Re: [Rd] Suggested dependencies in context of R CMD check

On 04/04/2016 01:56 PM, Duncan Murdoch wrote: On 04/04/2016 1:35 PM, Dirk Eddelbuettel wrote: On 4 April 2016 at 07:25, Hadley Wickham wrote: | On Sat, Apr 2, 2016 at 5:33 AM, Jan Górecki wrote: | | In principle, I believe a package should pass R CMD check if no |

Re: [Bioc-devel] readVcf appears to cause Windows i386 check error

There is a fresh build of your package now and it looks like this problem has cleared up. It seems there was a broken version of Biostrings installed, I'm investigating how it happened. Dan - Original Message - > From: "Riester, Markus" > To: "bioc-devel"

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

>If I recall correctly, some eigen vectors had their >direction flipped (negative values became positive and vice versa). >Did you notice anything of this kind when running 'make check' and >'make check recommended' ? It is important to us that numeric results >are reproducible between versions of

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

On Mon, Apr 4, 2016 at 7:39 PM, Jeroen Ooms wrote: > On Sun, Apr 3, 2016 at 6:44 PM, Ray Donnelly > wrote: > > I've started to look into building R for Windows using MSYS2 as both the > > build environment and tools + libraries provider (where

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

On Mon, Apr 4, 2016 at 12:29 PM, Duncan Murdoch wrote: > On 03/04/2016 9:44 PM, Ray Donnelly wrote: > >> Hi, >> >> Apologies for breaking the threading on this, I've only just signed up to >> the list and the last email was from September 2015. >> >> I've started to

[Bioc-devel] Bioconductor 3.3 release schedule has been updated to reflect R release delay

Bioconductors-- In case you missed it, R announced a delay in its release schedule: https://stat.ethz.ch/pipermail/r-announce/2016/000599.html Their full (updated) release schedule is at http://developer.r-project.org/ Accordingly, Bioconductor has updated its release schedule:

[Rd] debug/recover/.Internal

I was surprised by difference between using options(error=browser) and options(error=recover) when handling an error from sys.frame that I assume is related to the fact that the error is thrown from the .Internal and the 'which' parameter to the closure isn't available. >

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

On Sun, Apr 3, 2016 at 6:44 PM, Ray Donnelly wrote: > I've started to look into building R for Windows using MSYS2 as both the > build environment and tools + libraries provider (where possible). Thanks for your reply, and for the patches. Last time I had a look at this

Re: [Bioc-devel] readVcf appears to cause Windows i386 check error

Thanks for the report. Dan is looking into it. Valerie On 04/04/2016 08:44 AM, Riester, Markus wrote: > Hi, > > my package PureCN started to fail CHECK on Windows (i386 only, x64 seems to > work). > > http://bioconductor.org/spb_reports/PureCN_0.99.6_buildreport_20160402193854.html > > Looks

Re: [Bioc-devel] readVcf appears to cause Windows i386 check error

There are two installations of R on moscato2; one for the nightly builds and one for the single package builder. I can reproduce this problem on the latter but not the former. I will look into it further, pulling in others as necessary. Thanks for the report, Dan - Original Message -

Re: [Rd] Suggested dependencies in context of R CMD check

On 04/04/2016 1:35 PM, Dirk Eddelbuettel wrote: On 4 April 2016 at 07:25, Hadley Wickham wrote: | On Sat, Apr 2, 2016 at 5:33 AM, Jan Górecki wrote: | | In principle, I believe a package should pass R CMD check if no | suggested packages are installed. However, since this

Re: [Rd] Suggested dependencies in context of R CMD check

On 4 April 2016 at 07:25, Hadley Wickham wrote: | On Sat, Apr 2, 2016 at 5:33 AM, Jan Górecki wrote: | | In principle, I believe a package should pass R CMD check if no | suggested packages are installed. However, since this is not currently The relevant manual says

[Rd] Understanding POSIXct creation on different OSes.

Hello, Following Dirk's post here: https://github.com/Rdatatable/data.table/issues/1619 we would like to clarify if this is the right behaviour, and if so, the rationale behind it. Here's the summary (thanks to Dirk and Joshua): Sys.setenv("TZ"="America/Chicago") dates = as.Date("2016-03-02") +

[Bioc-devel] readVcf appears to cause Windows i386 check error

Hi, my package PureCN started to fail CHECK on Windows (i386 only, x64 seems to work). http://bioconductor.org/spb_reports/PureCN_0.99.6_buildreport_20160402193854.html Looks like a problem in VariantAnnotation to me, or is this something I need to fix? Thanks a lot, Markus

Re: [Rd] Suggested dependencies in context of R CMD check

Jan and Hadley, There's also the issue of tests, vignettes, or examples requiring Suggested packages (one of the core applications of Suggests, in fact). These are all checked by R CMD check, so to ensure any package which should pass check would do so without suggested packages installed would

Re: [Bioc-devel] dropping perceval and petty from supported platforms

Yes, you can remove it from devel. Dan - Original Message - > From: "Ramon Diaz-Uriarte" > To: "bioc-devel" > Cc: "ramon diaz" > Sent: Monday, April 4, 2016 2:30:34 AM > Subject: [Bioc-devel] dropping perceval and

Re: [Rd] Suggested dependencies in context of R CMD check

On Sat, Apr 2, 2016 at 5:33 AM, Jan Górecki wrote: > Dear R team, > > Are suggested dependencies mandatory in context of `R CMD check` when > using env var `_R_CHECK_FORCE_SUGGESTS_=FALSE`? > > Suggested dependencies are nice because are optional. > But that feature often

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

On 03/04/2016 9:44 PM, Ray Donnelly wrote: Hi, Apologies for breaking the threading on this, I've only just signed up to the list and the last email was from September 2015. I've started to look into building R for Windows using MSYS2 as both the build environment and tools + libraries

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

Hi, Apologies for breaking the threading on this, I've only just signed up to the list and the last email was from September 2015. I've started to look into building R for Windows using MSYS2 as both the build environment and tools + libraries provider (where possible). I've managed to get the

[Rd] Suggested dependencies in context of R CMD check

Dear R team, Are suggested dependencies mandatory in context of `R CMD check` when using env var `_R_CHECK_FORCE_SUGGESTS_=FALSE`? Suggested dependencies are nice because are optional. But that feature often isn't valid when trying to run `R CMD check` on them. I would like to use `export

[Bioc-devel] dropping perceval and petty from supported platforms

Dear All, In one of the packages I maintain, I have a .BBSoptions file with the single entry UnsupportedPlatforms: perceval, petty (because I used C++-11, etc). I understand this is no longer necessary, since those platforms are not supported anyway for 3.3