[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: [Rd] error handling in strcapture

Once again, nice catch. I've committed a check for this. Michael On Tue, Oct 4, 2016 at 2:37 PM, William Dunlap wrote: > It is also not catching the cases where the number of capture expressions > does not match the number of entries in proto. I think all of the following >

Re: [Rd] On implementing zero-overhead code reuse

@Konrad, you're right, that's exactly what I'm looking for. That's great stuff. Thanks! (And thanks also to Gabor Grothendieck, who suggested modules to me way back.) On Tue, Oct 4, 2016 at 7:07 AM, Konrad Rudolph wrote: > Check out ‹klmr/modules› on Github

Re: [Rd] error handling in strcapture

It is also not catching the cases where the number of capture expressions does not match the number of entries in proto. I think all of the following should give an error about the mismatch. > strcapture("(.)(.)", c("ab", "cde", "fgh", "ij", "lm"), proto=list(A="",B="",C="")) A B C 1 a b

Re: [Rd] error handling in strcapture

Hi Bill, This is a bug in regexec() and I will commit a fix. Thanks for the report, Michael On Tue, Oct 4, 2016 at 1:40 PM, William Dunlap wrote: > I noticed a problem in the strcapture from R-devel (2016-09-27 r71386), when > the text contains a missing value and perl=TRUE.

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: [Rd] error handling in strcapture

I noticed a problem in the strcapture from R-devel (2016-09-27 r71386), when the text contains a missing value and perl=TRUE. { # NA in text input should map to row of NA's in output, without warning r9p <- strcapture(perl = TRUE, "(.).* ([[:digit:]]+)", c("One 1", NA, "Fifty 50"),

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: [Rd] suggested addition to model.matrix

In addition, there is a formula method for data.frame that assumes the first column is the dependent variable. > z <- data.frame(X1=1:6,X2=letters[1:3],Y=log(1:6)) > formula(z) X1 ~ X2 + Y > colnames(model.matrix(formula(z), z)) [1] "(Intercept)" "X2b" "X2c" "Y" Spencer's

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

Re: [Rd] On implementing zero-overhead code reuse

Shower thoughts: Are you digging for something like what you'd use with a CI/CD pipeline? e.g. - building a workflow that pulls a tag from a couple of code repositories, checks them out into a workspace, installs prereqs, and then runs your code/tasks in a repeatable fashion? I'm not aware of a

[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

Re: [Rd] On implementing zero-overhead code reuse

Check out ‹klmr/modules› on Github (distinct from CRAN’s ‹modules›!). It looks pretty much exactly like what you want: https://github.com/klmr/modules It has an extensive README and vignette explaining the usage. Cheers, Konrad -- Konrad Rudolph On Sun, 2 Oct 2016 at 18:31 Kynn Jones

[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: