R help - Jan 2019 - g++ error causes non-zero exit status for package installation

On 5 January 2019 at 09:14, William Dunlap via R-help wrote:
| You would get these errors ("R: file or directory not found, version:
file
| or directory not found...") if you had a ~/.Rprofile file containing the
| line 'cat(version$version.string, sep="\n").

Well spotted -- very much so. That is bound to break use within src/Makevars
and alike. If you must do something in ~/.Rprofile either make it silent, or
make it conditional based on if (interactive()) { ...that_code_here... }

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

dirk & bill, you guys are incredible! the non-silent .Rprofile was the
problem!
making the code interactive didn't help either, only silenceing it helped!

thanks so much! i assume moving to r-sig-debian is now obsolete.

ps, @dirk: adding michael rutters ppa also helped, but the packages get
installed to R_LIBS_SITE, and not (as i am used to) to R_LIBS-USER.
but this was only a minor inconvinience (i like to keep the packages in one
directory).

thanks again!
winfried

Am Sa., 5. Jan. 2019 um 18:40 Uhr schrieb Dirk Eddelbuettel <edd at
debian.org
>:
>
> On 5 January 2019 at 09:14, William Dunlap via R-help wrote:
> | You would get these errors ("R: file or directory not found,
version:
> file
> | or directory not found...") if you had a ~/.Rprofile file containing
the
> | line 'cat(version$version.string, sep="\n").
>
> Well spotted -- very much so. That is bound to break use within
> src/Makevars
> and alike. If you must do something in ~/.Rprofile either make it silent,
> or
> make it conditional based on if (interactive()) { ...that_code_here... }
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>
	[[alternative HTML version deleted]]

On 5 January 2019 at 20:40, Winfried Moser wrote:
| dirk & bill, you guys are incredible! the non-silent .Rprofile was the
| problem!
| making the code interactive didn't help either, only silenceing it helped!

Good to know you have it fixed.
 
| thanks so much! i assume moving to r-sig-debian is now obsolete.
| 
| ps, @dirk: adding michael rutters ppa also helped, but the packages get
| installed to R_LIBS_SITE, and not (as i am used to) to R_LIBS-USER.
| but this was only a minor inconvinience (i like to keep the packages in one
| directory).

No, it is even more fine grained:

 - r-cran-* packages always install in /usr/lib/R/site-library

 - (One exception: Base R and recommended packages go to /usr/lib/R/library )

 - local "from source" installation goes by default to
/usr/local/lib/R/site-library
   
and the third part is much better for multi-user setting.  See the comments
in the file /etc/R/Renviron.site if you want to change this.

This has been our default since about 2003 or 2004 when Kurt Hornik and Fritz
Leisch convinced me of that approach in a Vienna bar. It is better.

And this discussion too belonged on r-sig-debian so let's stop here.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

On Sat, Jan 5, 2019 at 9:41 AM Dirk Eddelbuettel <edd at debian.org>
wrote:
>
>
> On 5 January 2019 at 09:14, William Dunlap via R-help wrote:
> | You would get these errors ("R: file or directory not found,
version: file
> | or directory not found...") if you had a ~/.Rprofile file containing
the
> | line 'cat(version$version.string, sep="\n").
>
> Well spotted -- very much so. That is bound to break use within
src/Makevars
> and alike. If you must do something in ~/.Rprofile either make it silent,
or
> make it conditional based on if (interactive()) { ...that_code_here... }
Interesting problem.  One way to workaround this startup issue with:

  PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"`

used by minqa:src/Makevars
(https://r-forge.r-project.org/scm/viewvc.php/pkg/minqa/src/Makevars?view=markup&root=optimizer),
could be to use something like:

  PKG_LIBS = `Rscript -e "cat('LDFLAGS:\n')" -e
"Rcpp:::LdFlags()" |
grep -A 999 "LDFLAGS:" | grep -v "LDFLAGS:"`

and analogously for src/Makevars.win.

But in the bigger picture, maybe there's room for an R/Rscript option
to silence all R startup stdout and/or stderr output?  For example,

  Rscript --quiet-startup -e "Rcpp:::LdFlags()"`

/Henrik

PS. It's probably better to output to stderr in .Rprofile, e.g. by
always using message() instead of cat(). However, that cannot be
assumed to always be the case.
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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On 5 January 2019 at 13:13, Henrik Bengtsson wrote:
| On Sat, Jan 5, 2019 at 9:41 AM Dirk Eddelbuettel <edd at debian.org>
wrote:
| >
| >
| > On 5 January 2019 at 09:14, William Dunlap via R-help wrote:
| > | You would get these errors ("R: file or directory not found,
version: file
| > | or directory not found...") if you had a ~/.Rprofile file
containing the
| > | line 'cat(version$version.string, sep="\n").
| >
| > Well spotted -- very much so. That is bound to break use within
src/Makevars
| > and alike. If you must do something in ~/.Rprofile either make it silent,
or
| > make it conditional based on if (interactive()) { ...that_code_here... }
| 
| Interesting problem.  One way to workaround this startup issue with:
| 
|   PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"`
| 
| used by minqa:src/Makevars
|
(https://r-forge.r-project.org/scm/viewvc.php/pkg/minqa/src/Makevars?view=markup&root=optimizer),

Nothing like 'Read the source, Luke!' :)

The *real* problem here is that command has been *obsolete* since early 2014
or for almost five years -- Rcpp does NOT require linking!

Hence the command is a null-op now, provided for backwards-compatibility:

     R> Rcpp:::LdFlags()
     R> 

Then again minqa has not been updated since 2014 either so there...

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org