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names lost in functions from packages installed by R-devel r74500

4 messages · Francois Rousset, Martin Maechler, Luke Tierney

Original
Francois Rousset
# 
Dear list members,

If I install with R-devel r74500 on Windows (sessionInfo below) the 
attached 'bugdemo' package with the single function

foo <- function() {
 ? named <- c("bar"=TRUE)
 ? print(named)
 ? return(named)
}

then run

 > bugdemo::foo()
[1] TRUE
[1] TRUE

The "bar" name is lost. It is not lost when I define foo in the R 
session instead of using its packaged version.

To reproduce:

=======================================

install.packages("bugdemo_0.1.1.tar.gz",type="source",repos=NULL)

bugdemo::foo()

=======================================

I also tested whether this was a problem with the "R CMD build" step or 
the "install.packages()" step by building with R 3.4.4 and installing 
with R-devel, and reciprocally, and the problem appears to be in the 
install step of R-devel.

F.

=============

 > sessionInfo()
R Under development (unstable) (2018-03-31 r74500)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252? LC_CTYPE=French_France.1252 
LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C?????????????????? LC_TIME=French_France.1252

attached base packages:
[1] stats???? graphics? grDevices utils???? datasets? methods base

other attached packages:
[1] bugdemo_0.1.1

loaded via a namespace (and not attached):
[1] compiler_3.6.0? tools_3.6.0???? withr_2.1.2 memoise_1.1.0?? 
digest_0.6.15?? devtools_1.13.5
 >
Martin Maechler
# 
> Dear list members,
    > If I install with R-devel r74500 on Windows (sessionInfo below) the 
    > attached 'bugdemo' package with the single function

    > foo <- function() {
    > ? named <- c("bar"=TRUE)
    > ? print(named)
    > ? return(named)
    > }

    > then run

    >> bugdemo::foo()
    > [1] TRUE
    > [1] TRUE

    > The "bar" name is lost. It is not lost when I define foo in the R 
    > session instead of using its packaged version.

    > To reproduce:

    > =======================================

    > install.packages("bugdemo_0.1.1.tar.gz",type="source",repos=NULL)

    > bugdemo::foo()



    > =======================================

    > I also tested whether this was a problem with the "R CMD build" step or 
    > the "install.packages()" step by building with R 3.4.4 and installing 
    > with R-devel, and reciprocally, and the problem appears to be in the 
    > install step of R-devel.

Confirmed.

It is a bug somewhere between the byte compiler and
(de)serialization .. really beyond my own expertise:

If you install  without byte compilation *),  foo() behaves as
expected, i.e., does not "lose" the names.

On the other hand, as you mention, if you define foo in the
globalenv, and call it, the JIT kicks in pretty quickly and you
can see that 'foo' is byte compiled as well, but it still does not break.

This is pretty important, so thank you very much for the nice
reproducible report!

Martin Maechler
ETH Zurich

---
*) R-devel CMD INSTALL --no-byte-compile -l ...

    > F.

    > =============

    >> sessionInfo()
    > R Under development (unstable) (2018-03-31 r74500)
    > Platform: x86_64-w64-mingw32/x64 (64-bit)
    > Running under: Windows 7 x64 (build 7601) Service Pack 1

    > Matrix products: default

    > locale:
    > [1] LC_COLLATE=French_France.1252? LC_CTYPE=French_France.1252 
    > LC_MONETARY=French_France.1252
    > [4] LC_NUMERIC=C?????????????????? LC_TIME=French_France.1252

    > attached base packages:
    > [1] stats???? graphics? grDevices utils???? datasets? methods base

    > other attached packages:
    > [1] bugdemo_0.1.1

    > loaded via a namespace (and not attached):
    > [1] compiler_3.6.0? tools_3.6.0???? withr_2.1.2 memoise_1.1.0?? 
    > digest_0.6.15?? devtools_1.13.5
    >> 


    > -- 
    > Fran?ois Rousset
    > CNRS research scientist 
    > <http://www.isem.univ-montp2.fr/recherche/teams/evolutionary-genetics/staff/roussetfrancois/?lang=en> 
    > - Institut des Sciences de l'Evolution (ISE-M)
    > Universit? de Montpellier - Dept. Scientifique B3ESTE

    > x[DELETED ATTACHMENT external: bugdemo_0.1.1.tar.gz, application/gzip]
    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel
Martin Maechler
# 
>> Dear list members,
    >> If I install with R-devel r74500 on Windows (sessionInfo below) the 
    >> attached 'bugdemo' package with the single function

    >> foo <- function() {
    >> ? named <- c("bar"=TRUE)
    >> ? print(named)
    >> ? return(named)
    >> }

    >> then run

    >>> bugdemo::foo()
    >> [1] TRUE
    >> [1] TRUE

    >> The "bar" name is lost. It is not lost when I define foo in the R 
    >> session instead of using its packaged version.

    >> To reproduce:

    >> =======================================

    >> install.packages("bugdemo_0.1.1.tar.gz",type="source",repos=NULL)

    >> bugdemo::foo()



    >> =======================================

    >> I also tested whether this was a problem with the "R CMD build" step or 
    >> the "install.packages()" step by building with R 3.4.4 and installing 
    >> with R-devel, and reciprocally, and the problem appears to be in the 
    >> install step of R-devel.

    > Confirmed.

    > It is a bug somewhere between the byte compiler and
    > (de)serialization .. really beyond my own expertise:

    > If you install  without byte compilation *),  foo() behaves as
    > expected, i.e., does not "lose" the names.

    > On the other hand, as you mention, if you define foo in the
    > globalenv, and call it, the JIT kicks in pretty quickly and you
    > can see that 'foo' is byte compiled as well, but it still does not break.

    > This is pretty important, so thank you very much for the nice
    > reproducible report!

    > Martin Maechler
    > ETH Zurich

    > ---
    > *) R-devel CMD INSTALL --no-byte-compile -l ...

This has been fixed now, both in R-devel (svn rev 74511)
and in R 3.5.0 alpha (r 74513).

I was wrong in that this was related to (de)serialization.
Rather I had forgotten that JIT (just in time) compilation and
explicit compilation may differ in their results.

Thank you again for the report!

Martin Maechler
ETH Zurich



    >> =============

    >>> sessionInfo()
    >> R Under development (unstable) (2018-03-31 r74500)

    [ ........... ]
Luke Tierney
#
On Tue, 3 Apr 2018, Martin Maechler wrote:

            

      
      
      
    

        
Actually the difference is that a function defined in a package is
compiled with more optimizations than one defined at session top
level.  A change had broken a piece of the optimization code, and has
now been fixed. Thanks for the report.

Best,

luke