Hi,
I am a graduate student at CMU and I am interested in studying scientific
software eco-systems such as Bioconductor.
I wanted to know if there is a publicly available issue tracker / bug
reports for Bioconductor or something that I can gain read-only access to.
Thank you all for your help.
Martin and Val.
I re-ran writeVcf on our (G)VCF data (34790518 ranges, 24 geno fields) with
profiling enabled. The results of summaryRprof for that run are attached,
though for a variety of reasons they are pretty misleading.
It took over an hour to write (3700+seconds), so it's definitely a
Hi Arun,
- Original Message -
From: Arun Kalyanasundaram arunk...@cs.cmu.edu
To: bioc-devel@r-project.org
Sent: Wednesday, August 27, 2014 10:01:44 AM
Subject: [Bioc-devel] Issue tracker for Bioconductor
Hi,
I am a graduate student at CMU and I am interested in studying
The profiling I attached in my previous email is for 24 geno fields, as I
said, but our typical usecase involves only ~4-6 fields, and is faster but
still on the order of dozens of minutes.
Sorry for the confusion.
~G
On Wed, Aug 27, 2014 at 11:45 AM, Gabe Becker becke...@gene.com wrote:
Hi, Arun. There is not such a system that covers the entire Bioconductor
project. Since packages are largely contributed by diverse developers,
there are many disparate bug tracking systems in use (and many packages
with no formal bug tracking). There is a facility in R to allow package
authors
Michael Friendly frien...@yorku.ca
on Tue, 26 Aug 2014 17:58:34 -0400 writes:
I'm updating the Lahman package of baseball statistics to the 2013
release. In addition to
the main data sets, the package also contains several convenience
functions that make use
of
The change would seem to be this
\item \command{R CMD check} now by default checks code usage
directly on the package namespace without loading and attaching
the package and its suggests and enhances.
and perhaps the remedies could be stated more clearly?
Putting the data
Hello,
I'm very new to R and don't know much about it yet. I would like
to develop R-programs that work with data of sizes of 10^10 - 10^11
data points. We have very-high-memory machines with ~256 GB, but it
would significantly help if I could store the data points in single
precision in RAM
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512
hi,
on OS X, when you try and use something which depends on X11, and you
don't have XQuartz installed, you receive an error message, it directs
you to download XQuartz, and then it euthanizes your process.
(my guess is that there is a skeleton
I have had similar notes, but in cases where the dataset was created
internally by a function:
* checking R code for possible problems ... NOTE
vm_diagnostics: no visible binding for global variable 'Median'
vm_diagnostics: no visible binding for global variable 'Index'
vm_diagnostics: no visible
Re solution 2, the following is in the function tabFarsDead()
the latest (0.55) version of gamclass:
data('FARS', package='gamclass', envir=environment())
FARS - get(FARS, envir=environment())
The second statement is, strictly, redundant, but it
makes the syntax checker happy. Another
On 8/27/2014 5:24 AM, Martin Maechler wrote:
Michael Friendly frien...@yorku.ca
on Tue, 26 Aug 2014 17:58:34 -0400 writes:
I'm updating the Lahman package of baseball statistics to the 2013
release. In addition to
the main data sets, the package also contains several
Mario,
On Aug 27, 2014, at 4:03 AM, Mario Emmenlauer ma...@emmenlauer.de wrote:
Hello,
I'm very new to R and don't know much about it yet. I would like
to develop R-programs that work with data of sizes of 10^10 - 10^11
data points. We have very-high-memory machines with ~256 GB, but it
On Aug 27, 2014, at 5:45 AM, Jonathon Love j...@thon.cc wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512
hi,
on OS X, when you try and use something which depends on X11, and you
don't have XQuartz installed, you receive an error message, it directs
you to download XQuartz, and
On 27/08/2014 14:43, Simon Urbanek wrote:
Mario,
On Aug 27, 2014, at 4:03 AM, Mario Emmenlauer ma...@emmenlauer.de wrote:
Hello,
I'm very new to R and don't know much about it yet. I would like
to develop R-programs that work with data of sizes of 10^10 - 10^11
data points. We have
On 8/27/2014 9:29 AM, Michael Friendly wrote:
It works in the sense that Lahman::Label(yearID) will
work even when Lahman is not in the search path,
but R-devel CMD check will still give the same NOTE,
though you can argue that that note is actally a false positive.
So, this would be
Using data() in a package with lazyloaded data seems like asking for trouble to
me. But you're making me curious (and I'm too lazy[*] to set up for rebuilding
the package myself):
Did you actually try putting battingLabels friends in the namespace? What
happened?
A workaround could be to use
I think the right answer _is_ to export the lazy data; the question is how to
do it. There's nothing particularly strange about exporting non-functions
(letters would be an example, save for the special status of package:base).
If you attach the package, the lazyloaded data appear in the
http://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Suggested-packages
suggests e.g. Lahman::battingLabels, and that does work for lazy-loaded
datasets (which is what these appear to be).
We have seen a couple of other instances in which this was needed for
code within the package.
On 8/27/2014 10:41 AM, peter dalgaard wrote:
Using data() in a package with lazyloaded data seems like asking for trouble to
me. But you're making me curious (and I'm too lazy[*] to set up for rebuilding
the package myself):
Did you actually try putting battingLabels friends in the
On Wed, Aug 27, 2014 at 12:51 PM, Michael Friendly frien...@yorku.ca wrote:
On 8/27/2014 10:41 AM, peter dalgaard wrote:
Using data() in a package with lazyloaded data seems like asking for
trouble to me. But you're making me curious (and I'm too lazy[*] to set up
for rebuilding the package
On 27 Aug 2014, at 19:51 , Michael Friendly frien...@yorku.ca wrote:
- Peter Dalgaard noted the change in R-devel, and nobody so far has suggested
a working remedy, so a clean solution
seems warranted.
Actually, both Peter Dalgaard and Brian Ripley suggested Lahman:battingLabels,
and,
On 27 Aug 2014, at 16:48 , Hadley Wickham h.wick...@gmail.com wrote:
I think the right answer _is_ to export the lazy data; the question is how
to do it. There's nothing particularly strange about exporting non-functions
(letters would be an example, save for the special status of
Dear list,
This is related to the change discussed in the thread no visible binding
for global variables for data sets in a package.
I went to look at the Check results for one of my packages (analogue) on
CRAN: http://cran.r-project.org/web/checks/check_results_analogue.html
Under the r-devel
Is that the cause of these NOTEs? Is the expectation that if I am using a
function from a package, even a package that I have in Depends:, that I
have to explicitly declare these imports in NAMESPACE?
Yes.
(Otherwise your package won't work if it's only attached and not
loaded. i.e. if
On 27 August 2014 15:24, Hadley Wickham h.wick...@gmail.com wrote:
Is that the cause of these NOTEs? Is the expectation that if I am using a
function from a package, even a package that I have in Depends:, that I
have to explicitly declare these imports in NAMESPACE?
Yes.
(Otherwise
- Original Message -
From: Gavin Simpson ucfa...@gmail.com
To: Hadley Wickham h.wick...@gmail.com
Cc: r-devel@r-project.org
Sent: Wednesday, August 27, 2014 3:01:53 PM
Subject: Re: [Rd] Re R CMD check checking in development version of R
On 27 August 2014 15:24, Hadley Wickham
On 28.08.2014 00:19, Gavin Simpson wrote:
On 27 August 2014 16:09, Dan Tenenbaum dtene...@fhcrc.org wrote:
- Original Message -
From: Gavin Simpson ucfa...@gmail.com
To: Hadley Wickham h.wick...@gmail.com
Cc: r-devel@r-project.org
Sent: Wednesday, August 27, 2014 3:01:53 PM
Subject:
On 27 August 2014 16:25, Uwe Ligges lig...@statistik.tu-dortmund.de wrote:
snip /
Again, I am happy to be re-educated on this though :-)
If you like, you can fill the search path with lots of packages (and make
masking of functions more likely), but you shoudl really import into your
On Wed, Aug 27, 2014 at 5:01 PM, Gavin Simpson ucfa...@gmail.com wrote:
On 27 August 2014 15:24, Hadley Wickham h.wick...@gmail.com wrote:
Is that the cause of these NOTEs? Is the expectation that if I am using
a
function from a package, even a package that I have in Depends:, that I
On Aug 27, 2014 5:24 PM, Hadley Wickham
snip /
I'd say: Depends is a historical artefact from ye old days before
package namespaces. Apart from depending on a specific version of R,
you should basically never use depends. (The one exception is, as
mentioned in R-exts, if you're writing
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