Bug 557152 – [R_Overlay] Ebuilds depending on recommended packages should use dev-lang/R[-minimal]

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description stilriv 2015-08-09 17:01:30 UTC]

sci-CRAN/nlme fails to build with following error
ERROR: dependency ‘lattice’ is not available for package ‘nlme’

Reproducible: Always

Steps to Reproduce:
emerge -1 --quiet-build=n -v sci-CRAN/nlme

[Comment 1 stilriv 2015-08-09 17:02:59 UTC]

Created attachment 408648 [details]
build.log

[Comment 2 stilriv 2015-08-09 17:04:07 UTC]

Created attachment 408650 [details]
fixed ebuild

[Comment 3 Andrew Savchenko 2015-08-16 11:12:41 UTC]

Please provide emerge --info output.

[Comment 4 Denis Dupeyron (RETIRED) 2015-08-19 22:19:27 UTC]

Please stop assigning these bugs to me. I am not the maintainer of the R overlay. Benda Xu (heroxbd) is.

[Comment 5 stilriv 2015-08-24 01:19:37 UTC]

Created attachment 410002 [details]
emerge --info

[Comment 6 Benda Xu 2015-08-24 06:35:24 UTC]

Hi stilriv,

Thanks for reporting.  In

  https://cran.r-project.org/web/packages/nlme/index.html

/Lattice/ is listed as a dependence.  Our ebuilds are generated from such official metadata.  The missing dependency is strange.

I will look into it.

Benda

[Comment 7 Benda Xu 2015-10-29 03:35:51 UTC]

Hi stilriv,

according to

  http://r.789695.n4.nabble.com/List-of-default-packages-that-come-with-R-td4661857.html

I tried with R-3.2.2:

> i <- installed.packages() 
> i[ i[,"Priority"] %in% c("base","recommended"), c("Package", "Priority")] 
           Package      Priority     
base       "base"       "base"       
boot       "boot"       "recommended"
class      "class"      "recommended"
cluster    "cluster"    "recommended"
codetools  "codetools"  "recommended"
compiler   "compiler"   "base"       
datasets   "datasets"   "base"       
foreign    "foreign"    "recommended"
graphics   "graphics"   "base"       
grDevices  "grDevices"  "base"       
grid       "grid"       "base"       
KernSmooth "KernSmooth" "recommended"
lattice    "lattice"    "recommended"
...

lattice should be shipped with R by default, shouldn't it?

[Comment 8 Benda Xu 2015-11-04 10:13:21 UTC]

Please specify how you installed R.  Feel free to reopen this bug.

[Comment 9 stilriv 2015-11-04 17:10:22 UTC]

Created attachment 416074 [details]
emerge =sci-CRAN/nlme-3.1.122::R_Overlay and bug searching

[Comment 10 stilriv 2015-11-04 17:11:01 UTC]

(In reply to Benda Xu from comment #8)
> Please specify how you installed R.  Feel free to reopen this bug.

// Sorry for long pings, I'm a little busy at work

I finally found source of the problem, that's because of 'minimal' use-flag of dev-lang/R

[Comment 11 Benda Xu 2015-11-05 00:54:28 UTC]

(In reply to stilriv from comment #10)
> (In reply to Benda Xu from comment #8)
> > Please specify how you installed R.  Feel free to reopen this bug.
> 
> // Sorry for long pings, I'm a little busy at work
> 
> I finally found source of the problem, that's because of 'minimal' use-flag
> of dev-lang/R

Ah-ha, probably the packages in R_Overlay should depend on dev-lang/R[-minimal].

Thanks a lot for your report.

[Comment 12 Benda Xu 2015-11-06 01:05:57 UTC]

Committed the fix in

  https://gitweb.gentoo.org/proj/R_overlay.git/commit/?id=8353fa3eae0021da37e807bb7ec04ed1789438fc