Re: [Rd] Base R examples that write to current working directory

2018-04-04 Thread Martin Maechler
> 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 or > switching to a

Re: [Rd] utils::unzip ignores overwrite argument, effectively

2018-04-04 Thread Tomas Kalibera
Thanks, fixed in R-devel. Tomas 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:

Re: [Rd] Base R examples that write to current working directory

2018-04-04 Thread Gabe Becker
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 directory. https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17403

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission Boom 0.8

2018-04-04 Thread Steven Scott
Thanks Dirk. IMO the package is in good shape otherwise. I'll wait hear from the CRAN maintainers. S 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

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission Boom 0.8

2018-04-04 Thread Dirk Eddelbuettel
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

[R-pkg-devel] CRAN Pre-Test Problems -- FSA Package

2018-04-04 Thread Derek Ogle
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

[R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission Boom 0.8

2018-04-04 Thread Steven Scott
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

Re: [Bioc-devel] Missed deadline

2018-04-04 Thread Kenneth Condon
Hi Gabe & Levi, Here is my current plan: 1 - complete the requirements checklist ( http://www.bioconductor.org/developers/package-submission/) 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

Re: [Bioc-devel] Missed deadline

2018-04-04 Thread Kasper Daniel Hansen
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. Unless you're

[Bioc-devel] BioC 3.7: build failing on Mac (merida2) because Cairo not available

2018-04-04 Thread Ramon Diaz-Uriarte
Dear All, A package I maintain (ADaCGH2) is giving an error during build (http://bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/merida2-buildsrc.html) because Cairo is not available. A quick look at other packages that depend on Cairo shows the same problem there. What should we do?

[Bioc-devel] Bioc-devel changes and SummarizedExperiment class

2018-04-04 Thread Leonard Goldstein
Hi Hervé, 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. Leonard -- > library(SGSeq) > > ## SGVariants object inherits from GRangesList >

Re: [Bioc-devel] Tensorflow support for bioconductor packages

2018-04-04 Thread Kieran Campbell
Hi all, 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

[Bioc-devel] problem in rbind with DelayedArray / HDF5Array package

2018-04-04 Thread Elizabeth Purdom
Hello, 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.

[Bioc-devel] web browser support missing in the build system? new package, IGV

2018-04-04 Thread Paul Shannon
Perhaps my newly submitted package times out because no web browser is available on the build systems? https://github.com/paul-shannon/IGV 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

Re: [Bioc-devel] Missed deadline

2018-04-04 Thread Gabe Becker
Kenneth, 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

Re: [Bioc-devel] problem in rbind with DelayedArray / HDF5Array package

2018-04-04 Thread Peter Hickey
Does `rbind(testhdf, DelayedArray(testdata))` give you what you want? On Wed, 4 Apr 2018 at 14:58 Elizabeth Purdom wrote: > Hello, > > I am trying to do a rbind a normal (in memory) matrix with a HDF5Matrix > object or DelayedArray object and I am hitting problems.

Re: [Bioc-devel] problem in rbind with DelayedArray / HDF5Array package

2018-04-04 Thread Elizabeth Purdom
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

Re: [Bioc-devel] problem in rbind with DelayedArray / HDF5Array package

2018-04-04 Thread Michael Lawrence
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