On Thu, Jun 17, 2010 at 5:22 AM, Patrick Burns pbu...@pburns.seanet.comwrote:
I agree with Hadley, and add that trying
to have an example be both an example and
a test may not be good for the example
aspect either.
Examples should make people who are ignorant
of the function twig as to how
The creation of a research compendium can be viewed as
a form of unit testing, and the fact that R has powerful tools
that support this process (Sweave) could be viewed as one of
its outstanding features (relating these comments back to
the topic of this thread).
If anything, a research
On Thu, Jun 17, 2010 at 9:23 AM, Hadley Wickham had...@rice.edu wrote:
The creation of a research compendium can be viewed as
a form of unit testing, and the fact that R has powerful tools
that support this process (Sweave) could be viewed as one of
its outstanding features (relating
On Thu, Jun 17, 2010 at 7:45 AM, Dominick Samperi djsamp...@gmail.com wrote:
On Thu, Jun 17, 2010 at 5:22 AM, Patrick Burns
pbu...@pburns.seanet.comwrote:
I agree with Hadley, and add that trying
to have an example be both an example and
a test may not be good for the example
aspect
On Thu, Jun 17, 2010 at 5:01 PM, Vincenzo Carey carey...@gmail.com wrote:
Rare is vague. Almost every software package in the Bioconductor
repository has a vignette; the informal advice to contributors is that
the vignette should take the reader through all the steps of a
substantively
On Wed, Jun 16, 2010 at 6:20 AM, Spencer Graves
spencer.gra...@structuremonitoring.com wrote:
Thanks. I added a row for Ruby and columns for Package manager and
Collaborative development platform to the table of Selected Repositories
in the Wikipedia entry for Software repository. Please
Thanks. I added rows for C++, Haskell, and PHP from your
stackoverflow.com reference. I skipped the rest because I wasn't sure
if they really fit and because I ran out of time for this right now.
More suggestions (including encouragement to study the stackoverflow.com
reference more) will
On Wed, Jun 16, 2010 at 12:20 AM, Spencer Graves
spencer.gra...@structuremonitoring.com wrote:
Hi, Gabor:
Thanks. I added a row for Ruby and columns for Package manager and
Collaborative development platform to the table of Selected Repositories
in the Wikipedia entry for Software
Hi Spencer,
I think it is the emphasis on documentation that makes the R
development process unique. Many other languages have equivalents to
CRAN and R-forge - few others require the attention to documentation
that R does.
Hadley
On Tue, Jun 15, 2010 at 8:45 PM, Spencer Graves
Hi, Hadley:
What about the encouragement to add unit tests, if only disguised
as examples?
I've found the unit tests to be a powerful tool to help improve
and maintain the quality of packages to which I contribute. To this
end, Sundar and I added a column Autochecks to the
What about the encouragement to add unit tests, if only disguised as
examples?
Examples are not unit tests. Examples are a convenient way of testing
some aspects of the package, but serve a rather different purpose to
tests. The R community does not emphase testing nearly as much as
other
Hello, All:
What thoughts might you have on The R Software Package
Development Process?
I'm looking for ideas, materials, references, and / or
collaborators for an article on this topic to be submitted to the
Communications of the ACM. My limited experience with other
On Tue, Jun 15, 2010 at 9:45 PM, Spencer Graves
spencer.gra...@structuremonitoring.com wrote:
Hello, All:
What thoughts might you have on The R Software Package Development
Process?
I'm looking for ideas, materials, references, and / or collaborators
for an article on this topic
Hi, Gabor:
Thanks. I added a row for Ruby and columns for Package manager
and Collaborative development platform to the table of Selected
Repositories in the Wikipedia entry for Software repository. Please
correct me if I'm wrong, but the Wiki page for Ruby suggested to me that
Hi,
Terry Therneau's question about package development reminded me of a
different issue. I maintain several packages along with a repository for
them at http://bioinformatics.mdanderson.org/OOMPA/;. Several people
are working on adding features or testing the packages. So, I often want
to
On 12/15/2008 10:31 AM, Kevin R. Coombes wrote:
Hi,
Terry Therneau's question about package development reminded me of a
different issue. I maintain several packages along with a repository for
them at http://bioinformatics.mdanderson.org/OOMPA/;. Several people
are working on adding
I knew that (but forgot to include it in my statement of the question).
Thanks for pointing it out.
Is there any way to convince the selection box (or its developers) to
include the version information that is already available?
Kevin
Duncan Murdoch wrote:
On 12/15/2008 10:31 AM,
On 12/15/2008 10:58 AM, Kevin R. Coombes wrote:
I knew that (but forgot to include it in my statement of the question).
Thanks for pointing it out.
Is there any way to convince the selection box (or its developers) to
include the version information that is already available?
The
Perhaps it would be sufficient as a first step to just display the version
that will be downloaded. That would still only let you pick one but at
least you would know which one.
On Mon, Dec 15, 2008 at 11:43 AM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 12/15/2008 10:58 AM, Kevin R. Coombes
Hi,
I have now spent some time looking at whether this is possible with one
repository. The _easy_ part is getting the selection list to display
more information. Right now, the code that determines what is displayed
is inside a function called explode_bundles that is defined internally
to
On 12 December 2008 at 11:05, Paul Gilbert wrote:
| Yes, there are several options for not distributing tests. I was
| thinking more about how to distribute them with a simple mechanism for
| anyone to run them, but in a way that they are not run by the usual R
| CMD check.
One scheme I
Using parse() is better for syntax errors;
pathnames - list.files(path=pkg/R, pattern=[.](r|R|s|S)$, full.names=TRUE);
for (pathname in pathnames) parse(pathname)
/Henrik
On Thu, Dec 11, 2008 at 4:00 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 11/12/2008 6:04 PM, Terry Therneau wrote:
Thanks to all for the replys. I've learned several things
First -- I didn't miss anything obvious in the documentation. This is good in
one sense at least: I wasn't being blind. I had one misunderstanding pointed
out, which is that I need not worry about my test suite being run with each
Duncan Murdoch wrote:
On 11/12/2008 6:04 PM, Terry Therneau wrote:
I'm making the move of the survival package from my own environment to,
and have stumbled into a vacuum. The R Extensions manual has really
nice
instructions about how to lay out the directories, order the files, and
run
A quick comment on two subjects:
First to get the line # from the command line:
cat pkg/R/* all.R
wc all.R
vim +LINE all.R (or pick you favorite method here...)
From there it should be easy enough to get context. At least enough
to grep back into the R directory.
Also, the use of unit-tests
Jeff Ryan wrote:
A quick comment on two subjects:
First to get the line # from the command line:
cat pkg/R/* all.R
wc all.R
vim +LINE all.R (or pick you favorite method here...)
The tmp file is also indicated in error message, so you can edit that,
go to the line number, find context,
I think the /tmp file gets removed:
ERROR: lazy loading failed for package 'xts'
** Removing '/private/tmp/Rinst625532301/xts'
ERROR
Installation failed.
Removing '/tmp/Rinst625532301'
At least it seems to when I run R CMD from the shell.
Yes, there are several options for not distributing
Mathieu Ribatet mathieu.ribatet at epfl.ch writes:
Dear Terry,
One way to locate which file is wrong - surely not the most brillant
way! You could do an R script that sources each of your .R files within
a for (file in file.names) loop.
When R will stop, it will indicate which file has
I'm making the move of the survival package from my own environment to,
and have stumbled into a vacuum. The R Extensions manual has really nice
instructions about how to lay out the directories, order the files, and
run tests for DISTRIBUTION of a product, but I can't find anything on how
to
Dear Terry,
One way to locate which file is wrong - surely not the most brillant
way! You could do an R script that sources each of your .R files within
a for (file in file.names) loop.
When R will stop, it will indicate which file has a wrong syntax and
more info.
Cheers,
Mathieu
Terry
Hi Terry
I suspect many people struggle with similar issues.
The new version of mvbutils contains a number of routines that facilitate
creation maintenance of a package, hopefully through its entire life-cycle:
from documenting your own stuff for personal use, through giving out
On 11/12/2008 6:04 PM, Terry Therneau wrote:
I'm making the move of the survival package from my own environment to,
and have stumbled into a vacuum. The R Extensions manual has really nice
instructions about how to lay out the directories, order the files, and
run tests for DISTRIBUTION of
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