From tobias.verbeke at openanalytics.eu  Sat Sep 21 21:39:12 2013
From: tobias.verbeke at openanalytics.eu (Tobias Verbeke)
Date: Sat, 21 Sep 2013 21:39:12 +0200 (CEST)
Subject: [Rd] regenerate Rscript after moving R installation
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Message-ID: <1021845929.1859.1379792352728.JavaMail.zimbra@openanalytics.eu>

Hi Dirk, 

Many thanks for your reaction.

----- Original Message -----
> From: "Dirk Eddelbuettel" <edd at debian.org>
> To: "Tobias Verbeke" <tobias.verbeke at openanalytics.eu>
> Cc: r-devel at r-project.org
> Sent: Saturday, September 21, 2013 9:00:12 PM
> Subject: Re: [Rd] regenerate Rscript after moving R installation
> 
> 
> On 21 September 2013 at 20:43, Tobias Verbeke wrote:
> | P.S. The background to this question is the usage of Rscript
> | calls in the Makevars files of some R packages on CRAN, so
> | the 'broken' Rscript prevents installation of certain R packages.
> 
> More details, please.
> 
> AFAICT there is no 'broken' Rscript per se.  Eg for Rcpp, and per hints from
> Kurt el al over the years, we have been doing this for a few years
> 
>   PKG_CXXFLAGS=-I../inst/include
>   PKG_LIBS=`$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS)
>   $(BLAS_LIBS) $(FLIBS)

The package that made me discover this was RcppEigen which has indeed

PKG_LIBS=`$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
 
> where a key part is the `$(R_HOME)/bin` which permits you to transparently
> switch between R-release, R-devel, R-beforeMove, R-afterMove, R-whatevr, ...
> simply by adjusting your shell's $PATH variable, or the R wrapper you for R
> CMD, or ...
> 
> It. Just. Works.

It is neat and certainly works, unless R is built on another location (on a build machine)
prior to being put on its final location.

If I read the strace output below correctly, the origin of the problem is the hardcoded
location of the R binary.

tobias at oa-laptop:/opt/architect/architect-stable/plugins/eu.openanalytics.architect.r.server.gtk.linux_stable/R/bin$ strace ./Rscript -e '2+2'
execve("./Rscript", ["./Rscript", "-e", "2+2"], [/* 51 vars */]) = 0
brk(0)                                  = 0x1eb6000
access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fc7563e1000
access("/etc/ld.so.preload", R_OK)      = -1 ENOENT (No such file or directory)
open("/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=161604, ...}) = 0
mmap(NULL, 161604, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7fc7563b9000
close(3)                                = 0
access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)
open("/lib/x86_64-linux-gnu/libc.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\200\30\2\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=1811128, ...}) = 0
mmap(NULL, 3925208, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7fc755e02000
mprotect(0x7fc755fb7000, 2093056, PROT_NONE) = 0
mmap(0x7fc7561b6000, 24576, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1b4000) = 0x7fc7561b6000
mmap(0x7fc7561bc000, 17624, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7fc7561bc000
close(3)                                = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fc7563b8000
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fc7563b7000
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fc7563b6000
arch_prctl(ARCH_SET_FS, 0x7fc7563b7700) = 0
mprotect(0x7fc7561b6000, 16384, PROT_READ) = 0
mprotect(0x601000, 4096, PROT_READ)     = 0
mprotect(0x7fc7563e3000, 4096, PROT_READ) = 0
munmap(0x7fc7563b9000, 161604)          = 0
brk(0)                                  = 0x1eb6000
brk(0x1ed7000)                          = 0x1ed7000
execve("/home/builduser/architect/stable/R-build/sources/R-3.0.1/bin/R", ["/home/builduser/architect/stable/"..., "--slave", "--no-restore", "-e", "2+2", "--args"], [/* 52 vars */]) = -1 ENOENT (No such file or directory)
dup(2)                                  = 3
fcntl(3, F_GETFL)                       = 0x8002 (flags O_RDWR|O_LARGEFILE)
fstat(3, {st_mode=S_IFCHR|0620, st_rdev=makedev(136, 3), ...}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fc7563e0000
lseek(3, 0, SEEK_CUR)                   = -1 ESPIPE (Illegal seek)
write(3, "Rscript execution error: No such"..., 51Rscript execution error: No such file or directory
) = 51
close(3)                                = 0
munmap(0x7fc7563e0000, 4096)            = 0
exit_group(-1)                          = ?
 
> So if you borked your Rscript somewhere, just use another and quickly rebuild
> R for the new location. It is after all a cheap build (and cheaper still if
> you use tricks like ccache which I am a huge fan of, or 'make -j8', or ...)

There is no way to build again since R itself is shipped (in a Debian/Ubuntu package
and as part of Architect) prior to being installed and used on another computer.
The buildstamp that is part of the final installation path of the application is 
generated after the R build (since R is only one component), so changing the --prefix
on the build machine would not work (currently).

I hope this gives more background to the question and would be curious if there are alternatives
to rapidly regenerate the Rscript executable only.

(My other alternative of messing with the path in a hex editor has not been successful :-)

Best wishes,
Tobias

P.S. Architect can be installed from

http://deb.openanalytics.eu/howto.html

sudo apt-get install architect

> 
> Dirk
> 
> PS  ccache is at http://ccache.samba.org/ and should be in any sane Linux
> distro
> 
> --
> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
>



[Rd] regenerate Rscript after moving R installation
Tobias Verbeke