[Bioc-devel] builds of last 2 days

Dear all, I re-cloned my package (canceR ), following this tutorial . And I commit some changes (05 May), and I bump version from 1.18.2 to 1.18.3. Actually I am seeing

[Bioc-devel] Fwd: canceR problems reported in the Multiple platform build/check report for BioC 3.6

Dear Admin, Following this link https://master.bioconductor.org/checkResults/3.6/bioc-LATEST/canceR/malbec1- buildsrc.html, I did not find any built issue in malbec1 for 3.6 version. Thanks, Karim -- Forwarded message -- From: Date: Mon, Dec 11, 2017 at 8:57 PM Subject: canceR pr

Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

LCMS proteomics experiment quantifies 7000 > proteins. Retrieving annotation for these through biomaRt would be slow (an > overnight activity). I want something that works instantaneously. > > · From what I remember you can actually not access the uniprot > summary (which

Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

Hi, I general LCMSMS generate mass/charge data of Amino Acid or peptides. The goal in to identify which protein belong the peptides. The Software used with LCMSMS can match the peptides to Uniprot database , and ranks putative proteins by scores. Could the tell us what is the interest of org.Hs.un

Re: [Bioc-devel] denied access to git

Thank You Dr. Morgan, When I cloned a repository with git clone , it automatically creates a remote connection called *origin* pointing back to the cloned repository. I tried to update bioCancer using old scenario 1: - git clone https://github.com/Bioconductor-mirror/bioCancer - cd bioCan

[Bioc-devel] denied access to git

Dear admin, I re-submit my ssh key to the google form. Maybe I need to wait to get approved. Actually I do not have access to push updates for bioCancer package. bioCancer Mezhoud$ git remote -v originhttps://github.com/Bioconductor-mirror/bioCancer (fetch) originhttps://github.com/Bioco

Re: [Bioc-devel] commit changes with scenario 1

Thanks Dr Dan, I have multiple files to commit. How can I specify multiple files names? git commit -m " resolve prblm" -a "file1.R, file2.R" Thanks karim On Mon, Aug 8, 2016 at 6:33 PM, Dan Tenenbaum wrote: > > > - Original Message - > > From: &

[Bioc-devel] commit changes with scenario 1

I am trying to commit some changes to bioCancer . the issue is no changes added to commit. Please, here is commands. Thanks - git clone https://github.com/Bioconductor-mirror/bioCancer - cd bioCancer/ - ../update_remotes.sh Already on

Re: [Bioc-devel] check shiny app: issue with global variables: input$Vars is not found

ables declared within the ui-function body need to be addressed by > input$. > > I hope that helps. > > Cheers, > > Stefan > > On Tue, May 3, 2016 at 1:57 PM Karim Mezhoud wrote: > >> Dear R, >> usually, Shiny app uses global variables saved in a session

[Bioc-devel] check shiny app: issue with global variables: input$Vars is not found

Dear R, usually, Shiny app uses global variables saved in a session. These variables can be returned by client web page (checkbox or select). for example: FUN1 <- function(input$var1){ a <- input$car1 + input$globalVar2 return (a) } when I run check package I got error like object input$globalV

Re: [Bioc-devel] package submission - problem with vignette

Hi, I don't know why I have to use %\VignetteEncoding{UTF-8} instead %\usepackage[UTF8]{inputenc} it works. On Tue, Apr 12, 2016 at 8:38 AM, Karim Mezhoud wrote: > Dear Lara and Dan, > In my case I am having this error. Thanks > > * creating vignettes ... ERROR

Re: [Bioc-devel] package submission - problem with vignette

ckage. In DESCRIPTION file I added: Suggests: BiocStyle, AnnotationHub, knitr, rmarkdown, testthat (>= 0.10.0), rappdirs VignetteBuilder: knitr In Rmd file, I started by: --- title: "bioCancer: Interactive Multi-OMICS Cancers Data Visualization and Analysis"

Re: [Bioc-devel] import except on Window Machine

t; Source package written to /Volumes/DATA/radiant On Mon, Apr 11, 2016 at 6:10 PM, Dan Tenenbaum wrote: > roxygen2 does not support the new syntax. Do you still get the same error > if you write your NAMESPACE manually? > > - Original Message - > > From: "Kar

Re: [Bioc-devel] import except on Window Machine

is the sessionInfo() in your R-3.3? It might be too old to > have the new feature. It needs to be at svn rev r70426 or newer. > > Dan > > > - Original Message - > > From: "Karim Mezhoud" > > To: "Lihua Zhu" > > Cc: "Dan Tenenbau

Re: [Bioc-devel] import except on Window Machine

Dear Julie, Are you using roxigen2 to edit NAMESPACE file? Are you using R 3.4? Thanks In my case, When I used R 3.3 I get this error: ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer * installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ * install

[Bioc-devel] mascato2 check error

Dear BioC devel, I did not understand the following error check message. http://www.bioconductor.org/checkResults/3.3/bioc-LATEST/canceR/moscato2-checksrc.html Any suggestion is welcome. Thank you Karim ### Running command: ### ### rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir canceR.buil

Re: [Bioc-devel] namespace question

unfortunately, Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for help Bioconductor does not yet support R version 3.4.0 On Tue, Apr 5, 2016 at 9:17 PM, Michael Lawrence wrote: > You need R 3.4 for right now. > > On Tue, Apr 5, 2016 at 1:16 PM, Karim Mezhoud wrote: >

Re: [Bioc-devel] new package: annotate function interaction from Reactome DB

Dear bioC devel, I write an annotate package named reactomeFI to avoid the big size files in /extdata folder. Finally when compressed the txt file to RDS format I reduce enough the size of files. reactomeFI provides annotation that do not exist in any other package (to my knowledge). Nor reactome.

[Bioc-devel] annotate package not need vignette?

Hi, if yes, how to a avoid biocCheck failure? Thanks Karim [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] big file ReactomeFI --> bioC annotate package

ot that > working you can open a new ticket on the package tracker. > > Feel free to write me at valerie.obench...@roswellpark.org if you have > other questions. > > Valerie > > > > > On 04/05/2016 02:18 AM, Karim Mezhoud wrote: > > Dear bioC de

Re: [Bioc-devel] namespace question

ks/R.framework/Versions/3.3/Resources/library/bioCancer’ Exited with status 1 On Tue, Apr 5, 2016 at 8:58 PM, Michael Lawrence wrote: > Yea, with the closing ) > > On Tue, Apr 5, 2016 at 12:37 PM, Karim Mezhoud wrote: > > If I include manually the exception, I hve to writ

Re: [Bioc-devel] namespace question

e > with the warning or just importFrom(shiny, ...). Maybe there is some > way to manually patch the NAMESPACE with Roxygen? > > Honestly, I would recommend against using Roxygen to manage your > NAMESPACE. Just write the thing... > > > > On Tue, Apr 5, 2016 at 11:07 AM, Kar

Re: [Bioc-devel] namespace question

them for that. But do we want this kind > of > >>>>> things to work? I'm worried debugging NAMESPACE files would become a > >>>>> full-time job... > >>>>> > >>>>>> I guess one could have implemented NAMESPACE

[Bioc-devel] big file ReactomeFI --> bioC annotate package

Dear bioC developer, I included in my bioCancer/inst/extdata a Reactome FI database (/ http://reactomews.oicr.on.ca:8080/caBigR3WebApp2015/FIsInGene_031516_with_annotations.txt.zip ) Gene1Gene2AnnotationDirectionScore 16-5-5CDC42predicted-0.82 16-5-5RHOJpred

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

thing On Fri, Apr 1, 2016 at 9:48 PM, Dan Tenenbaum wrote: > Sorry, about that, please try again. > > Dan > > > - Original Message - > > From: "Karim Mezhoud" > > To: "Dan Tenenbaum" > > Sent: Friday, April 1, 2016 1:36:30 PM >

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

NO thing in the file On Fri, Apr 1, 2016 at 6:24 PM, Dan Tenenbaum wrote: > Can you send me the output of > > git diff? > > So: > > git diff > diff.txt > > and send me diff.txt? > > Dan > > > - Original Message - > > From: "Kari

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

ory is an svn repository, so > instead of pushing you want to do > > git svn dcommit --add-author-from > > I'll take a look at your earlier email later today. > > Dan > > > - Original Message - > > From: "Karim Mezhoud" > > To: "Dan Te

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

ervname provided, or not known fatal: Could not read from remote repository. Please make sure you have the correct access rights On Fri, Apr 1, 2016 at 1:09 AM, Karim Mezhoud wrote: > Hi, > I repeated several times the clone And I success for one time the > commit but with m

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

run me again. I am stopping in case you still have something valuable there. rebase refs/remotes/git-svn-devel: command returned error: 1 On Tue, Mar 29, 2016 at 8:12 PM, Dan Tenenbaum wrote: > > > > > - Original Message - > > From: "Karim Mezhoud" > &

Re: [Bioc-devel] namespace question

I think "From" is needed to specify which package we want to exlude functions. I think excludeFrom (package, function) seems to be intuitive. thanks, Karim On Thu, Mar 31, 2016 at 9:54 PM, Hervé Pagès wrote: > On 03/31/2016 12:55 PM, Michael Lawrence wrote: > >> Probably should just stick

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

Thank you, I am in devel branch (git checkout devel) . when I "git svn rebase" I get all changed files with message: needs update. How can I update. km On Tue, Mar 29, 2016 at 4:16 PM, Dan Tenenbaum wrote: > > > - Original Message ----- > > From: "Karim

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

Dear Dr Dan, Thank you for this note. In my case (canceR), I am using sweave and having: checking PDF version of manual ... [8s/19s] OK during R CMD Check. I need to sync devel version using git-mirrors ( https://www.bioconductor.org/developers/how-to/git-mirrors/). I am following scenario 2.

[Bioc-devel] new package: canceR

suggestions. Karim Mezhoud [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Package submission with library requirement

Yes, just an error by copy/paste [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Package submission with library requirement

Hi, Before you submit your package, please make sure that it satisfies all our guidelines here. http://www.bioconductor.org/developers/package­guidelines/ Be sure that you tested it with the appropriate version of R. To work out which version that is, please have a look at this site here: htt

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

[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

[Bioc-devel] built BioC packages using RStudio

and reload the project; In attached file the log informations. Any suggestion? I need to fill the doc informations (title, manual, vignette, description). Can I do these directly from Rd files located in Man folder? Thanks! Karim Mezhoud ___ Bioc-devel