Re: [gentoo-science] Errors installing Rcpp using R_Overlay

[Benda Xu <heroxbd@gentoo.org>]

Hi Neil,

Sorry to getting back to you late.  I have not forgotten these issues.

Neil Shephard <nshephard@gmail.com> writes:

> Thanks for the comprehensive reply and explanations. 
>
> Whilst I've no existing contact with the R development team I will
> make inquiries about moving "SystemRequirements" from free text to a
> more machine-readable format.
>
> I'm also keen to help provide feedback on R_Overlay and help with its
> development where I can, to which end I have as advised re-emerged
> =dev-lang/R-3.4.4 with USE=minimal and tried installing packages I
> use. Quite a few packages still fail unfortunately, I'm emerging the
> following....
>
> [...]

> 1) Outdated ebuilds
>
> Quite a few src packages could not be retrieved...
>
> # grep '404 Not Found' /var/tmp/portage/sci-CRAN/*/temp/build.log -B3 | grep contrib
> /var/tmp/portage/sci-CRAN/ggHorizon-0.1/temp/build.log---2018-03-22 10:10:21-- http://cran.r-project.org/src/contrib/ggHorizon_0.1.tar.gz
> /var/tmp/portage/sci-CRAN/ggimage-0.0.2/temp/build.log---2018-03-22 10:10:35-- http://cran.r-project.org/src/contrib/ggimage_0.0.2.tar.gz
> /var/tmp/portage/sci-CRAN/igraph-1.1.2/temp/build.log---2018-03-22 10:09:30-- http://cran.r-project.org/src/contrib/igraph_1.1.2.tar.gz
> /var/tmp/portage/sci-CRAN/lubridate-1.7.0/temp/build.log---2018-03-26 11:15:41-- http://cran.r-project.org/src/contrib/lubridate_1.7.0.tar.gz
> /var/tmp/portage/sci-CRAN/Rcpp-0.12.15/temp/build.log---2018-03-22 09:11:46-- http://cran.r-project.org/src/contrib/Rcpp_0.12.15.tar.gz
> /var/tmp/portage/sci-CRAN/rgl-0.95.1441/temp/build.log---2018-03-26 11:23:58-- http://cran.r-project.org/src/contrib/rgl_0.95.1441.tar.gz
> /var/tmp/portage/sci-CRAN/xml2-0.1.2/temp/build.log---2018-03-26 11:15:01-- http://cran.r-project.org/src/contrib/xml2_0.1.2.tar.gz
>
> I suspect that this is down to the SystemRequirements issue you've
> highlighted exists meaning outdated ebuilds exist in R_Overlay.

I am exposing a set of unmatched strings in the description field at 

   http://roverlay.dev.gentoo.org/unresolved.html

For example, I can see the rgl case,

> 2018-05-27 05:06:10 INFO     DependencyResolver.UNRESOLVABLE: 0x7, 'XQuartz (on OSX)'
> 2018-05-27 05:06:10 INFO     DependencyResolver.UNRESOLVABLE: 0x7, 'zlib(optional)'
> 2018-05-27 05:06:10 INFO     DependencyResolver.UNRESOLVABLE: 0x7, 'libpng (>=1.2.9'
> 2018-05-27 05:06:10 INFO     DependencyResolver.UNRESOLVABLE: 0x7, 'pandoc (>=1.14'
> 2018-05-27 05:06:10 INFO     DependencyResolver.UNRESOLVABLE: 0x7, 'needed for vignettes)'
> 2018-05-27 05:06:10 INFO     EbuildCreation.rgl.depres: Cannot satisfy dependencies!
> 2018-05-27 05:06:10 INFO     EbuildCreation.rgl: Cannot create an ebuild for this package (status=-2).
> 2018-05-27 05:06:10 DEBUG    OverlayCreator.R_Overlay.sci-CRAN.rgl: removing 0.99.16 from rgl

These are non-machine readable strings that calls for special
treatments.  We should make a better parser for these.

> 2) Checksums failed
>
> Three packages failed to emerge due to Checksums of the fetched src not matching
>
> # grep 'checksum' -i /var/tmp/portage/sci-CRAN/*/temp/build.log -B60 | grep contrib
> /var/tmp/portage/sci-CRAN/Matrix-1.2.12/temp/build.log---2018-03-26 12:34:13-- http://cran.r-project.org/src/contrib/Matrix_1.2-12.tar.gz
> /var/tmp/portage/sci-CRAN/mvtnorm-1.0.7/temp/build.log---2018-03-26 12:33:25-- http://cran.r-project.org/src/contrib/mvtnorm_1.0-7.tar.gz
> /var/tmp/portage/sci-CRAN/nloptr-1.0.4/temp/build.log---2018-03-26
> 12:33:05-- http://cran.r-project.org/src/contrib/nloptr_1.0.4.tar.gz

Hmmm, it looks like the upstream has silently replaced the tarballs.  Duh.

> 3) 'File Not Found'
>
> The majority failed after the build and installation had occurred
> within R and control had returned to Portage with "File Not Found"
> errors similar to the following...

This has been my silly typo...  Now fixed.

Cheers,
Benda