[Bioc-devel] Harman not building on Windows due to mzR

Hi there, I notice the Harman package which I maintain is not building on Windows. See: http://bioconductor.org/checkResults/3.4/bioc-LATEST/Harman/? This is arising from the vignette and is due to the package msmsEDA not being present. If I keep peeling the dependencies back, I get to mzR,

Re: [Bioc-devel] Why can't NAMESPACE be a strict subset of DESCRIPTION Imports?

- Original Message - > From: "Martin Morgan" > To: "McDavid, Andrew" , "bioc-devel" > > Sent: Tuesday, October 4, 2016 2:09:27 PM > Subject: Re: [Bioc-devel] Why can't NAMESPACE be a strict

Re: [Bioc-devel] Why can't NAMESPACE be a strict subset of DESCRIPTION Imports?

On 10/04/2016 05:07 PM, McDavid, Andrew wrote: BiocCheck throws a warning when a package is listed as Imports: in DESCRIPTION but not used in the NAMESPACE. This may happen when a developer uses the fully qualified names of objects within a package. I am unclear as to the rationale for this

[Bioc-devel] Why can't NAMESPACE be a strict subset of DESCRIPTION Imports?

BiocCheck throws a warning when a package is listed as Imports: in DESCRIPTION but not used in the NAMESPACE. This may happen when a developer uses the fully qualified names of objects within a package. I am unclear as to the rationale for this warning. Per Hadley: It's common for packages

Re: [Bioc-devel] package submission from bitbucket

Hi Lori, Thank you for the information and for the quick response! Thanks! Lauren On Tue, Oct 4, 2016 at 1:01 PM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > Lauren, > > > Thank you for your interest in submitting to Bioconductor. > > Currently we only support the use of github

Re: [Bioc-devel] package submission from bitbucket

Lauren, Thank you for your interest in submitting to Bioconductor. Currently we only support the use of github for package submission. After the package has been accepted through the review process, it does not have to remain in github. Lori Shepherd Bioconductor Core Team Roswell Park

[Bioc-devel] package submission from bitbucket

Hello Bioconductor Core Team, We use bitbucket to host all our software repositories. Is there a way to submit a bitbucket URL for a new bioconductor package or does it need to be from github? If it has to be in github, do we need to maintain the original repository that created the initial

Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

- Original Message - > From: "Hervé Pagès" > To: "Dan Tenenbaum" > Cc: "Philipp Angerer" , "bioc-devel" > > Sent: Tuesday, October 4, 2016 10:16:34 AM > Subject: Re:

Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

On 10/04/2016 09:56 AM, Dan Tenenbaum wrote: - Original Message - From: "Hervé Pagès" To: "Philipp Angerer" , "bioc-devel" Sent: Tuesday, October 4, 2016 9:23:29 AM Subject: Re: [Bioc-devel]

Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

- Original Message - > From: "Hervé Pagès" > To: "Philipp Angerer" , "bioc-devel" > > Sent: Tuesday, October 4, 2016 9:23:29 AM > Subject: Re: [Bioc-devel] tokay1 (windows) build server cannot use

Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

Dear all, linux builders have both IPython 3+ and Jupyter installed, see https://github.com/Bioconductor/BBS-provision-cookbook/blob/master/recipes/default.rb#L256-L264 For consistency, maybe it would make sense to have them both on Windows too. Cheers, Andrzej On Tue, Oct 4, 2016 at 6:23 PM,

Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

Hi Philipp, On 10/04/2016 12:13 AM, Angerer, Philipp via Bioc-devel wrote: Hi, Looking at my package’s build report, the devel version isn’t built anymore on windows: http://bioconductor.org/checkResults/devel/bioc-LATEST/destiny/tokay1-buildsrc.html The release version is built just fine

[Bioc-devel] Statistical Scalability for Streaming Data - 1/2 day workshop in London

Perhaps interesting for some: http://www.turing-gateway.cam.ac.uk/tgmw39.shtml ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] PKG_LIBS in make child processes

Hi all, I have a subtle question related to how R CMD SHLIB handles variables in make child processes. In more detail: I am the maintainer of the 'msa' package which has been in Bioconductor since April 2015. This package integrates three open-source libraries for multiple sequence alignment.

[Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

Hi, Looking at my package’s build report, the devel version isn’t built anymore on windows: http://bioconductor.org/checkResults/devel/bioc-LATEST/destiny/tokay1-buildsrc.html The release version is built just fine with moscato2: