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

Are you discussing statistics of the same dimension as the data (unusual) or summary statistics? We should think about a MAE version of summary statistics, but that is not captured in current representation I would say. Best, Kasper On Mon, Oct 23, 2017 at 4:50 PM, Vincent Carey wrote: > no ans

Re: [Bioc-devel] No build report today & Automatic build/check failure notifications activated for BioC 3.7

On 10/23/2017 02:24 PM, Hervé Pagès wrote: Hi developers, The builds completed in time today but the build/check report couldn't be generated in time. So no updated build/check report today, sorry! Some of you might have received an automatic build/check failure notification today. Please note

Re: [Bioc-devel] cellbaseR build

Many thanks! On Tue, Oct 24, 2017 at 12:03 AM, Hervé Pagès wrote: > Hi Mohammed, > > Packages that fail to pass build/check on release day won't propagate > to the BioC 3.6 repositories. They'll propagate later when they pass > build/check. > > Hopefully the CellBase web services will be back so

[Bioc-devel] No build report today & Automatic build/check failure notifications activated for BioC 3.7

Hi developers, The builds completed in time today but the build/check report couldn't be generated in time. So no updated build/check report today, sorry! Some of you might have received an automatic build/check failure notification today. Please note that this notification is based on the build

Re: [Bioc-devel] cellbaseR build

Hi Mohammed, Packages that fail to pass build/check on release day won't propagate to the BioC 3.6 repositories. They'll propagate later when they pass build/check. Hopefully the CellBase web services will be back soon. Thanks for keeping an eye on the build results for your package! Cheers, H

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 wro

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 'colna

[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?

Hi Hervé, Thanks for the suggestion. I actually checked first that they were the same length, but identical() would be safer and simplify my code. Elizabeth > On Oct 23, 2017, at 10:40 PM, Hervé Pagès wrote: > > Hi Elizabeth, > > Thanks for troubleshooting this. > > Note that testing with id

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

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 'colnames1' and 'colnames2' have different lengths

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

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 'colnames1' and 'colnames2' have different lengths. Cheers, H. On 10/23/2017 01:06 PM, Eliz

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

FYI, that seems to be a locale issue, as the locale defines the sort order. The first one is sorting alphabetically in a case-insensitive manner, eg aAbBcC etc, the second is sorting in a case sensitive manner, where capital letters all come before lower-case letters, e.g. ABC...YZabc... You can

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 other

[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: [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 > > rsecFluidigm<-RSEC(rsecFluidigm,isCount=TRU

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 mailto:martin.mor...@roswellpark.org>> 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

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 ONLY when I >> run R CMD BUILD. I

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

On 10/23/2017 09:47 AM, 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 ONLY when I run R CMD BUILD. I can’t recreate the error

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 o

[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 ima

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 on behalf of Carles Hernández Se

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 t

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; bioc-devel@r-p

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 connec

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 2.5.39 and create a html_doc