Recent and upcoming changes to R-devel

On 07/05/2011 04:21 PM, Duncan Murdoch wrote:

On 05/07/2011 10:17 AM, Tobias Verbeke wrote:

Dear Duncan,

On 07/05/2011 03:25 PM, Duncan Murdoch wrote:

On 05/07/2011 6:52 AM, Tobias Verbeke wrote:

L.S.

On 07/05/2011 02:16 AM, Mark.Bravington at csiro.au wrote:

I may have misunderstood, but:

Please could we have an optional installation that does not*not*

byte-compile base and recommended?

Reason: it's not possible to debug byte-compiled code-- at least not

with the 'debug' package, which is quite widely used. I quite often
end up using 'mtrace' on functions in base/recommended packages to
figure out what they are doing. And sometimes I (and others)
experiment with changing functions in base/recommended to improve
functionality. That seems to be harder with BC versions, and might
even be impossible, as best I can tell from hints in the documentation
of 'compile').

Personally, if I had to choose only one, I'd rather live with the

speed penalty from not byte-compiling. But of course, if both are
available, I could install both.

I completely second this request. All speed improvements and the byte
compiler in particular are leaps forward and I am very grateful and
admiring towards the people that make this happen.

That being said, 'moving away' from the sources (with the lazy loading
files and byte-compilation) may be a step back for R package

developers

that (during development and maybe on separate development

installations

[as opposed to production installations of R]) require
the sources of all packages to be efficient in their work.

As many of you know there is an open source Eclipse/StatET visual
debugger ready and for that application as well (similar to Mark's
request) presence of non-compiled code is highly desirable.

For the particular purpose of debugging R packages, I would even plead
to go beyond the current options and support the addition of an
R package install option that allows to include the sources (e.g. in
a standard folder Rsrc/) in installed packages.

I am fully aware that one can always fetch the source tarballs from
CRAN for that purpose, but it would be much more easy if a simple
installation option could put the R sources of a package in a separate
folder [or archive inside an existing folder] such that R development
tools (such as the Eclipse/StatET IDE) can offer inspection of sources
or display them (e.g. during debugging) out of the box.

If one has the srcref, one can always load the absolutely correct

source

code this way, even if one doesn't know the parent function with
the source attribute.

Any comments?

I think these requests have already been met. If you modify the body of
a closure (as trace() does), then the byte compiled version is
discarded, and you go back to the regular interpreted code. If you
install packages with the R_KEEP_PKG_SOURCE=yes environment variable
set, the you keep all source for all functions. (It's attached to the
function itself, not as a file that may be out of date.) It's possible

Can you expand on when files put inside a package at install time will be out of date compared to the source information attached to a function ?

I (naively) thought the source information was created and attached at install time as well and that it did not change afterwards either.

I guess the arguments for files is that they have precise locations and allow for easy indexing by development tools external to R (but may be corrected here as well).

that byte compiling turns off R_KEEP_PKG_SOURCE, but that is something
that is either easily fixed, or avoided by re-installing without byte
compiling.

Many thanks for your reaction. Is the R_KEEP_PKG_SOURCE=yes environment
variable also supported during R installation ?

Yes, other than the error you saw below, which is a temporary problem.
Not sure which function exceeded the length limit, but the length limit
is going away before 2.14.0 is released.

Thanks again, Duncan, for the clarification.

Is it useful (or just whimsical) to have an R
function that would allow for a given stock CRAN
Windows R installation with stock Windows CRAN binary
add-on packages to add the source information that
would be useful e.g. for a debugger post factum?

I can imagine something like

update.packages(., checkSourcesKept = TRUE)

as I don't think this can currently be solved
with a combination of INSTALL_opts="--with-keep.source"
and type="source" given that there will not be a check
for the presence of source information to determine
which packages require being updated (or in this
case 'completed' with source information).

The alternative scenario would be to expect users
that want this functionality to compile R and all
add-on packages from source (also on Windows or
Mac).

I hope I'm not overlooking anything, but when compiling

ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz

a few minutes ago I encountered the following issue:

[...]

building package 'tools'
mkdir -p -- ../../../library/tools
make[4]: Entering directory
`/home/tobias/rAdmin/R-devel/src/library/tools'
mkdir -p -- ../../../library/tools/R
mkdir -p -- ../../../library/tools/po
make[4]: Leaving directory
`/home/tobias/rAdmin/R-devel/src/library/tools'
make[4]: Entering directory
`/home/tobias/rAdmin/R-devel/src/library/tools'
make[5]: Entering directory
`/home/tobias/rAdmin/R-devel/src/library/tools/src'
making text.d from text.c
making init.d from init.c
making Rmd5.d from Rmd5.c
making md5.d from md5.c
gcc -std=gnu99 -I../../../../include -I/usr/local/include
-fvisibility=hidden -fpic -g -O2 -c text.c -o text.o
gcc -std=gnu99 -I../../../../include -I/usr/local/include
-fvisibility=hidden -fpic -g -O2 -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -I/usr/local/include
-fvisibility=hidden -fpic -g -O2 -c Rmd5.c -o Rmd5.o
gcc -std=gnu99 -I../../../../include -I/usr/local/include
-fvisibility=hidden -fpic -g -O2 -c md5.c -o md5.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o tools.so text.o init.o
Rmd5.o md5.o -L../../../../lib -lR
make[6]: Entering directory
`/home/tobias/rAdmin/R-devel/src/library/tools/src'
make[6]: `Makedeps' is up to date.
make[6]: Leaving directory
`/home/tobias/rAdmin/R-devel/src/library/tools/src'
make[6]: Entering directory
`/home/tobias/rAdmin/R-devel/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[6]: Leaving directory
`/home/tobias/rAdmin/R-devel/src/library/tools/src'
make[5]: Leaving directory
`/home/tobias/rAdmin/R-devel/src/library/tools/src'
make[4]: Leaving directory
`/home/tobias/rAdmin/R-devel/src/library/tools'
Error in parse(n = -1, file = file) :
function is too long to keep source (at line 2967)
Error: unable to load R code in package ?tools?
Execution halted

[...]

tobias at openanalytics:~/rAdmin$ echo $R_KEEP_PKG_SOURCE
yes

I do not have this issue when R_KEEP_PKG_SOURCE is set
to 'false' during compilation.

Best,
Tobias

P.S. One could even consider a post-install option e.g. to add 'real'
R sources (and source references) to Windows packages (which are by
definition already 'installed' and for which such information is not
by default included in the CRAN binaries of these packages).

Prof Brian Ripley wrote:
There was an R-core meeting the week before last, and various

planned

changes will appear in R-devel over the next few weeks.

These are changes planned for R 2.14.0 scheduled for Oct 31.

As we

are sick of people referring to R-devel as '2.14' or '2.14.0',

that

version number will not be used until we reach 2.14.0 alpha. You
will be able to have a package depend on an svn version number

when

referring to R-devel rather than using R (>= 2.14.0).

All packages are installed with lazy-loading (there were 72 CRAN
packages and 8 BioC packages which opted out). This means that

the

code is always parsed at install time which inter alia simplifies

the

descriptions. R 2.13.1 RC warns on installation about packages

which

ask not to be lazy-loaded, and R-devel ignores such requests

(with a

warning).

In the near future all packages will have a name space. If the
sources do not contain one, a default NAMESPACE file will be

added.

This again will simplify the descriptions and also a lot of

internal

code. Maintainers of packages without name spaces (currently

42% of

CRAN) are encouraged to add one themselves.

R-devel is installed with the base and recommended packages
byte-compiled (the equivalent of 'make bytecode' in R 2.13.x, but
done less inefficiently). There is a new option R CMD INSTALL
--byte-compile to byte-compile contributed packages, but that

remains

optional.
Byte-compilation is quite expensive (so you definitely want to

do it

at install time, which requires lazy-loading), and relatively few
packages benefit appreciably from byte-compilation. A larger

number

of packages benefit from byte-compilation of R itself: for

example

AER runs its checks 10% faster. The byte-compiler technology is
thanks to Luke Tierney.

There is support for figures in Rd files: currently with a

first-pass

implementation (thanks to Duncan Murdoch).