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

[Neil Shephard]

Hi Benda,

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....


# Tidyverse...
emerge -av tidyverse
# ggplot2 extensions
emerge -av ggridges ggraph ggrepel ggnetwork ggmosaic gglasso ggimage
ggforce gge ggalt ggROC ggHorizon ggExtra ggbeeswarm
# Recommended (not necessarily the recommend version though, will pull in
latest from CRAN)
emerge -av KernSmooth MASS Matrix boot class sci-CRAN/cluster
sci-CRAN/codetools foreign lattice mgcv nlme nnet rpart spatial survival
# Modelling
emerge -av lme4 glmnet Hmisc rms epitools
# Sample Size
emerge -av pwr TrialSize longpower simglm clusterPower samplesize PowerTOST
# Miscellaneous
emerge -av blockrand bookdown sci-CRAN/shiny rmarkdown

Of particular note is that the Recommended packages (
https://cran.r-project.org/src/contrib/3.4.4/Recommended/) that were
explicitly removed by using USE=minimal emerge =dev-lang/R-3.4.4 they
mostly failed to build.

A total of 69 packages failed to build directly, slightly more failed
because some of these 69 were dependencies.  Of those that explicitly
failed it appears (to me) that they fall into three groups...

1) Outdated ebuilds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.


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


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...

 * Package:    sci-CRAN/abind-1.4.5
 * Repository: R_Overlay
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
* installing *source* package ‘abind’ ...
** package ‘abind’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (abind)
Traceback (most recent call last):
  File "/usr/lib/portage/python3.5/doins.py", line 611, in <module>
    sys.exit(main(sys.argv[1:]))
  File "/usr/lib/portage/python3.5/doins.py", line 602, in main
    os.path.dirname(source)):
  File "/usr/lib/portage/python3.5/doins.py", line 450, in _doins
    return install_runner.install_file(source, os.path.dirname(dest))
  File "/usr/lib/portage/python3.5/doins.py", line 386, in install_file
    return self._ins_runner.run(source, dest_dir)
  File "/usr/lib/portage/python3.5/doins.py", line 195, in run
    sstat = os.stat(source)
FileNotFoundError: [Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/abind-1.4.5/work/abindy'
 * ERROR: sci-CRAN/abind-1.4.5::R_Overlay failed (install phase):
 *   doins failed
 *
 * If you need support, post the output of `emerge --info
'=sci-CRAN/abind-1.4.5::R_Overlay'`,
 * the complete build log and the output of `emerge -pqv
'=sci-CRAN/abind-1.4.5::R_Overlay'`.
 * The complete build log is located at
'/var/tmp/portage/sci-CRAN/abind-1.4.5/temp/build.log'.
 * The ebuild environment file is located at
'/var/tmp/portage/sci-CRAN/abind-1.4.5/temp/environment'.
 * Working directory:
'/var/tmp/portage/sci-CRAN/abind-1.4.5/work/abind-1.4.5'
 * S: '/var/tmp/portage/sci-CRAN/abind-1.4.5/work/abind-1.4.5'


Having looked at a few of these it appears there is a common theme as the
files that can not be found all refer to the
"/var/tmp/portage/sci-CRAN/[pkg]/work/[pkg]y" directory, that is the letter
'y' has been appended to the package name...

# grep 'FileNotFound'  /var/tmp/portage/sci-CRAN/*/temp/build.log
/var/tmp/portage/sci-CRAN/abind-1.4.5/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/abind-1.4.5/work/abindy'
/var/tmp/portage/sci-CRAN/acepack-1.4.1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/acepack-1.4.1/work/acepacky'
/var/tmp/portage/sci-CRAN/backports-1.1.2/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/backports-1.1.2/work/backportsy'
/var/tmp/portage/sci-CRAN/bitops-1.0.6-r1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/bitops-1.0.6-r1/work/bitopsy'
/var/tmp/portage/sci-CRAN/blockrand-1.3-r1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/blockrand-1.3-r1/work/blockrandy'
/var/tmp/portage/sci-CRAN/boot-1.3.20/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/boot-1.3.20/work/booty'
/var/tmp/portage/sci-CRAN/class-7.3.14/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/class-7.3.14/work/classy'
/var/tmp/portage/sci-CRAN/cluster-2.0.6/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/cluster-2.0.6/work/clustery'
/var/tmp/portage/sci-CRAN/codetools-0.2.15/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/codetools-0.2.15/work/codetoolsy'
/var/tmp/portage/sci-CRAN/cubature-1.3.11/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/cubature-1.3.11/work/cubaturey'
/var/tmp/portage/sci-CRAN/epitools-0.5.10/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/epitools-0.5.10/work/epitoolsy'
/var/tmp/portage/sci-CRAN/evaluate-0.10.1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/evaluate-0.10.1/work/evaluatey'
/var/tmp/portage/sci-CRAN/fftwtools-0.9.8/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/fftwtools-0.9.8/work/fftwtoolsy'
/var/tmp/portage/sci-CRAN/forcats-0.3.0/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/forcats-0.3.0/work/forcatsy'
/var/tmp/portage/sci-CRAN/foreign-0.8.69/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/foreign-0.8.69/work/foreigny'
/var/tmp/portage/sci-CRAN/Formula-1.2.2/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/Formula-1.2.2/work/Formulay'
/var/tmp/portage/sci-CRAN/ggalt-0.4.0/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/ggalt-0.4.0/work/ggalty'
/var/tmp/portage/sci-CRAN/ggbeeswarm-0.6.0/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/ggbeeswarm-0.6.0/work/ggbeeswarmy'
/var/tmp/portage/sci-CRAN/ggExtra-0.7/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/ggExtra-0.7/work/ggExtray'
/var/tmp/portage/sci-CRAN/ggforce-0.1.1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/ggforce-0.1.1/work/ggforcey'
/var/tmp/portage/sci-CRAN/gglasso-1.4/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/gglasso-1.4/work/gglassoy'
/var/tmp/portage/sci-CRAN/ggmosaic-0.1.2/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/ggmosaic-0.1.2/work/ggmosaicy'
/var/tmp/portage/sci-CRAN/ggnetwork-0.5.1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/ggnetwork-0.5.1/work/ggnetworky'
/var/tmp/portage/sci-CRAN/ggrepel-0.7.0/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/ggrepel-0.7.0/work/ggrepely'
/var/tmp/portage/sci-CRAN/ggridges-0.4.1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/ggridges-0.4.1/work/ggridgesy'
/var/tmp/portage/sci-CRAN/ggROC-1.0/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/ggROC-1.0/work/ggROCy'
/var/tmp/portage/sci-CRAN/highr-0.6/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/highr-0.6/work/highry'
/var/tmp/portage/sci-CRAN/hms-0.4.2/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/hms-0.4.2/work/hmsy'
/var/tmp/portage/sci-CRAN/iterators-1.0.9/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/iterators-1.0.9/work/iteratorsy'
/var/tmp/portage/sci-CRAN/jpeg-0.1.8-r1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/jpeg-0.1.8-r1/work/jpegy'
/var/tmp/portage/sci-CRAN/KernSmooth-2.23.15/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/KernSmooth-2.23.15/work/KernSmoothy'
/var/tmp/portage/sci-CRAN/lattice-0.20.35/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/lattice-0.20.35/work/latticey'
/var/tmp/portage/sci-CRAN/latticeExtra-0.6.28/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/latticeExtra-0.6.28/work/latticeExtray'
/var/tmp/portage/sci-CRAN/locfit-1.5.9.1-r1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/locfit-1.5.9.1-r1/work/locfity'
/var/tmp/portage/sci-CRAN/markdown-0.8/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/markdown-0.8/work/markdowny'
/var/tmp/portage/sci-CRAN/MASS-7.3.49/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/MASS-7.3.49/work/MASSy'
/var/tmp/portage/sci-CRAN/MatrixModels-0.4.1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/MatrixModels-0.4.1/work/MatrixModelsy'
/var/tmp/portage/sci-CRAN/minqa-1.2.4/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/minqa-1.2.4/work/minqay'
/var/tmp/portage/sci-CRAN/mnormt-1.5.5/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/mnormt-1.5.5/work/mnormty'
/var/tmp/portage/sci-CRAN/nipals-0.4/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/nipals-0.4/work/nipalsy'
/var/tmp/portage/sci-CRAN/nlme-3.1.131.1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/nlme-3.1.131.1/work/nlmey'
/var/tmp/portage/sci-CRAN/nnet-7.3.12/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/nnet-7.3.12/work/nnety'
/var/tmp/portage/sci-CRAN/png-0.1.7-r1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/png-0.1.7-r1/work/pngy'
/var/tmp/portage/sci-CRAN/polspline-1.1.12/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/polspline-1.1.12/work/polspliney'
/var/tmp/portage/sci-CRAN/proto-1.0.0/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/proto-1.0.0/work/protoy'
/var/tmp/portage/sci-CRAN/pwr-1.2.2/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/pwr-1.2.2/work/pwry'
/var/tmp/portage/sci-CRAN/rematch-1.0.1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/rematch-1.0.1/work/rematchy'
/var/tmp/portage/sci-CRAN/rpart-4.1.13/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/rpart-4.1.13/work/rparty'
/var/tmp/portage/sci-CRAN/rstudioapi-0.7/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/rstudioapi-0.7/work/rstudioapiy'
/var/tmp/portage/sci-CRAN/samplesize-0.2.4/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/samplesize-0.2.4/work/samplesizey'
/var/tmp/portage/sci-CRAN/selectr-0.3.2/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/selectr-0.3.2/work/selectry'
/var/tmp/portage/sci-CRAN/shiny-1.0.5/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/shiny-1.0.5/work/shinyy'
/var/tmp/portage/sci-CRAN/SparseM-1.77/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/SparseM-1.77/work/SparseMy'
/var/tmp/portage/sci-CRAN/spatial-7.3.11/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/spatial-7.3.11/work/spatialy'
/var/tmp/portage/sci-CRAN/TeachingDemos-2.10/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/TeachingDemos-2.10/work/TeachingDemosy'
/var/tmp/portage/sci-CRAN/tiff-0.1.5-r1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/tiff-0.1.5-r1/work/tiffy'
/var/tmp/portage/sci-CRAN/TrialSize-1.3-r1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/TrialSize-1.3-r1/work/TrialSizey'
/var/tmp/portage/sci-CRAN/viridis-0.5.0/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/viridis-0.5.0/work/viridisy'
/var/tmp/portage/sci-CRAN/zoo-1.8.1/temp/build.log:FileNotFoundError:
[Errno 2] No such file or directory:
b'/var/tmp/portage/sci-CRAN/zoo-1.8.1/work/zooy'


As this is a looong post I've put my emerge --info into a Pastebin post
https://pastebin.com/Zc44aF1K

Cheers,

Neil

--
*Natural selection is a mechanism for generating an exceedingly high **degree
of improbability.* - R.A. Fisher

*Ignorance more frequently begets confidence than does knowledge* - by
Charles Darwin

PGP Public : https://pgp.mit.edu/pks/lookup?op=get&search=0x0E7ECE9C10D7B4A0

Website - http://kimura.no-ip.info/
Photos - http://www.flickr.com/photos/slackline/


On 22 March 2018 at 23:57, Benda Xu <heroxbd@g.o> wrote:

> Hi Neil,
>
> Thank you!
>
> Neil Shephard <nshephard@×××××.com> writes:
>
> > Thanks for taking the time to resolve this, that has worked nicely and
> > Rcpp now emerges.
> >
> > I continued trying to replace all the packages I have installed
> > directly through R with emerges from R_Overlay and opted to emerge the
> > meta-package tidyverse which pulls in a ton of packages as well as
> > more explicit packages that aren't pulled in. In doing so I've
> > encountered three problems....
> >
> > 1. Some ebuilds try to pull in old versions.
>
> > 2. Some ebuilds from R_Overlay require "USE=minimal dev-lang/R" whilst
> > others require "USE=-minimal dev-lang/R" which makes it difficult to
> > emerge things.
>
> > 3. I found one package that is on CRAN but for which there is no ebuild.
> >
> > 1. Old Versions
> > ============
> >
> > I found the following old version were pulled in....
> >
> > | Package | R_Overlay Version | CRAN version |
> > |-----------|-------------------|---------------|
> > | xml2 | 0.1.2 | 1.2.0 |
> > | lubridate | 1.7.0 | 1.7.3 |
>
> This is because the parser fails on the new version.  Taking xml2 for
> example, the "system requirements" field on CRAN is:
>
>   libxml2: libxml2-dev (deb), libxml2-devel (rpm)
>
> The parser did not know "(deb)" this maps to dev-libs/libxml2, nor it
> could match 'libxml2-devel'.
>
>
> Before I had to fix these cornor cases manually.  I am thinking of
> exposing the configuration file so that users can contribute to the new
> parsing rules.
>
> > 2. dev-lang/R [-]minimal conflicts
> > ==========================
> >
> > Tried emerging a bundle of packages and get conflicts relating to the
> > USE=minimal, also resulted in some slot conflicts that I couldn't
> > see. Its mostly the 'virtual/[pkg]' that require -minimal....
> >
> > emerge -av ggridges ggraph ggrepel ggnetwork ggmosaic gglasso ggimage
> > ggforce gge ggalt ggROC ggHorizon ggExtra ggbeeswarm lme4 glmnet rpart
> > caret survival Hmisc rms epitools pwr TrialSize longpower simglm
> > clusterPower samplesize PowerTOST blockrand bookdown ...
> >
> > !!! Multiple package instances within a single package slot have been
> pulled
> > !!! into the dependency graph, resulting in a slot conflict:
> >
> > dev-lang/R:0
> >
> > The following USE changes are necessary to proceed:
> > (see "package.use" in the portage(5) man page for more details)
> > # required by sci-CRAN/survival-2.41.3::R_Overlay
> > # required by sci-CRAN/multcomp-1.4.8::R_Overlay
> > # required by sci-CRAN/rms-5.1.2::R_Overlay
> > # required by rms (argument)
> >>=dev-lang/R-3.4.4 minimal
> >
> > Strangely virtual/rpart is listed as requiring USE=-minimal but the
> > rpart package itself requires USE=minimal.
>
> The short answer is, reinstall R with USE=minimal.
>
> Long story: dev-lang/R[-minimal] installs a set of R-recommended packages,
>
>   https://cran.r-project.org/src/contrib/3.3.3/Recommended/
>
> The packages are bundled with R.  Then some package foo in R_Overlay,
> depends on Matrix-1.4.  It is not a problem for R, because it does not
> track files and Matrix-1.4 overwrites the bundled Matrix-1.2.8.  Portage
> is strict on file collisions.  Therefore, we have introduced the
> virtuals.  If you read the virtual ebuilds, e.g. matrix, it speaks for
> itself
>
> DESCRIPTION="Virtual of a R recommended package"
> RDEPEND="
>         || (
>                 dev-lang/R[-minimal]
>                 sci-CRAN/Matrix
>         )"
>
> > 3. Missing ebuild for one package
> > ==========================
> >
> > I was going to try emergeing the blogdown package (
> https://cran.r-project.org/web/packages/blogdown/) but there is no ebuild
> for it in
> > R_Overlay...
> >
> > # emerge -av blogdown
> >
> > emerge: there are no ebuilds to satisfy "blogdown".
> >
> > emerge: searching for similar names...
> > emerge: Maybe you meant any of these: sci-CRAN/bookdown,
> > sci-BIOC/ballgown, app-admin/logmon?
>
> Reading CRAN blogdown
>
> SystemRequirements: Hugo (<https://gohugo.io>) and Pandoc
> (<http://pandoc.org>)
>
> The parser will not know it is hugo (not yet packaged in Gentoo) and
> app-text/pandoc.
>
> > One minor caeveat is that I'm using a locally bumped version of R as
> > the bugreport I've filed for bumping in portage
> > (https://bugs.gentoo.org/632364) hasn't been addressed yet. I'm
> > currently using =dev-lang/R-3.4.4
>
> Thanks for the bug report.
>
> > I'm unsure how the ebuilds in R_Overlay are generated, is it
> > automatically based on available builds?
>
> Yes, it has been a Google summer of code project by André Erdmann
> mentored by calchan:
>
>   https://blogs.gentoo.org/calchan/2015/04/05/why-we-do-
> not-have-nor-want-r-packages-in-the-tree/
>
> Now I find myself the only one left to do the server maintenance with
> our infra team.
>
> > Thanks for yours and others work on this, having R packages managed by
> > portage is a real boon, as it removes the need to update.packages(ask
> > = FALSE) so regularly.
>
> You're welcome.  I myself is an active user of it.
>
> > If there is something I can do to help please let me know.
>
> Keep on discussion.
>
> If you have a connection with R development team, can we talk to them to
> impose a machine-readable format on the "SystemRequirements:"?
>
> Cheers,
> Benda
>