Re: [Rd] Revert to R 3.2.x code of logicalSubscript in subscript.c?

Suharto, If you're interested in performance with subscripting, you might want to look at pqR (pqR-project.org). It has some substantial performance improvements for subscripting over R Core versions. This is especially true for the current development version of pqR (probably leading to a new

[Bioc-devel] Encoding issues with citations (Windows only)

Hi, I've been using knitcitations for a while to handle citations in HTML vignettes. I had been using knitcitations::read.bibtex() until I realized that it no longer reads the entries in the order that were given in the bib file**. So I made a change and it all works... except on Windows. I

Re: [R-pkg-devel] Category (Subjection) in R documentation for package

On 02/10/2017 8:10 AM, Mohammad Tanvir Ahamed wrote: Thanks. But @section makes some section in individual functions help file. No, I said to put it in the package help file, not an individual function help file. But I am in interested to add section in main index file of the package.

Re: [Bioc-devel] Query regarding size limit and including external datasets

The data definitely does not belong in the software package. We are a little schizophrenic about Experiment Data at the moment; my own feeling is that ExperimentHub is the right place, especially for data over say 10 Mb. This is more labor intensive and harder to version, but potentially

Re: [Bioc-devel] Several ssh keys ?

On 10/02/2017 10:50 AM, Bernat Gel wrote: Don't want to be alarmist, but is there anything in place to prevent a "malicious agent" inserting a new ssh key to the form and gaining access to our git repo? Maybe it would be sufficient to send an email to the maintainer whenever a new key is added

[Bioc-devel] Changes in 'digest' mode

Bioc-devel subscribers! The 'digest' mode was previously configured to send mail daily, or whenever the size of the digest exceeded a threshold, whichever came first. It is now configured to send the digest on a daily basis, hopefully reducing frequency for those preferring this form of

Re: [Bioc-devel] git clone failed from git.bioconductor.org

On Mon, Oct 2, 2017 at 3:07 PM, Juan David Henao Sanchez < judhena...@unal.edu.co> wrote: > Hi, > > I'm trying to clone my package from git.bioconductor.org as: > > git clone g...@git.bioconductor.org:packages/coexnet.git > > But, I recive the next message: > > == > Clonar en

Re: [Bioc-devel] git clone failed from git.bioconductor.org

You don’t seem to have an SSH public key on our system. Please submit your SSH public key. https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform If you have more questions, bioconductor.org/developers/how-to/git/faq/ Nitesh > On Oct 2, 2017, at

[Bioc-devel] git clone failed from git.bioconductor.org

Hi, I'm trying to clone my package from git.bioconductor.org as: git clone g...@git.bioconductor.org:packages/coexnet.git But, I recive the next message: == Clonar en «coexnet»... Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you

Re: [Bioc-devel] Several ssh keys ?

Don't want to be alarmist, but is there anything in place to prevent a "malicious agent" inserting a new ssh key to the form and gaining access to our git repo? Maybe it would be sufficient to send an email to the maintainer whenever a new key is added so we have a clue something has gone

Re: [R-pkg-devel] Confusion over CRAN build error for package Brundle

Dear Uwe, Thanks for your response. Andy On Mon, 2 Oct 2017 at 13:16 Uwe Ligges wrote: > > > On 02.10.2017 08:23, Andrew Holding wrote: > > Forgive me for possibly being naive. I have run the current version of my > > > > package, Brundle, through the test

Re: [Bioc-devel] write access to RTNduals and RTNsurvival

Thank you Martin, that makes sense to me. In this case, the next package that my lab contribute to bioc I will probably submit it myself. The structure of a laboratory involves team members coming and going, and we need to ensure continuous maintenance. This is certainly an issue that is not

Re: [Bioc-devel] write access to RTNduals and RTNsurvival

Hello Nitesh, Thank you very much for the support. I totally agree with that. Best, Vinicius On Mon, Oct 2, 2017 at 10:44 AM Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > Hi Mauro > > Please always forward your git questions to bioc-devel. There is more than > one person handling

Re: [Bioc-devel] write access to RTNduals and RTNsurvival

On 10/02/2017 09:57 AM, m castro wrote: Hi Nitesh, Thank you. In the submission of these packages, Vinicius and Clarice had included all the team as maintainers (I can confirm in the packages' homepages, below), not sure why it did not work at that occasion. We encourage just a single

Re: [Bioc-devel] write access to RTNduals and RTNsurvival

Hi Mauro, You should have access to those packages now. Please let me know if it has worked. Best, Nitesh > On Oct 2, 2017, at 9:57 AM, m castro wrote: > > Hi Nitesh, > > Thank you. > > In the submission of these packages, Vinicius and Clarice had included >

Re: [Bioc-devel] write access to RTNduals and RTNsurvival

Hi Nitesh, Thank you. In the submission of these packages, Vinicius and Clarice had included all the team as maintainers (I can confirm in the packages' homepages, below), not sure why it did not work at that occasion. http://bioconductor.org/packages/RTNduals/

Re: [Bioc-devel] write access to RTNduals and RTNsurvival

Hi Mauro Please always forward your git questions to bioc-devel. There is more than one person handling the issues about git. RTNsurvival, — Clari Groeneveld is the maintainer hence you don’t have write access. RTNduals — Vinicius Chagas is the listed maintainer on our system. This issue

Re: [Bioc-devel] external dependencies

Dear Martin and Vincent, Thanks for your feedback. Here is the current package repository: https://github.com/gogleva/SecretSanta I still need to run more tests on mac and clean the code a bit. But probably this would be sufficient to say whether the package is compatible with Bioconductor in

Re: [Bioc-devel] external dependencies

I'd also comment that if you make the package visible I would be willing to have a look at the issues involved in porting to windows. No guarantees but at least get some sense of context. On Mon, Oct 2, 2017 at 9:04 AM, Martin Morgan wrote: > I want to add,

Re: [Bioc-devel] external dependencies

I want to add, though, that OS-specific functionality and system requirements greatly limit the utility of your package and, like the OS-specific dependencies your package depends on, serves as a kind of virus that makes any other package that uses yours also not operable on the unsupported

Re: [Bioc-devel] external dependencies

Dear Lori, Thanks a lot for the clarification. I will incorporate os checks in my unit tests and examples. Thanks, Anna On 2 October 2017 at 12:30, Shepherd, Lori wrote: > You can still submit to bioconductor despite this limitation. You could > also do a os

Re: [Rd] calling R API functions after engine shutdown

If this is not considered to be safe, then I guess my message can be seen as a heads-up: If R_ReleaseObject ever does something that is not safe after the R engine has shut down, you will start to see crashes from packages like “minqa”. In FastR, we ended up adding a global flag that disables

Re: [R-pkg-devel] Confusion over CRAN build error for package Brundle

On 02.10.2017 08:23, Andrew Holding wrote: Forgive me for possibly being naive. I have run the current version of my package, Brundle, through the test systems on win-builder, and the development and stable tests both pass. The package builds on my desktop (MacOS) still runs fine. Yet for

Re: [R-pkg-devel] Category (Subjection) in R documentation for package

--- Begin Message --- Thanks.  But @section makes some section in individual functions help file.  But I am in interested to add section in main index file of the package.  This is more or less like sort functions by alphabetic order on the main help index of the package. But here I want to add

[Bioc-devel] new package submission (pcxn) Abnormal build result

Hi all, Today I submitted a new package called "pcxn" in bioconductor and I got the following Abnormal built result: Warning in fun(libname, pkgname) : no display name and no $DISPLAY environment variable Error: processing vignette 'usingPCxNdb.Rnw' failed with diagnostics: chunk 4 (label =

Re: [Bioc-devel] external dependencies

You can still submit to bioconductor despite this limitation. You could also do a os check in the examples and tests that fail on windows and make a comment that this is the case. If the program is not meant to run in windows there is options to handle that as well and the review assigned to

[R-pkg-devel] Confusion over CRAN build error for package Brundle

Forgive me for possibly being naive. I have run the current version of my package, Brundle, through the test systems on win-builder, and the development and stable tests both pass. The package builds on my desktop (MacOS) still runs fine. Yet for the last two days I the package has caused

[Bioc-devel] external dependencies

Dear Bioconductor Team, I have written a package and was planning to submit it to Bioconductor one day. The package provides a set of wrapper functions around several existing command line tools to construct scalable and reproducible pipelines for secretome prediction. The package requires

Re: [R-pkg-devel] Category (Subjection) in R documentation for package

In roxygen2 you do @section Section name: The colon is important. David On 1 October 2017 at 19:50, Duncan Murdoch wrote: > On 01/10/2017 12:42 PM, Mohammad Tanvir Ahamed via R-package-devel wrote: > >> I am building package R-studio (Roxygen2). >> In the package