incoming checks fail due to non-staged installation

OK, here is what I think is going on.

There is a bug in the check code, that creates a false positive when
the package installation is performed with `--merge-multiarch`. In
this case the x64 architecture uses a non-staged install,
deliberately, but the check code still picks this up and reports it as
a NOTE.

Reproducing it is not easy, because of several reasons:
- win-builder uses package-specific configuration, in this case your
package is listed in

https://svn.r-project.org/R-dev-web/trunk/CRAN/QA/Uwe/make/config/MergeMultiarch
,
so `--merge-multiarch` is added automatically.
- R CMD check cannot pass --merge-multiarch to R CMD INSTALL because
--merge-multiarch only works on tarballs, and R CMD check runs INSTALL
on a directory.
- However, R CMD check has an undocumented --install=... option, which
can be used to pick up the installation output from a certain file. I
am pretty sure that win-builder uses this. I.e. it calls R CMD INSTALL
first, putting the output to a file, and then calls R CMD check with
the --install= option pointing to that file as the install output.

In summary, I think this an R CMD check bug, added in this commit:

https://github.com/wch/r-source/commit/44e8faeb1ed30a7603e79988639da7e4e358d497

It can be fixed easily by using a slightly different message for the
--merge-multiarch case, or maybe even by not specifying
--no-staged-install here:

https://github.com/wch/r-source/blob/be469e86046389a0213f22e8b5c7b3227558bb01/src/library/tools/R/install.R#L1913
and here:

https://github.com/wch/r-source/blob/be469e86046389a0213f22e8b5c7b3227558bb01/src/library/tools/R/install.R#L1938
because --libs-only implies --no-staged-install anyway. I am not
entirely certain, but Tomas and/or Prof Ripley will know for sure.

If you want submit your package before the bug is fixed, I suggest you
explain this directly to CRAN when you submit your package.

Best,
Gabor

On Tue, Mar 26, 2019 at 3:18 PM David Kepplinger
<david.kepplinger at gmail.com> wrote:

Dear G?bor,

Oddly, it does emit a NOTE due to the non-staged install, as can be seen

at https://win-builder.r-project.org/86i67mqTD9YY

The package source can be found at

https://github.com/dakep/pense-rpkg/tree/release/1.2.2

Thanks for your help,
David


On Tue, Mar 26, 2019, 3:28 AM G?bor Cs?rdi, <csardi.gabor at gmail.com>

wrote:

Hi David,

if you only see

install for i386
* installing *source* package 'pense' ...
** using staged installation
[....]
install for x64
* installing *source* package 'pense' ...
** using non-staged installation
[...]

then everything is fine, there is no NOTE here, AFAICT.

If you see a NOTE about this, please post 1) a link to your package,
and 2) a link to the win-builder output.

Thanks,
Gabor

On Tue, Mar 26, 2019 at 12:13 AM David Kepplinger
<david.kepplinger at gmail.com> wrote:

Dear Community,

The issue persists and I don't know if it is something I can fix or

if it's

a false positive from the CRAN incoming checks. As a result, the

package is

archived as the old version has other issues with the new R version.

Does someone have an idea how I can fix the issue? I have asked the

CRAN

team last week to flag the issue as a false positive, but I haven't

heard

back so I assume it's something I have to fix.

Thanks,
David

On Wed, Mar 13, 2019 at 3:34 PM David Kepplinger <

david.kepplinger at gmail.com>

wrote:

Thank you, Max, for the clarification.
I have added the option "StagedInstall: yes" to the DESCRIPTION

file, but

it doesn't seem to be forcing a staged installation for x64 on

Windows. I

get the same NOTE now from winbuilder, but with more explanation

which

could help isolate the problem:

install for i386
* installing *source* package 'pense' ...
** using staged installation
[...]
install for x64
* installing *source* package 'pense' ...
not using staged install with --libs-only
** using non-staged installation
[...]


Best,
David

On Wed, Mar 13, 2019 at 1:21 PM Maxime Turgeon <
maxime.turgeon at mail.mcgill.ca> wrote:

Hi David,

Non-staged installation is something new in R-devel:

https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html

Package maintainers can opt out of it (through DESCRIPTION), and

I'm

assuming CRAN wants a quick way to know if that was the case when
diagnosing a submission.

To resolutely opt *in* (which will eventually be the default), you

could

try adding "StagedInstall: yes" to your DESCRIPTION file.

Of course, one question still remains: why was the behaviour

different

for the two architectures.

Max
------------------------------
*From:* R-package-devel <r-package-devel-bounces at r-project.org> on
behalf of David Kepplinger <david.kepplinger at gmail.com>
*Sent:* March 13, 2019 3:39 PM
*To:* r-package-devel at r-project.org
*Subject:* [R-pkg-devel] CRAN incoming checks fail due to

non-staged

installation

Dear Community,

I am trying to update the pense package on CRAN to fix `autoreconf`
problems, but the incoming checks fail for Windows (r-devel) with

2 NOTEs.

The first NOTE is a HTTP 403 for a http://doi.org URL which I

already

know
about and can not change, but the other NOTE is more obscure to

me. It

says

* checking whether package 'pense' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used


and when I check the install log, it says

install for i386
* installing *source* package 'pense' ...
** using staged installation
[....]
install for x64
* installing *source* package 'pense' ...
** using non-staged installation
[...]


Is this a false positive or is there something I can do to force

using a

staged installation for both architectures on Windows?

Best,
David

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