[R-pkg-devel] Trying to remove dot file

Hello Everyone, I am trying to eliminate a warning from my package so that it will pass the devtools check. * checking package subdirectories ... WARNING Subdirectory 'man' contains invalid file names: '._PlotMDS.Rd' Please remove or rename the files. I tried using "dot_clean -m

Re: [Bioc-devel] Modeling (statistic, p-value) pairs in MultiAssayExperiment

no answers yet? would it work to put your matrices as separate assays in a SummarizedExperiment? as long as they are conformant in dimensions and dimnames I think that would work. That SummarizedExperiment would then work well in an MAE. On Mon, Oct 23, 2017 at 1:00 PM, Francesco Napolitano

Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

On 10/23/2017 01:42 PM, Martin Morgan wrote: On 10/23/2017 04:40 PM, Hervé Pagès wrote: Hi Elizabeth, Thanks for troubleshooting this. Note that testing with identical()/checkIdentical() is safer than with 'any(sort(colnames1) != sort(colnames2))'. The latter won't do the right thing if

[Bioc-devel] cellbaseR build

Hi All I am the maintainer of cellbaseR, a client for the CellBase Annotation database, Unfortunately, The web services are down at the moment which results in build errors, but this is not due to a fault in R package, I hope this does not disqualify my package from Bioconductor release as I know

Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

Dear Martin, Just for completeness, I figured out the discrepancy and solved my problem. In my check, I check that the column names contain the expected names and I didn’t want to make the order required in a certain way so I used sort -- but only of one side because I naively assumed the

[Bioc-devel] Modeling (statistic, p-value) pairs in MultiAssayExperiment

Hi, I'm trying to build a MultiAssayExperiment. However, in my case each assay should ideally include two matrices: one with a statistic and another one with the corresponding p-value. I'm currently managing each of them simply as a list of two matrices, but assay class expects table-like data. I

Re: [Rd] range function with finite=T and logical parameters

> Lukas Stadler > on Mon, 23 Oct 2017 15:56:55 +0200 writes: > Hi! > I was wondering about the behavior of the range function wrt. logical NAs: >> range(c(0L, 1L, NA), finite=T) > [1] 0 1 >> range(c(F, T, NA), finite=T) > [1] NA NA

Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

> > I can reproduce the error with > > clusterExperiment/vignettes master$ R_DEFAULT_PACKAGES= LC_COLLATE=C R -f > clusterExperimentTutorial.R > > leading to > > > ## > > recallRSEC > >

Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

On 10/23/2017 09:59 AM, Elizabeth Purdom wrote: On Oct 23, 2017, at 3:47 PM, Martin Morgan > wrote: On 10/23/2017 09:26 AM, Elizabeth Purdom wrote: Hello, I am updating an existing package and I am getting an error in

Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

> On Oct 23, 2017, at 3:47 PM, Martin Morgan > wrote: > > On 10/23/2017 09:26 AM, Elizabeth Purdom wrote: >> Hello, >> I am updating an existing package and I am getting an error in running my >> vignette (and a similar error in an example in help pages) but

[Rd] range function with finite=T and logical parameters

Hi! I was wondering about the behavior of the range function wrt. logical NAs: > range(c(0L, 1L, NA), finite=T) [1] 0 1 > range(c(F, T, NA), finite=T) [1] NA NA The documentation is quite clear that "finite = TRUE includes na.rm = TRUE”, so that I would have assumed that these two snippets

Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

On 10/23/2017 09:26 AM, Elizabeth Purdom wrote: Hello, I am updating an existing package and I am getting an error in running my vignette (and a similar error in an example in help pages) but ONLY when I run R CMD BUILD. I can’t recreate the error in any session where I can debug and figure

[Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

Hello, I am updating an existing package and I am getting an error in running my vignette (and a similar error in an example in help pages) but ONLY when I run R CMD BUILD. I can’t recreate the error in any session where I can debug and figure out what is happening. So my question is how can I

[Bioc-devel] Cannot reproduce Bioc build server errors for annotatr package

Hello all, I’m getting some CHECK errors in the examples and tests for the annotatr package (http://bioconductor.org/checkResults/devel/bioc-LATEST/annotatr/ ) that I cannot reproduce using the bioconductor/devel_core2 Docker

Re: [R-pkg-devel] Add appveyor in package with RcppGSL dependency

@Dirk, yes, we checked the revdeps but only SimInf seems to have appveyor working. Thank you for the advices. @Jenny Thank you! Now we'll do our homework and return with feedback, hopefully having a complete solution :) Julio On Sun, Oct 22, 2017 at 7:51 PM Jennifer Bryan

Re: [R-pkg-devel] Fw: [CRAN-pretest-archived] CRAN submission nnfor 0.9

Dear Nikos, Your examples are taking too much time. Make them run faster. Or remove some of them. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team

[R-pkg-devel] Fw: [CRAN-pretest-archived] CRAN submission nnfor 0.9

Dear all, I am facing a problem with a package I am trying to submit. I am getting three notes, for which I am not sure what could be done. Any help is greatly appreciated. Please here for the summary: https://win-builder.r-project.org/incoming_pretest/171023_084642_nnfor_09/00check.log or look

Re: [Bioc-devel] EXTERNAL: Re: IMPCdata push permissions to git repo

What are the packages you are trying to access? Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel

Re: [Bioc-devel] EXTERNAL: R version dependence of a new package

Dear Lori, many thanks for your detailed explanations. I think that it makes sense from Bioconductor maintenance's point of view to require that the R version of a package should be the same of the R version in a Bioconductor release which includes the package, because it's the safest option. On

Re: [Rd] Illegal Logical Values

On 10/21/2017 04:14 PM, Radford Neal wrote: On Fri, 2017-10-20 at 14:01 +, brodie gaslam via R-devel wrote: I'm thinking of this passage: Logical values are sent as 0 (FALSE), 1 (TRUE) or INT_MIN = -2147483648 (NA, but only if NAOK is true), and the compiled code should return one of

Re: [Bioc-devel] Package failure due to GenomicFeatures update

Thank you Herve! Then, I will pull the code from github to update my code, too. Hopefully my package will also go through by 24th :) Best, Bora From: Hervé Pagès [hpa...@fredhutch.org] Sent: Monday, October 23, 2017 6:17 AM To: Uyar, Bora;

Re: [Bioc-devel] IMPCdata push permissions to git repo

Hi all, In my case I got the same error: $ git fetch --all Fetching origin Fetching upstream The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be established. ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q. Are you sure you want to continue

Re: [Bioc-devel] Superscript in BiocStyle 2.5.39 html document seems to be not working

Hi Stefan, thanks for reporting this. Should be fixed in BiocStyle 2.5.42. Best, Andrzej On Mon, Oct 23, 2017 at 7:55 AM, Stefan Mutter wrote: > Hi, > > > I am currently writing a vignette for a package that we want to submit to > Bioconductor. I am using BiocStyle