R devel - May 2018 - Debugging "SETLENGTH() cannot be applied to an ALTVEC object."?

Hi all,
I wish to push a new version of a package (heatmaply).

I sent it to winbuild with no issues but after submitting it to CRAN I got
an update that it breaks on Debian, see:

package heatmaply_0.15.0.tar.gz does not pass the incoming checks
automatically, please see the following pre-tests:
Windows: <https://win-builder.r-project.org/incoming_pretest/
heatmaply_0.15.0_20180502_082353/Windows/00check.log>
Status: OK
Debian: <https://win-builder.r-project.org/incoming_pretest/
heatmaply_0.15.0_20180502_082353/Debian/00check.log>
Status: 1 ERROR, 1 WARNING



Looking at the errors I get, they are all of the type:
"SETLENGTH() cannot be applied to an ALTVEC object."
I assume this is somehow related to changes in R 3.5.0 (maybe related to
this
<https://github.com/wch/r-source/commit/0ba66a2bc236ae5b009af910688575aa4adddd2c>?),
but I'm not sure how to debug it (as I don't have this environment
set-up),
not am I sure what is actually causing the issue.

Any suggestions would be most appreciated.

(I debated if to post it here or on r-package-devel, and it seems a more
general R issue than package development issue - but feel free to correct
me about this if you think otherwise)

Cheers,
Tal






----------------Contact
Details:-------------------------------------------------------
Tal Galili, Ph.D. in Statistics

Tal.Galili at gmail.com

www.r-statistics.com (English)
www.biostatistics.co.il (Hebrew)  | www.talgalili.com (Hebrew)
----------------------------------------------------------------------------------------------

	[[alternative HTML version deleted]]

Tal,

I don't have a debian machine at my fingertips, but I don't see that
error
when installing heatmaply into a clean library in R 3.5.0 (that takes a
while...).

I suspect you're hitting old installed versions of packages in that build
on that machine, especially since the failure is not universal, but I don't
have any visibliity into the internals of that system so I have no way of
knowing if that's true or not.

You can use Gabor's builder.r-hub.io to try checking your package on the
Debian VMs over there. If it can pass there that would be more evidence
that something more complicated is going on.

Sorry I couldn't be more direct help.
~G

On Fri, May 4, 2018 at 12:46 PM, Tal Galili <tal.galili at gmail.com>
wrote:
> Hi all,
> I wish to push a new version of a package (heatmaply).
>
> I sent it to winbuild with no issues but after submitting it to CRAN I got
> an update that it breaks on Debian, see:
>
> package heatmaply_0.15.0.tar.gz does not pass the incoming checks
> automatically, please see the following pre-tests:
> Windows: <https://win-builder.r-project.org/incoming_pretest/
> heatmaply_0.15.0_20180502_082353/Windows/00check.log>
> Status: OK
> Debian: <https://win-builder.r-project.org/incoming_pretest/
> heatmaply_0.15.0_20180502_082353/Debian/00check.log>
> Status: 1 ERROR, 1 WARNING
>
>
>
> Looking at the errors I get, they are all of the type:
> "SETLENGTH() cannot be applied to an ALTVEC object."
> I assume this is somehow related to changes in R 3.5.0 (maybe related to
> this
> <https://github.com/wch/r-source/commit/0ba66a2bc236ae5b009af910688575
> aa4adddd2c>?),
> but I'm not sure how to debug it (as I don't have this environment
set-up),
> not am I sure what is actually causing the issue.
>
> Any suggestions would be most appreciated.
>
> (I debated if to post it here or on r-package-devel, and it seems a more
> general R issue than package development issue - but feel free to correct
> me about this if you think otherwise)
>
> Cheers,
> Tal
>
>
>
>
>
>
> ----------------Contact
> Details:-------------------------------------------------------
> Tal Galili, Ph.D. in Statistics
>
> Tal.Galili at gmail.com
>
> www.r-statistics.com (English)
> www.biostatistics.co.il (Hebrew)  | www.talgalili.com (Hebrew)
> ------------------------------------------------------------
> ----------------------------------
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

-- 
Gabriel Becker, Ph.D
Scientist
Bioinformatics and Computational Biology
Genentech Research

	[[alternative HTML version deleted]]

The Debian failure is in R-devel, and you should see the same failure
in R-devel on all platforms. A recent change in R-devel has unmasked
an issue in data.table that needs to be fixed. The data.table
maintainer is working on this.

Best,

luke

On Fri, 4 May 2018, Tal Galili wrote:
> Hi all,
> I wish to push a new version of a package (heatmaply).
>
> I sent it to winbuild with no issues but after submitting it to CRAN I got
> an update that it breaks on Debian, see:
>
> package heatmaply_0.15.0.tar.gz does not pass the incoming checks
> automatically, please see the following pre-tests:
> Windows: <https://win-builder.r-project.org/incoming_pretest/
> heatmaply_0.15.0_20180502_082353/Windows/00check.log>
> Status: OK
> Debian: <https://win-builder.r-project.org/incoming_pretest/
> heatmaply_0.15.0_20180502_082353/Debian/00check.log>
> Status: 1 ERROR, 1 WARNING
>
>
>
> Looking at the errors I get, they are all of the type:
> "SETLENGTH() cannot be applied to an ALTVEC object."
> I assume this is somehow related to changes in R 3.5.0 (maybe related to
> this
>
<https://github.com/wch/r-source/commit/0ba66a2bc236ae5b009af910688575aa4adddd2c>?),
> but I'm not sure how to debug it (as I don't have this environment
set-up),
> not am I sure what is actually causing the issue.
>
> Any suggestions would be most appreciated.
>
> (I debated if to post it here or on r-package-devel, and it seems a more
> general R issue than package development issue - but feel free to correct
> me about this if you think otherwise)
>
> Cheers,
> Tal
>
>
>
>
>
>
> ----------------Contact
> Details:-------------------------------------------------------
> Tal Galili, Ph.D. in Statistics
>
> Tal.Galili at gmail.com
>
> www.r-statistics.com (English)
> www.biostatistics.co.il (Hebrew)  | www.talgalili.com (Hebrew)
>
----------------------------------------------------------------------------------------------
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu