Re: [Bioc-devel] RankProd (development) - install and build error in oaxaca

Hi Francesco, gmp is installed on oaxaca, but not Rmpfr. Both are CRAN packages. As you can see by visiting several CRAN package landing pages, CRAN doesn't provide Mac binaries for r-devel yet: http://cran.fhcrc.org/web/packages/Rmpfr/index.html Our Mac and Windows builders always try to

Re: [Bioc-devel] Build OK in devel, Mac OS error in release (CausalR)

Hi Glyn, Looks like the problem went away today: https://bioconductor.org/checkResults/3.4/bioc-LATEST/CausalR/morelia-buildsrc.html AFAIK we didn't touch anything on morelia recently. The only thing we did a couple of days ago was reboot the machine (which had not been rebooted for months).

Re: [Bioc-devel] incomplete vignette on macosx

Hi Renan, I'm not familiar with Rhtml vignettes and I couldn't get to the bottom of this but it seems to me that the calls to dev.new() in your plotting functions somehow get in the way and confuse the knit engine. If I remove them the problem goes away i.e. the images get generated and embedded

Re: [Bioc-devel] Build error: Dependency 'Biobase' is not available

Hi Shraddha, On 10/26/2016 11:12 AM, Shraddha Pai wrote: Hello BioC developers, I'm not sure why the nightly build of my package IdeoViz is reporting this error on tokay (see message below). It seems to me that not having Biobase installed is such a fundamental problem that the package should

Re: [Rd] BUG?: On Linux setTimeLimit() fails to propagate timeout error when it occurs (works on Windows)

Spencer also had tools and rsconnect loaded (via a namespace) but it doesn't seem to make a difference for me if I load them. It also doesn't seem to matter for me whether it is CRAN R, locally built R, Terminal, R.app. However, RStudio differs > setTimeLimit(elapsed=1) Error: reached elapsed

Re: [Bioc-devel] Build error: Dependency 'Biobase' is not available

Hi Hervé, Thank you for the feedback, that makes sense. Thanks also to all the BioC system admins for maintaining such a large system of interdependent packages. BioC makes complex genomics data analysis so easily accessible to community researchers. Regards, Shraddha On Wed, Oct 26, 2016 at

[Bioc-devel] Build error: Dependency 'Biobase' is not available

Hello BioC developers, I'm not sure why the nightly build of my package IdeoViz is reporting this error on tokay (see message below). It seems to me that not having Biobase installed is such a fundamental problem that the package should have been flagged when it first got submitted (sometime in

Re: [Bioc-devel] ignoreSelf Option for findOverlaps of GenomicRanges Query

On 10/26/2016 06:21 AM, Michael Lawrence wrote: There is only one general method for this case, on Vector,missing, so it's consistent by definition. Note that ignoreSelf and ignoreRedundant are defunct (and maybe even removed now). Yep, defunct in release. Just removed them now in devel

Re: [Rd] improve 'package not installed' load errors?

This might be a good opportunity for developing some error classes for signaling these errors that can be used to programmatically do something more useful at the library/require. I can try to help with that. Best, luke On Wed, 26 Oct 2016, Martin Maechler wrote: Duncan Murdoch

Re: [Bioc-devel] ignoreSelf Option for findOverlaps of GenomicRanges Query

Hi Dario, The situation for a GenomicRanges object is no different from the situation for a IRanges object. In both case, when subject is missing, the findOverlaps,Vector,missing method is called. This method accepts the 'drop.self' and 'drop.redundant' arguments thru the ellipsis: >

Re: [Bioc-devel] RankProd (development) - install and build error in oaxaca

Hi Got similar error here http://bioconductor.org/checkResults/3.5/bioc-LATEST/fCCAC/tokay2-buildsrc.html "there is no package called 'Biobase'" Best, Pedro On 26 Oct 2016, at 13:51, Francesco Del Carratore wrote: > Hi All, > I just noticed that there is an error

[Bioc-devel] RankProd (development) - install and build error in oaxaca

Hi All, I just noticed that there is an error in build report of the development version of my package ( http://bioconductor.org/checkResults/3.5/bioc-LATEST/RankProd/oaxaca-install.html ). There are no problems for the release version of the package, apparently the dependencies "Rmpfr" and "gmp"

[Bioc-devel] Build OK in devel, Mac OS error in release (CausalR)

Hi All, We currently have the same version of our package CausalR up in devel and release, but while devel is showing build OK for all 3 platforms, release is showing an build error for Mac OS. The error is related to the vignette building: * creating vignettes ... ERROR Error in texi2dvi(file

[Rd] A few typos in config.site

I noticed the following typos in the file "config.site": The word "compilier" should be "compiler", occurs twice (in the R-devel version). Also, "It not" should be "If not" and "overriden" should be "overridden". -- Mikko Korpela Department of Geosciences and Geography University of Helsinki

Re: [Rd] improve 'package not installed' load errors?

On 26/10/2016 5:52 AM, Martin Maechler wrote: Duncan Murdoch on Mon, 24 Oct 2016 14:54:16 -0400 writes: > On 24/10/2016 1:51 PM, Kevin Ushey wrote: >> Hi R-devel, >> >> One of the more common issues that new R users see, and become stumped >>

[Bioc-devel] ignoreSelf Option for findOverlaps of GenomicRanges Query

Good day, For an IRanges object, findOverlaps has ignoreSelf and ignoreRedundant options. However, these aren't available for a GenomicRanges input object, even though the subject parameter is optional and a query GRanges object can be overlapped with itself. Could this be changed to be

Re: [Rd] improve 'package not installed' load errors?

> Duncan Murdoch > on Mon, 24 Oct 2016 14:54:16 -0400 writes: > On 24/10/2016 1:51 PM, Kevin Ushey wrote: >> Hi R-devel, >> >> One of the more common issues that new R users see, and become stumped >> by, is error messages during package

Re: [Rd] BUG?: On Linux setTimeLimit() fails to propagate timeout error when it occurs (works on Windows)

> On 26 Oct 2016, at 04:44, Henrik Bengtsson wrote: > ... > This looks like a bug to me. Can anyone on macOS confirm whether this > is also a problem there or not? > Tried it on macOS El Capitan and got this (running in R.app with R version 3.3.2 RC

Re: [Rd] BUG?: On Linux setTimeLimit() fails to propagate timeout error when it occurs (works on Windows)

On 26 Oct 2016, at 04:44 , Henrik Bengtsson wrote: > This looks like a bug to me. Can anyone on macOS confirm whether this > is also a problem there or not? I don't know whether it is a problem ( ;-) ), but it does the same thing (checked Mavericks, Yosemite and

Re: [Rd] BUG?: On Linux setTimeLimit() fails to propagate timeout error when it occurs (works on Windows)

> Spencer Graves > on Tue, 25 Oct 2016 22:02:29 -0500 writes: > On 10/25/2016 9:44 PM, Henrik Bengtsson wrote: >> setTimeLimit(elapsed=1) causes a timeout error whenever a call takes >> more than one second. For instance, this is how it works