Re: [Bioc-devel] BiocCheck error

Hi Marek, Thanks for pointing this out in release. I have applied the patch to BiocCheck version 1.38.1. FWIW, this issue was first opened here https://github.com/Bioconductor/BiocCheck/issues/135 Best regards, Marcel On 1/25/24 9:24 AM, Marek Gierlinski (Staff) wrote: > Yes, it must be this.

Re: [Bioc-devel] BiocCheck error

Yes, it must be this. I�ve installed the devel version and the error is gone. Marek From: Kern, Lori Date: Thursday, 25 January 2024 at 14:13 To: James W. MacDonald , Marek Gierlinski (Staff) , bioc-devel@r-project.org Subject: Re: BiocCheck error I believe this bug with BiocCheck is fixed in

Re: [Bioc-devel] BiocCheck error

ject.org Subject: Re: [Bioc-devel] BiocCheck error Are you subscribed to the bioc-devel mailing list? -Original Message- From: Bioc-devel On Behalf Of Marek Gierlinski (Staff) Sent: Thursday, January 25, 2024 5:51 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] BiocCheck error When

Re: [Bioc-devel] BiocCheck error

Yes, I am. And BiocCheck used to work for me before, suddenly it is crashing with error. Marek From: James W. MacDonald Date: Thursday, 25 January 2024 at 14:07 To: Marek Gierlinski (Staff) , bioc-devel@r-project.org Subject: RE: BiocCheck error Are you subscribed to the bioc-devel mailing l

Re: [Bioc-devel] BiocCheck error

Are you subscribed to the bioc-devel mailing list? -Original Message- From: Bioc-devel On Behalf Of Marek Gierlinski (Staff) Sent: Thursday, January 25, 2024 5:51 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] BiocCheck error When running BiocCheck::BiockCheck() on my package

[Bioc-devel] BiocCheck error

When running BiocCheck::BiockCheck() on my package, it gets through almost everything and then produces an error: ... * Checking for bioc-devel mailing list subscription... * NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel mailing list (requires admin credenti

Re: [Bioc-devel] BiocCheck not available in bioc-devel docker container

HI Mike, Thanks so much for taking the time to go through everything so carefully. It's very much appreciated. I originally found the issue with BiocCheck by instantiating the bioc-devel container locally. That one's sorted now so the devel version of ngsReports builds on r-devel using linux. A f

Re: [Bioc-devel] BiocCheck not available in bioc-devel docker container

Hi Stevie, To follow up on this, BiocCheck is missing from devel because some changes in R-devel tripped up a few unit tests, and the package hasn't been built successfully. It looks like Marcel has fixed those issues ( https://code.bioconductor.org/browse/BiocCheck/commits/master) and it should

Re: [Bioc-devel] BiocCheck not available in bioc-devel docker container

Hi Stevie, It might be helpful to link to the workflow runs so people can see exactly what you're doing and what's happening. Hopefully I'm looking in the right place at https://github.com/steveped/ngsReports/actions/runs I'm not sure about the error message regarding BiocCheck. However there a

[Bioc-devel] BiocCheck not available in bioc-devel docker container

Hi, I also can't get my github actions bioc-check workflow running for devel, so I checked the bioc-devel docker image & can't seem to install BiocCheck on that container. Is this likely to be available for devel soon? Error from my local installation of the container below: BiocManager::install

[Bioc-devel] BiocCheck fails during Github action workflow

Hi, this question probably relates to Bioc docker images, thus asking here first. I am using biocthis GitHub action and I recently noticed that it started to fail with a BiocCheck message: "ERROR: dependencies ‘Genomi

Re: [Bioc-devel] BiocCheck and version requirement

> I believe in the past we tried suggesting removing a R dependency >> > altogether but that R CMD check complained not having an R dependency? >> > Maybe someone remembers more about this. >> > >> > >> > >> > >> > Lori Shepherd >

Re: [Bioc-devel] BiocCheck and version requirement

; > > > > Lori Shepherd > > > > Bioconductor Core Team > > > > Roswell Park Comprehensive Cancer Center > > > > Department of Biostatistics & Bioinformatics > > > > Elm & Carlton Streets > > > > Buffalo, New York 14263 > > > >

Re: [Bioc-devel] BiocCheck and version requirement

ive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ________ > From: Kasper Daniel Hansen > Sent: Thursday, April 8, 2021 1:33 PM > To: Kern, Lori > Cc: bioc-devel > S

Re: [Bioc-devel] BiocCheck and version requirement

ics Elm & Carlton Streets Buffalo, New York 14263 From: Kasper Daniel Hansen Sent: Thursday, April 8, 2021 1:33 PM To: Kern, Lori Cc: bioc-devel Subject: Re: [Bioc-devel] BiocCheck and version requirement But why is it even a warning? The submission polic

Re: [Bioc-devel] BiocCheck and version requirement

l Hansen > *Sent:* Thursday, April 8, 2021 9:44 AM > *To:* bioc-devel > *Subject:* [Bioc-devel] BiocCheck and version requirement > > The latest BiocCheck (well, it may have been around for a bit) _requires_ > the package to have a R >= 4.1 dependency. > > That seems new t

Re: [Bioc-devel] BiocCheck and version requirement

Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Kasper Daniel Hansen Sent: Thursday, April 8, 2021 9:44 AM To: bioc-devel Subject: [Bioc-devel] BiocCheck and version requirem

[Bioc-devel] BiocCheck and version requirement

The latest BiocCheck (well, it may have been around for a bit) _requires_ the package to have a R >= 4.1 dependency. That seems new to me. Right now it's a bit irritating, because if you're submitting a package that works with latest stable release, you are now prohibited from installing it from G

Re: [Bioc-devel] BiocCheck space indentation in Rmakrdown vignette documents

Thanks, Martin, that is actually my bug report. I'm considering doing a pull-request with a fix. However, I don't have a clear idea yet on how to deal with the YAML portion of a .rmd file. Regards Carlos A. Catania (AKA Harpo) El dom., 26 jul. 2020 a las 10:14, Martin Morgan () escribió: > See a

Re: [Bioc-devel] BiocCheck space indentation in Rmakrdown vignette documents

Hello, Mike, Thanks for your answer and info about the review process. As recommended by Lori we filled a bug report about the issue. Thanks again and best regards Carlos A. Catania (AKA Harpo) El sáb., 25 jul. 2020 a las 17:56, Mike Smith () escribió: > Hi Carlos, > > I don't think you need t

Re: [Bioc-devel] BiocCheck space indentation in Rmakrdown vignette documents

See also this issue https://github.com/Bioconductor/BiocCheck/issues/100 . On 7/25/20, 4:57 PM, "Bioc-devel on behalf of Mike Smith" wrote: Hi Carlos, I don't think you need to worry about this. The 4 space indentation is a style recommendation (not a requirement), and if the

Re: [Bioc-devel] BiocCheck space indentation in Rmakrdown vignette documents

Hi Carlos, I don't think you need to worry about this. The 4 space indentation is a style recommendation (not a requirement), and if the only place that your code isn't meeting that recommendation is the YAML header then I can't imagine that any reviewer will worry too much about this. The revie

[Bioc-devel] BiocCheck space indentation in Rmakrdown vignette documents

Hello BioConductor Team, We are in the final steps prior to submitting a new package to Bioconductor. As recommended, we want our package to pass BiocCheck with no Errors, Warnings, or Notes. However, we have a problem regarding the indentation of a vignette written rmarkdown. -- BEGIN BiocCheck

[Bioc-devel] BiocCheck-a-thon!

Join us for 'BiocCheck-a-thon', a week-long virtual hackathon to improve BiocCheck and the consistency and quality of Bioconductor packages! See https://github.com/Bioconductor/BiocCheck/wiki for details; starting May 18. Martin Morgan Bioconductor __

Re: [Bioc-devel] BiocCheck error

>>> situation? >> >> But then isn't it going to be somewhat painful to keep the 2 repos in >> sync? Sounds like using some kind of alias or redirect mechanism would >> be better but you would need to ask the Git or GitHub experts on how to >>

Re: [Bioc-devel] BiocCheck error

>sync? Sounds like using some kind of alias or redirect mechanism would >be better but you would need to ask the Git or GitHub experts on how to >do this. > >H. > >> >> Zhezhen >> -------- >&

Re: [Bioc-devel] BiocCheck error

--- > *From:* Pages, Herve > *Sent:* Wednesday, August 21, 2019 7:47 PM > *To:* Zhezhen Wang ; Martin Morgan > ; Vincent Carey > *Cc:* bioc-devel@r-project.org > *Subject:* Re: [Bioc-devel] BiocCheck error > Note that t

Re: [Bioc-devel] BiocCheck error

s. H. > > Zhezhen > > *From:* Pages, Herve > *Sent:* Wednesday, August 21, 2019 7:47 PM > *To:* Zhezhen Wang ; Martin Morgan > ; Vincent Carey > *Cc:* bioc-devel@r-project.org > *Subject:* Re: [Bioc-dev

Re: [Bioc-devel] BiocCheck error

? Zhezhen From: Pages, Herve Sent: Wednesday, August 21, 2019 7:47 PM To: Zhezhen Wang ; Martin Morgan ; Vincent Carey Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] BiocCheck error Note that the name of the package (BioTIP) differs from the name of the

Re: [Bioc-devel] BiocCheck error

From: Martin Morgan > Sent: Tuesday, August 20, 2019 11:15 AM > To: Zhezhen Wang ; Vincent Carey > > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] BiocCheck error > > I think this is from BiocCheck, needing access to CRAN / Bioconductor to look > at pac

Re: [Bioc-devel] BiocCheck error

I see, thank you Martin! Zhezhen From: Martin Morgan Sent: Tuesday, August 20, 2019 11:15 AM To: Zhezhen Wang ; Vincent Carey Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] BiocCheck error I think this is from BiocCheck, needing access to CRAN

Re: [Bioc-devel] BiocCheck error

AM To: Zhezhen Wang Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] BiocCheck error If your package that generates the error is in a github repo, please give the details. If it is already in Bioconductor please give the name of the package and ensure we can get

Re: [Bioc-devel] BiocCheck error

The github repo is https://github.com/xyang2uchicago/NPS From: Vincent Carey Sent: Tuesday, August 20, 2019 10:52 AM To: Zhezhen Wang Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] BiocCheck error If your package that generates the error is in a

Re: [Bioc-devel] BiocCheck error

If your package that generates the error is in a github repo, please give the details. If it is already in Bioconductor please give the name of the package and ensure we can get access to the code that is generating the error. In general it is very hard to help unless we can reproduce the error yo

[Bioc-devel] BiocCheck error

Hi I am running BiocCheck on my new package and I get the following error message * Checking for deprecated package usage... Warning in readLines(file, skipNul = TRUE) : InternetOpenUrl failed: 'The server name or address could not be resolved' Error in readLines(file, skipNul = TRUE) : can

Re: [Bioc-devel] BiocCheck error

Martin, Thank you. yes, you are right. Now it works, I also changed outputs to tempfile() or tempdir(). Aimin On Tue, Apr 10, 2018 at 6:07 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > Hi Aimin -- the problem is that your vignette has two VignetteEngine > commands in it > > Pathw

Re: [Bioc-devel] BiocCheck error

Hi Aimin -- the problem is that your vignette has two VignetteEngine commands in it PathwaySplice/vignettes master$ grep VignetteEngine * tutorial.Rmd: %\VignetteEngine{knitr::rmarkdown} tutorial.Rmd: %\VignetteEngine{knitr::knitr} Also, please avoid writing to files in the user system, repla

[Bioc-devel] BiocCheck error

I used "R CMD check PathwaySplice_1.3.0.tar.gz", and get it passed without errors and warnings. However I get the following error when I use "R CMD BiocCheck PathwaySplice_1.3.0.tar.gz" R CMD BiocCheck PathwaySplice_1.3.0.tar.gz This is BiocCheck version 1.15.8. BiocCheck is a work in progress.

Re: [Bioc-devel] BiocCheck - warning: files are over 5MB

Good day, You could make use of the package named BSgenome.Celegans.UCSC.ce11. It contains the DNA sequences of all of the chromosomes of the roundworm and doesn't add any size to your package. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Austra

Re: [Bioc-devel] BiocCheck - warning: files are over 5MB

On 03/10/2018 09:03 AM, Pariksheet Nanda wrote: Hi Claris, On Sat, Mar 10, 2018 at 2:49 AM, Claris Baby via Bioc-devel < bioc-devel@r-project.org> wrote: [1] "The following files are over 5MB in size: 'dataset/Caenorhabditis_elegans.WBcel235.dna.chromosome.I.fa'." This as well as other d

Re: [Bioc-devel] BiocCheck - warning: files are over 5MB

> disk efficient compression algorithm Whoops, meant to say compression format. Pariksheet [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] BiocCheck - warning: files are over 5MB

Hi Claris, On Sat, Mar 10, 2018 at 2:49 AM, Claris Baby via Bioc-devel < bioc-devel@r-project.org> wrote: > > [1] "The following files are over 5MB in size: > 'dataset/Caenorhabditis_elegans.WBcel235.dna.chromosome.I.fa'." > This as well as other data like .gff files, that are being used > for

[Bioc-devel] BiocCheck - warning: files are over 5MB

Dear all,I am trying to run BiocCheck("/home/package_name", list(`no-check-vignettes`=TRUE)) There is no error but I am getting the following warning. $warning [1] "The following files are over 5MB in size: 'dataset/Caenorhabditis_elegans.WBcel235.dna.chromosome.I.fa'." This as well as other

Re: [Bioc-devel] BiocCheck requires example for a function withnoargument.

sday, May 31, 2017 20:51 > *To: *Arman Sh > *Cc: *Michael Lawrence ; > bioc-devel@r-project.org > *Subject: *Re: [Bioc-devel] BiocCheck requires example for a function > withnoargument. > > > > And nothing shows up in the list? > > > > On Wed, May 31, 2017 at 8

Re: [Bioc-devel] BiocCheck requires example for a function with no argument.

On 05/31/2017 11:29 AM, Arman Sh wrote: Hi every one, BiocCheck is really annoying. My package contains three functions. Two of them are flexible with multiple argument. The third one is requires internet to check available data types and returns the result as an excel file. It’s a simple fun

Re: [Bioc-devel] BiocCheck requires example for a function with noargument.

> examples. The following pages do not:" > > > > Best regards, arman > > > > *From: *Michael Lawrence > *Sent: *Wednesday, May 31, 2017 20:12 > *To: *Arman Sh > *Cc: *bioc-devel@r-project.org > *Subject: *Re: [Bioc-devel] BiocCheck requires example

Re: [Bioc-devel] BiocCheck requires example for a function with no argument.

You could embed the example in \dontrun{}. Does BiocCheck detect cases where the entire example is not run? Btw, I'm pretty suspicious about this R function that takes no arguments and downloads an Excel file. Seems like the file could be bundled with the package, or internally lazily downloaded a

[Bioc-devel] BiocCheck requires example for a function with no argument.

Hi every one, BiocCheck is really annoying. My package contains three functions. Two of them are flexible with multiple argument. The third one is requires internet to check available data types and returns the result as an excel file. It’s a simple function with no argument. So there is no exa

Re: [Bioc-devel] BiocCheck Local and Single Package Builder Discrepancy

- Original Message - > From: "David Kuo" > To: "bioc-devel" > Sent: Friday, April 1, 2016 1:13:47 PM > Subject: [Bioc-devel] BiocCheck Local and Single Package Builder Discrepancy > Hi, > > I'm observing different results from executing

[Bioc-devel] BiocCheck Local and Single Package Builder Discrepancy

Hi, I'm observing different results from executing BiocCheck, version 1.7.9 locally and the build output. The tar.gz output locally shows no Warnings and outputs this: == * Checking for support site registration... * Maintainer is registered at support site!

Re: [Bioc-devel] BiocCheck not passing at test check phase

- Original Message - > From: "Marcel Ramos" > To: "bioc-devel" > Sent: Tuesday, February 9, 2016 11:54:17 AM > Subject: [Bioc-devel] BiocCheck not passing at test check phase > Hi everyone, > I am running into trouble when running BiocCheck from withi

[Bioc-devel] BiocCheck not passing at test check phase

Hi everyone, I am running into trouble when running BiocCheck from within RStudio and the command line. This check is for a package that would be going into the development branch. After running BiocCheck::BiocCheck("biocMultiAssay"), I get the following error: * Checking unit tests... Warning in

Re: [Bioc-devel] BiocCheck failing

- Original Message - > From: "Samuel E Zimmerman" > To: bioc-devel@r-project.org > Sent: Wednesday, September 30, 2015 2:02:06 PM > Subject: [Bioc-devel] BiocCheck failing > > Hi everyone, > > I just submitted a package to Bioconductor. All the tests

[Bioc-devel] BiocCheck failing

Hi everyone, I just submitted a package to Bioconductor. All the tests passed except for the BiocCheck step in the "Mac OS X Mavericks (10.9.5)/x86_64" OS. The version of BiocCheck used was 1.5.9 and the error is below. Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was rea

Re: [Bioc-devel] BiocCheck required import

- Original Message - > From: "Thomas Lin Pedersen" > To: "Dan Tenenbaum" > Cc: bioc-devel@r-project.org > Sent: Thursday, September 3, 2015 10:50:19 AM > Subject: Re: [Bioc-devel] BiocCheck required import > > It might be related to the

Re: [Bioc-devel] BiocCheck required import

riginal Message - >> From: "Thomas Dybdal Pedersen" >> To: "Dan Tenenbaum" >> Cc: bioc-devel@r-project.org >> Sent: Thursday, September 3, 2015 8:25:36 AM >> Subject: Re: [Bioc-devel] BiocCheck required import >> >> Sure, sorry. It

Re: [Bioc-devel] BiocCheck required import

- Original Message - > From: "Thomas Dybdal Pedersen" > To: "Dan Tenenbaum" > Cc: bioc-devel@r-project.org > Sent: Thursday, September 3, 2015 8:25:36 AM > Subject: Re: [Bioc-devel] BiocCheck required import > > Sure, sorry. Its avail

Re: [Bioc-devel] BiocCheck required import

t.org >> Sent: Thursday, September 3, 2015 7:55:42 AM >> Subject: Re: [Bioc-devel] BiocCheck required import >> >> What's the name of the package? > > I mean, is the source available somewhere? > Dan > > >> Dan >> >> >> - Origina

Re: [Bioc-devel] BiocCheck required import

- Original Message - > From: "Dan Tenenbaum" > To: "Thomas Lin Pedersen" > Cc: bioc-devel@r-project.org > Sent: Thursday, September 3, 2015 7:55:42 AM > Subject: Re: [Bioc-devel] BiocCheck required import > > What's the name of the packa

Re: [Bioc-devel] BiocCheck required import

What's the name of the package? Dan - Original Message - > From: "Thomas Lin Pedersen" > To: bioc-devel@r-project.org > Sent: Thursday, September 3, 2015 1:03:42 AM > Subject: [Bioc-devel] BiocCheck required import > > I’m polishing up a package fo

[Bioc-devel] BiocCheck required import

I’m polishing up a package for release and gets this “REQUIRED” message from BiocCheck that kinds of baffles me: * REQUIRED: Packages (IRanges, Biostrings) which provide reverse, reverse (used in trailsToGraph, trailsToGraph) should be imported in the NAMESPACE file, otherwise pac

Re: [Bioc-devel] BiocCheck examples error when using imported package functions

Hi Please disregard this thread, I've realised it's an error with our code Thanks Glyn From: Glyn Bradley Sent: 16 January 2015 15:32 To: 'bioc-devel@r-project.org' Subject: BiocCheck examples error when using imported package functions Hi, Our package uses igraph. We have imports: igraph i

[Bioc-devel] BiocCheck examples error when using imported package functions

Hi, Our package uses igraph. We have imports: igraph in the DESCRIPTION file and import(igraph)in the NAMESPACE But when we try to write examples for our functions that use igraph functions to create then use igraph objects from our input, BiocCheck fails on them. How can we use igraph in our exa

Re: [Bioc-devel] BiocCheck result

- Original Message - > From: "Karim Mezhoud" > To: "Dan Tenenbaum" > Cc: bioc-devel@r-project.org > Sent: Friday, January 2, 2015 12:15:31 PM > Subject: Re: [Bioc-devel] BiocCheck result > > > > > Dear Dr Dan, > Thanks, > &

Re: [Bioc-devel] BiocCheck result

- > > From: "Karim Mezhoud" > > To: bioc-devel@r-project.org > > Sent: Friday, January 2, 2015 4:22:44 AM > > Subject: [Bioc-devel] BiocCheck result > > > > Dear all, > > > > I have these comments and did not found solution for sil

Re: [Bioc-devel] BiocCheck result

- Original Message - > From: "Karim Mezhoud" > To: bioc-devel@r-project.org > Sent: Friday, January 2, 2015 4:22:44 AM > Subject: [Bioc-devel] BiocCheck result > > Dear all, > > I have these comments and did not found solution for silencing them.

[Bioc-devel] BiocCheck result

Dear all, I have these comments and did not found solution for silencing them. 1 - What about Vignette? 2 - The version is "package.0.99.0.tar.gz" 3 - In wich file can I clarify permanent objects. To avoid <<- I create new Environment with myGlobalEnv <- new.env(parent = emptyenv()) I have many

Re: [Bioc-devel] BiocCheck Error 'duplicate label install'?

- Original Message - > From: "Charles Determan Jr" > To: bioc-devel@r-project.org > Sent: Wednesday, December 31, 2014 11:41:09 AM > Subject: [Bioc-devel] BiocCheck Error 'duplicate label install'? > > Greetings, > > Apologies if this is a d

[Bioc-devel] BiocCheck Error 'duplicate label install'?

Greetings, Apologies if this is a double post, I was over zealous in my initial submission that I didn't wait for my membership to be confirmed. I have 'finished' creating a package I would like to submit to bioconductor. As per the instructions on the bioconductor website I am trying to get the

Re: [Bioc-devel] BiocCheck crash with package vignette?

Thanks Dan, this solved the problem ! / Leo On Mon, Sep 15, 2014 at 6:42 PM, Dan Tenenbaum wrote: > Hi Leo, > > - Original Message - > > From: "Leo Lahti" > > To: bioc-devel@r-project.org > > Sent: Monday, September 15, 2014 10:19:55 AM > >

Re: [Bioc-devel] BiocCheck crash with package vignette?

Hi Leo, - Original Message - > From: "Leo Lahti" > To: bioc-devel@r-project.org > Sent: Monday, September 15, 2014 10:19:55 AM > Subject: [Bioc-devel] BiocCheck crash with package vignette? > > Dear Bioc developers, > > The BioC guidelines request

[Bioc-devel] BiocCheck crash with package vignette?

Dear Bioc developers, The BioC guidelines request that package authors run BiocCheck successfully before package submission. To get this working in Linux, I copied the BiocCheck script to /usr/lib/R/bin as adviced and it seemed to work. However, I am now bumping into problems with BiocCheck relate

Re: [Bioc-devel] BiocCheck

- Original Message - > From: "Dan Tenenbaum" > To: "Kasper Daniel Hansen" > Cc: bioc-devel@r-project.org > Sent: Friday, June 13, 2014 4:24:27 PM > Subject: Re: [Bioc-devel] BiocCheck > > > > - Original Message - > &g

Re: [Bioc-devel] BiocCheck

- Original Message - > From: "Kasper Daniel Hansen" > To: bioc-devel@r-project.org > Sent: Wednesday, May 28, 2014 7:20:00 AM > Subject: [Bioc-devel] BiocCheck > > 1) The hash bang in the BiocCheck script currently requires > intervention at > instal

Re: [Bioc-devel] BiocCheck

On Thu, May 29, 2014 at 2:47 PM, Dan Tenenbaum wrote: > #!/bin/sh > > R_SCRIPT="suppressPackageStartupMessages(library(methods))" > R_SCRIPT="$R_SCRIPT; suppressPackageStartupMessages(library(methods))" > R_SCRIPT="$R_SCRIPT; suppressPackageStartupMessages(library(BiocCheck))" > R_SCRIPT="$R_SCRI

Re: [Bioc-devel] BiocCheck

- Original Message - > From: "Kasper Daniel Hansen" > To: "Dan Tenenbaum" > Cc: bioc-devel@r-project.org > Sent: Thursday, May 29, 2014 10:51:56 AM > Subject: Re: [Bioc-devel] BiocCheck > > > This is the content of the Sweave script in

Re: [Bioc-devel] BiocCheck

-- > > From: "Kasper Daniel Hansen" > > To: bioc-devel@r-project.org > > Sent: Wednesday, May 28, 2014 7:20:00 AM > > Subject: [Bioc-devel] BiocCheck > > > > 1) The hash bang in the BiocCheck script currently requires > > intervention at > >

Re: [Bioc-devel] BiocCheck

Hi Kasper, - Original Message - > From: "Kasper Daniel Hansen" > To: bioc-devel@r-project.org > Sent: Wednesday, May 28, 2014 7:20:00 AM > Subject: [Bioc-devel] BiocCheck > > 1) The hash bang in the BiocCheck script currently requires > intervention at

[Bioc-devel] BiocCheck

1) The hash bang in the BiocCheck script currently requires intervention at install time. It would be much more convenient if the script could read of the location of R, in the same way as (say) the Sweave script can. In fact, I modified the BiocCheck script as per the Sweave script but ran into

Re: [Bioc-devel] BiocCheck: Allowed formats for vignette source

- Original Message - > From: "Julian Gehring" > To: bioc-devel@r-project.org > Sent: Tuesday, April 1, 2014 10:04:08 AM > Subject: [Bioc-devel] BiocCheck: Allowed formats for vignette source > > Hi, > > BiocCheck:::getVigSources check for vignett

[Bioc-devel] BiocCheck: Allowed formats for vignette source

Hi, BiocCheck:::getVigSources check for vignette source files in the 'vignettes' directory. Currently, this includes 'Rmd', 'Rnw', 'Rrst'. Shouldn't this also include 'rhtml' and 'rtex' which are valid source formats (see http://yihui.name/knitr/demo/minimal/). Best wishes Julian __