Re: [Rd] Setting the path to Rtools for package compilation on Windows

I can confirm the behaviour that you report.  Usually I put Rtools in c:\programs\Rtools and modify the path accordingly. Recently (don't recall for how long) I have encountered the same problems as you have and I have resorted to moving Rtools to c:\Rtools I have no idea as how to proceed;

[Rd] Setting the path to Rtools for package compilation on Windows

Hi all, I'm trying to set up the Windows Rtools toolset for building packages with compiled code. I installed for Windows R-3.4.3 from CRAN and installed Rtools-3.4 in a custom location M:\R\R-3.4.3 and M:\R\Rtools-3.4 Following the instructions, in shell, I set

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 13 February 2018 at 01:05, Dirk Eddelbuettel wrote: > > On 12 February 2018 at 22:16, Baptiste Auguie wrote: > | As far as I can tell Armadillo added specialised methods for banded > | matrices; the routines used to solve non-banded matrices probably haven't > | changed. > |

[R-pkg-devel] CMake on win-builder

Dear all, I am trying to create a R interface to a C++ library which itself uses cmake as its build tool. For experimenting the idea, I copy the entire source of the library to a sub-directory of "inst" and call "cmake" in the "configure" script, then call "make", which generates a static

[Rd] Fix minor typo in error message from grDevices

Hi, I fixed a minor typo in an error message from grDevices. Please see attached for a patch to revision 74246. Thanks, John Index: src/library/grDevices/src/colors.c === --- src/library/grDevices/src/colors.c (revision 74246) +++

Re: [Bioc-devel] release build of ChemmineR failing

Andrzej, Sorry, I didn't realize that line was coming from my own Makefile. The Makefile was there for historic reasons, but I think can be removed now, so that will probably fix the problem. Kevin On 02/08/2018 02:39 AM, Andrzej Oleś wrote: > Dear Kevin, > > thank you for reporting the

Re: [Bioc-devel] rsvg on mac

Valerie, I'm not sure I understand. I looked at another package that is currently installed on the mac devel machine, DiagrammeR (https://cran.r-project.org/package=DiagrammeR), and it has the same set of links on the CRAN site as rsvg does. In particular, it does not show a r-devel

Re: [Bioc-devel] Issues with GenomicRanges updates

Hi Nathan, You're right, there was a remaining issue. It should be fixed in IRanges 2.13.26. Make sure to also get S4Vectors 0.17.32 (IRanges 2.13.26 requires it). The 2 updated packages should become available via biocLite() in about 24 hours but you can get them now directly from

[Rd] [parallel] fixes load balancing of parLapplyLB

Dear R-Devel List, **TL;DR:** The function **parLapplyLB** of the parallel package has [reportedly][1] (see also attached RRD output) not been doing its job, i.e. not actually balancing the load. My colleague Dirk Sarpe and I found the cause of the problem and we also have a patch to fix it

Re: [Bioc-devel] Help with GWASTools

Hi, Try the following. Just print "bed.fn" to see if they are imported correctly. And use "snpgdsBED2GDS(... verbose=TRUE)" to print more detailed information or error log. Qian Liu Bioconductor Core Team Roswell Park Cancer Institute library(SNPRelate) (bed.fn <- system.file("extdata",

Re: [Bioc-devel] Access to push to pacakges Polyester and Ballgown

Hi Jack, Have you gone through the steps outlined here? https://bioconductor.org/developers/how-to/git/ Specifically, have you added ssh keys? https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform If you have not added keys, you'll need to.

[Bioc-devel] Access to push to pacakges Polyester and Ballgown

Hi Bioc team, I'm currently maintaining the packages Ballgown and polyester. However, I haven't been able to access the new system since the change in system. I'm wondering if I would be able to be give access? I have included the maintainers on file for those packages as well. Best, Jack

Re: [Bioc-devel] warning: checking Rd cross-references

On 02/12/2018 07:01 AM, Claris Baby via Bioc-devel wrote: Dear all,I am trying to build a package for RNA-seq analysis combining different existing packages in bioconductor and am facing problem while trying to run Check PackageThere is no error but a warning saying checking Rd

Re: [Bioc-devel] Issues with GenomicRanges updates

Hi Herve, The updates have indeed solved those issues for that sample -- However, when you try to apply a more complicated function, I am getting the same error. Here's a reproducible example of the error again, this time using the latest GenomicRanges and IRanges packages:

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 12 February 2018 at 22:16, Baptiste Auguie wrote: | As far as I can tell Armadillo added specialised methods for banded | matrices; the routines used to solve non-banded matrices probably haven't | changed. | | Coming back to the error itself, what puzzles me is that it seems to be |

[Bioc-devel] warning: checking Rd cross-references

Dear all,I am trying to build a package for RNA-seq analysis combining different existing packages in bioconductor and am facing problem while trying to run Check PackageThere is no error but a warning saying checking Rd cross-references ... WARNING Missing link or links in documentation object

[Bioc-devel] "Error: duplicate commits" when pushing FamAgg to Bioconductor git

Dear all, I'm unable to push my recent changes to FamAgg to the Bioconductor git repo (see below for the error message). I did try the suggested fix but without any success - seems the duplicated commits are in Bioconductor and not github. thankful for any help or advise The error message is:

Re: [Bioc-devel] Bug in Biostrings::reverse?

I have been able to make it work now, sorry for the previous email. Best, Leandro. On Mon, Feb 12, 2018 at 4:52 AM, Leandro Roser wrote: > > Dear BioC, > > > Using the devel version of Biostrings (2.47.9) i am obtaining an error > message with the 'reverse' function

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 12 February 2018 at 04:52, Dirk Eddelbuettel wrote: > > On 11 February 2018 at 19:13, Baptiste Auguie wrote: > | Hi, > | > | Sorry I never found the time to put this issue to rest. My cda package > has > | now been removed from CRAN because Armadillo's update on 'banded > |

Re: [Rd] makeCluster hangs

Also using R-devel might help - the forking support in parallel has been made more robust against race conditions, but the changes are probably too substantial to port to 3.4.x. If you find how to cause a race condition using parallel/forking in R-devel, a report would be greatly appreciated.