Hi Luke,
Do you mean bins or bin pairs?
If you want to just bin the coverage in terms of the linear genome,
there should be ways to do that outside of InteractionSet or
GenomicInteractions. This is just dealing with standard genomic interval
data; extract the anchor coordinates and plug it
> On Mar 22, 2019, at 7:25 PM, peter dalgaard wrote:
>
>
>
>> On 22 Mar 2019, at 18:07 , Martin Maechler
>> wrote:
>>
>> gives (on Linux R 3.5.3, Fedora 28)
>>
>> d=10 d=7 d=2 d=1 d=0
>> [1,] "123456" "123456" "123456" "1e+05" "%#4.0-1e"
>>
> On 22 Mar 2019, at 18:07 , Martin Maechler wrote:
>
> gives (on Linux R 3.5.3, Fedora 28)
>
> d=10 d=7 d=2 d=1 d=0
> [1,] "123456" "123456" "123456" "1e+05" "%#4.0-1e"
> [2,] "12345.6""12345.6""12346" "12346" "%#4.0-1e"
> [3,]
Hi Peter and Rolf,
In fact there was a missing EOL at the end, but I had already fixed
that. It was an error in a previous function (delim.table) and Rolf's
little function spotted it. Thanks to both of you for quick and
helpful answers.
Jim
On Fri, Mar 22, 2019 at 9:49 PM Rolf Turner wrote:
>
Not a CRAN maintainer, but from my experience, it sounds like you're
hitting some very unusual hiccup here - that's unfortunate. I just
had a look around at ftp://cran.r-project.org/incoming/ and your
package is not there anymore. Just a wild guess but I wonder if your
email reply back to CRAN
Maybe the question arises whether to store a reduced representation like, say,
singleCellExperiment does?
In any event, I agree that endomorphism will be expected by users and, like
tximport collapsing many transcripts into each gene, the sensible thing to do
is just to return a binned (less
Why is this not "just" a function which transforms one GI into another GI?
Thats what it seems to me.
On Fri, Mar 22, 2019 at 12:31 PM Luke Klein wrote:
> I am writing a package that will extend the GenomicInteractions class. I
> am a statistician, so I may not know best practices when it
Hi Koustav,
From a Build System point of view, we certainly don't want packages to
write files to the user's home (or to the current directory, which might
be different from the user's home) during 'R CMD build' and 'R CMD
check'. (Note that there is actually no guarantee that the current
> peter dalgaard
> on Fri, 22 Mar 2019 17:30:19 +0100 writes:
> FWIW, it doesn't seem to be happening on Mac OS:
>> format(2^30, digits=0)
> [1] "1.e+09"
>> prettyNum(12345.6, digits=0)
> [1] "1.e+04"
> A glibc misfeature?
It seems (and note we are talking
In response to Vince’s comment:
My package already has an implementation for checking if the file exists and
then to explicitly require the user’s permission for removing the file
In response to Lori’s comment:
In my implementation of BiocFileCache, if a user provides a filename without an
I am writing a package that will extend the GenomicInteractions class. I am a
statistician, so I may not know best practices when it comes to extending
existing classes (eg. should I make a new slot or simply add a column to the
`elementMetadata`? Are there existing functions that already do
FWIW, it doesn't seem to be happening on Mac OS:
> format(2^30, digits=0)
[1] "1.e+09"
> prettyNum(12345.6, digits=0)
[1] "1.e+04"
A glibc misfeature?
-pd
> On 22 Mar 2019, at 10:10 , Martin Maechler wrote:
>
> Thank you, Robert for raising this here !
>
>> Robert McGehee
>>on
Dear all,
if I understand correctly, the main problem stems from the fact that the
function has set a default value for "Output.Filename” argument.
Would it then be ok to have NO default value for Output.Filename? So as to
force the user to specify one
Or alternatively, the solution
To chime and expand a bit on Vince's comments:
I feel Bioconductor's position when accepting packages , with few exceptions,
is that nothing should be written or saved to a users directory without the
expressed permission of the user for fear of overwriting a users own directory
or files
Guidelines on this topic do not seem to be present in our web
site; there is a link to Wickham's guide but I don't see that it
confronts the topic. I will make some unofficial and possibly
wrong remarks.
Suppose my function has to create a file "foo.txt". If I do it
in the working folder, I
Hello,
My package HiCBricks was submitted and accepted under the previous 3.8 release
of Bioconductor.
At the time, during package review, my reviewer had expressed reservations
towards my package creating
files in the current working directory.
[REQUIRED] CreateLego() creates HDF5 files in
Hi,
Thanks for this. To be clear, I did not intend to use scientific notation, I
just happened to stumble upon this when using prettyNum on numbers large enough
that R switched to scientific notation and I noticed the problem. I just made
this artificial example just to show with an example
Dear List,
section "6.3 Random number generation" of WRE [1] lists unif_rand(),
norm_rand() and exp_rand() as the interface to R's RNG. Now
R_ext/Random.h also has
double R_unif_index(double);
Can this be also treated as an official API function that may be called
from a package?
Thanks
Hello,
we have resubmitted the package 'volesti'. I got the email and
confirmed submission. Later I got the confirmation email starting:
"The following package was uploaded to CRAN:..." and then the email on
automated check complaining about the same 2 notes as in the previous
submission. I
The final day to submit new packages to the Bioconductor contributions tracker
to have a shot at being included in the upcoming 3.9 release is Friday April
5th.
Please note: submission by this date does not guarantee it will be included -
the package must undergo an official review and be
Hi all,
The release of Bioconductor 3.9 will be on Tuesday April 30:
https://www.bioconductor.org/developers/release-schedule/
Over the next weeks we'll announce key dates on the on bioc-devel@r-project.org
mailing list. Thanks in advance for cleaning up packages and getting those last
On 22/03/19 11:18 PM, Jim Lemon wrote:
Hi,
I have been attempting to check a new version of the prettyR package,
and have struck a difficult problem. The check fails at the
installation, and when I track the error, it is "Unexpected end of
input" in the xtab function. I have tried a number of
It could use a little whitespace, but I (and the Rstudio script editor) can't
spot anything wrong, like mismatching braces or parens, and all
else-at-beginning-of-line is inside the function.
Could it be an incomplete last line?
-pd
> On 22 Mar 2019, at 11:18 , Jim Lemon wrote:
>
> Hi,
> I
Hi,
I have been attempting to check a new version of the prettyR package,
and have struck a difficult problem. The check fails at the
installation, and when I track the error, it is "Unexpected end of
input" in the xtab function. I have tried a number of things as I
thought that it was a
Full schedule is available on developer.r-project.org.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk Priv: pda...@gmail.com
Thank you, Robert for raising this here !
> Robert McGehee
> on Thu, 21 Mar 2019 20:56:19 + writes:
> R developers,
> Seems I get a bad result ("%#4.0-1e" in particular) when trying to use
prettyNum digits=0 with scientific notation. I tried on both my Linux box and
on
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