Hi Benda,
[Sending this to gentoo-science mailing list as accidentally replied
direct, have also discovered a few other packages that have incorrect
versions]
Hi Benda,
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 |
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
(dev-lang/R-3.4.4:0/0::slack, installed) pulled in by
dev-lang/R[-minimal] required by (virtual/cluster-0:0/0::R_Overlay,
ebuild scheduled for merge)
^^^^^^^^
dev-lang/R[-minimal] required by (virtual/KernSmooth-0:0/0::R_Overlay,
installed)
^^^^^^^^
dev-lang/R[-minimal] required by (virtual/MASS-0:0/0::R_Overlay,
installed)
^^^^^^^^
dev-lang/R[-minimal] required by (virtual/Matrix-0:0/0::R_Overlay,
installed)
^^^^^^^^
dev-lang/R[-minimal] required by (virtual/codetools-0:0/0::R_Overlay,
ebuild scheduled for merge)
^^^^^^^^
dev-lang/R[-minimal] required by (virtual/class-0:0/0::R_Overlay,
ebuild scheduled for merge)
^^^^^^^^
dev-lang/R[-minimal] required by (virtual/foreign-0:0/0::R_Overlay,
installed)
^^^^^^^^
dev-lang/R[-minimal] required by (virtual/lattice-0:0/0::R_Overlay,
installed)
^^^^^^^^
dev-lang/R[-minimal] required by (virtual/nlme-0:0/0::R_Overlay,
installed)
^^^^^^^^
dev-lang/R[-minimal] required by (virtual/survival-0:0/0::R_Overlay,
ebuild scheduled for merge)
^^^^^^^^
dev-lang/R[-minimal] required by (virtual/rpart-0:0/0::R_Overlay,
ebuild scheduled for merge)
^^^^^^^^
dev-lang/R[-minimal] required by (virtual/nnet-0:0/0::R_Overlay, ebuild
scheduled for merge)
^^^^^^^^
(dev-lang/R-3.4.4:0/0::slack, ebuild scheduled for merge) pulled in by
dev-lang/R[minimal] required by (sci-CRAN/Matrix-1.2.12:0/0::R_Overlay,
ebuild scheduled for merge)
^^^^^^^
dev-lang/R[minimal] required by
(sci-CRAN/nlme-3.1.131.1:0/0::R_Overlay, ebuild scheduled for merge)
^^^^^^^
dev-lang/R[minimal] required by (sci-CRAN/rpart-4.1.13:0/0::R_Overlay,
ebuild scheduled for merge)
^^^^^^^
dev-lang/R[minimal] required by
(sci-CRAN/survival-2.41.3:0/0::R_Overlay, ebuild scheduled for merge)
^^^^^^^
dev-lang/R[minimal] required by
(sci-CRAN/lattice-0.20.35:0/0::R_Overlay, ebuild scheduled for merge)
^^^^^^^
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.
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?
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
I'm unsure how the ebuilds in R_Overlay are generated, is it automatically
based on available builds?
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.
If there is something I can do to help please let me know.
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
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