> Gabe Becker
> on Tue, 3 Apr 2018 21:16:12 -0700 writes:
> Martin et al,
> I have submitted a patch on bugzilla which fixes all of the examples I
> could easily find which were not already writing only to temporary files
> switching to a
Thanks, fixed in R-devel.
On 12/20/2017 02:38 PM, Gábor Csárdi wrote:
It does give a warning, but then it overwrites the files, anyway.
Reproducible example below.
This is R 3.4.3, but it does not seem to be fixed in R-devel:
Martin et al,
I have submitted a patch on bugzilla which fixes all of the examples I
could easily find which were not already writing only to temporary files or
switching to a temp directory before writing files to the working
Thanks Dirk. IMO the package is in good shape otherwise. I'll wait hear
from the CRAN maintainers.
On Wed, Apr 4, 2018 at 2:53 PM, Dirk Eddelbuettel wrote:
> On 4 April 2018 at 14:15, Steven Scott wrote:
> | These appear to be caused by an ill formed std::set or
On 4 April 2018 at 14:15, Steven Scott wrote:
| These appear to be caused by an ill formed std::set or std::function in the
| STL implementation of the host machine. If I'm reading that wrong someone
| please let me know.
AFAICT it needs C++11 explicitly set which that machine (with a new
I recently submitted a new version (v0.8.19) of my FSA package to CRAN. It was
rejected at the pre-test level because of problems with automatic checks. There
were three links for me to see what these problems were.
The first link from CRAN was to a win-builder check log
I've been trying to update the Boom package to the next version, and it
hasn't been going so well. Hoping someone can help me figure out what next
steps I should take.
I got the attached mail from auto-check. From what I can tell the new
version of Boom (0.8.0) has two issues. Some long path
Hi Gabe & Levi,
Here is my current plan:
1 - complete the requirements checklist (
2 - get feedback the in-house NGS team, and then from the rest of in-house
bioinformatics (others who use R more may spot some issues)
3 - set up pull
This is a subjective question. As a paper reviewer I like to see the
package accepted. That increases trust. As a package reviewer I like some
idea of what the package actually does, so a statement like "we implement X
which is described in (XX, in preparation), is also irritating.
A package I maintain (ADaCGH2) is giving an error during build
because Cairo is not available. A quick look at other packages that depend
on Cairo shows the same problem there.
What should we do?
Some recent changes in bioc-devel are causing trouble with
SummarizedExperiment objects if the rowRanges slot inherits from
GRangesList. Please see example below.
Thanks in advance for your help.
> ## SGVariants object inherits from GRangesList
Thanks for your replies. I had a look at the greta package
(https://github.com/greta-dev/greta) on CRAN that uses tensorflow,
which seemingly exports the install_tensorflow function but still
requires the user to call it, so it looks like that's the best way to
go for now. I'll submit our
I am trying to do a rbind a normal (in memory) matrix with a HDF5Matrix object
or DelayedArray object and I am hitting problems. I’m using the development
version of R and bioconductor (as of 2 weeks ago) and HDF5Array_1.7.9,
DelayedArray_0.5.23 — see sessionInfo at end of email.
Perhaps my newly submitted package times out because no web browser is
available on the build systems?
The build times out on linux and OS X at the “creating vignettes” stage. But
since the package is a wrapper around igv.js running in the browser, no
I agree with Kasper. I generally like the approach of getting the software
out there sooner rather than later. Especially if the paper you are talking
about is a method paper about the software algorithm, rather than a result
paper. In that case, getting it into a public, DOI'ed
Does `rbind(testhdf, DelayedArray(testdata))` give you what you want?
On Wed, 4 Apr 2018 at 14:58 Elizabeth Purdom
> I am trying to do a rbind a normal (in memory) matrix with a HDF5Matrix
> object or DelayedArray object and I am hitting problems.
Yes that does get around the problem, thanks!
I would note, though, that for me at least, its a workaround and not ideal
functionality, since to use it in my function means that I now I have to have
two different code snippets depending on whether my input object (here
`testhdf`) is a matrix
I'm surprised that DelayedMatrix inherits from DataTable. Originally
at least, DataTable was meant to represent a data.frame-like object,
not a matrix-like object. Since rbind2() and cbind2() assume that
DataFrame is a valid default implementation of DataTable, they will
coerce the matrix to a
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