Fix hardcoding of paths in R binary

[kcrisman]

See this thread on sage-support.

Here is how I got the optional package automap to install into a 
binary sage R. 
Go into the sage directory and edit the following files: 
local/bin/R and local/lib/R/bin/R 
and change all the hard-set user variables "/scratch/...." to the true 
locations of R_HOME_DIR, R_HOME, R_INCLUDE_DIR, R_SHARE_DIR and for 
good measure, R_DOC_DIR. Replace the default string EVERYWHERE in the 
file. 
I then exported SAGE_HOME as well (Not sure that this is needed.), and 
run local/bin/R 
Inside R, install.packages("automap") 
No more build errors, and when I restart R, automap loads using 
library. Just have to try it out from sage now. 
Any chance there's a script to find all of these hard-set strings and 
change them to correct values? 

---

Related (R package):

• Move the RPy package outside of the R package #9906
• Handle preset R_PROFILE or R_HOME variables #9847
• R's spkg-install needs a good overhaul. #8274
• R breaks if SAGE_LOCAL undefined #10967

---

New spkg: http://boxen.math.washington.edu/home/palmieri/SPKG/r-2.15.2.p2.spkg

CC: @nexttime @jhpalmieri

Component: packages: standard

Keywords: R spkg R.sh.in libR.pc pkg-config hard-coded package installation R_HOME_DIR sd32 r-project

Author: John Palmieri

Reviewer: Karl-Dieter Crisman, Jeroen Demeyer

Merged: sage-5.9.rc0

Issue created by migration from https://trac.sagemath.org/ticket/9668

[nexttime]

Description changed:

--- 
+++ 
@@ -17,3 +17,11 @@
 Any chance there's a script to find all of these hard-set strings and 
 change them to correct values? 
 ```
+
+---
+
+Related (R package):
+* #9906
+* #9847
+* #8274
+

[nexttime]

comment:2

IIRC I have some "almost" ready R spkg for #9906, which also does a lot of clean-up in spkg-install...

[kcrisman]

comment:3

Well, I would certainly welcome and help review this. Anything which cleans up parts of #8274 could be commented there, and perhaps even a new ticket opened if there isn't much left.

But what about #9668 (this ticket) itself? Does the stuff that is "almost" ready at #9906 address that?

[nexttime]

comment:4

Replying to @kcrisman:

But what about #9668 (this ticket) itself? Does the stuff that is "almost" ready at #9906 address that?

Not yet, i.e. not all of it. See this comment there.

[nexttime]

comment:5

Replying to @nexttime:

Replying to @kcrisman:

But what about #9668 (this ticket) itself? Does the stuff that is "almost" ready at #9906 address that?

Not yet, i.e. not all of it. See this comment there.

Ok, a bit more subtle than I expected (R is quite weird, failed to build inbetween), but I now have a p6 that fixes both the R scripts and the pkg-config file (libR.pc).

---

There was another issue with R someone reported on sage-devel which was caused by a "complicated" setting of an environment variable, in this case PAGER, but that's certainly an upstream problem and rather exotic.

[kcrisman]

comment:6

Replying to @nexttime:

Replying to @nexttime:

Replying to @kcrisman:

But what about #9668 (this ticket) itself? Does the stuff that is "almost" ready at #9906 address that?

Not yet, i.e. not all of it. See this comment there.

Ok, a bit more subtle than I expected (R is quite weird, failed to build inbetween), but I now have a p6 that fixes both the R scripts and the pkg-config file (libR.pc).

Okay, I'll watch this space.

There was another issue with R someone reported on sage-devel which was caused by a "complicated" setting of an environment variable, in this case PAGER, but that's certainly an upstream problem and rather exotic.

Agreed.

[kcrisman]

comment:7

See also #10967. We should probably either incorporate that here, or make a followup spkg there.

[kcrisman]

Description changed:

--- 
+++ 
@@ -24,4 +24,4 @@
 * #9906
 * #9847
 * #8274
-
+* #10967

[nexttime]

comment:8

Replying to @kcrisman:

See also #10967. We should probably either incorporate that here, or make a followup spkg there.

Almost certainly the former.

[Note to myself:]

The problem is that removing any reference to SAGE_ROOT and SAGE_LOCAL disables the script being "automatically" relocated in the first place.

I'll then have to guess SAGE_ROOT if none of Sage's variables are defined. We also have two copies of the R script, one in local/bin/, and one in local/lib/R/bin/.

[nexttime]

Dependencies: #9906

[nexttime]

Changed keywords from none to R spkg R.sh.in libR.pc pkg-config hard-coded package installation R_HOME_DIR