Re: [Bioc-devel] help with lack of permission on new package

ncer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Krutik Patel Sent: Tuesday, July 25, 2023 3:21 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] help with lack of permis

Re: [Bioc-devel] help with lack of permission on new package

ly 25, 2023 3:21 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] help with lack of permission on new package Dear Bioc team, please find attached word doc with screenshots. I am having trouble updating a newly submitted package. I do know the ssh keys were added to biocredentials and gi

Re: [Bioc-devel] help with lack of permission on new package

Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Krutik Patel Sent: Tuesday, July 25, 2023 3:21 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] help with lack of permission on new package Dear Bioc team, please find attached word

[Bioc-devel] help with lack of permission on new package

Dear Bioc team, please find attached word doc with screenshots. I am having trouble updating a newly submitted package. I do know the ssh keys were added to biocredentials and github, but I lack permission to fetch from git@git.bioconductor. Any guidance would be very helpful. Many thanks, Kru

Re: [Bioc-devel] Help fixing version and resync existing package epidecodeR

Hi Kandarp, Please email the bioc-devel@r-project.org for questions on git. You can try to use the documentation we have on our website, http://bioconductor.org/developers/how-to/git/sync-existing-repositories/. The problem is to sync your Github repo with the Bioconductor git repo, hence i

Re: [Bioc-devel] Help for R package check

ive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Xiaowen Chen Sent: Thursday, October 15, 2020 9:10 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Help for R packag

[Bioc-devel] Help for R package check

Hi bioc-devel, I pushed the epihet to Bioconductor on Wen. And this morning I checked the result on the website “bioconductor.org/checkResults/devel/bioc-LATEST/epihet/. “ And I found the window environment there are error “ERROR: dependency 'ReactomePA' is not available for package 'epihet'”

Re: [Bioc-devel] Help me check if I push my package to git bioconductor

n Sent: Monday, September 28, 2020 8:40 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Help me check if I push my package to git bioconductor Hi there, I have followed http://secure-web.c

[Bioc-devel] Help me check if I push my package to git bioconductor

Hi there, I have followed http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ to push to both Bioconductor and GitHub repositories. However, I went to the website https://github.com/Bioconductor, I did not find my R package “epihet”, 1. Could you help me to check it?

Re: [Bioc-devel] Help finding helpful diagnostic info in the build results report

Hi Lillian, For the most part skipping happens because there is a hierarchy to the package testing. If you can't BUILD a package, then you automatically can't CHECK or build a binary version (BUILD BIN), so the build system will simply skip trying those steps if it fails at the BUILD stage. (The

[Bioc-devel] Help finding helpful diagnostic info in the build results report

The newest build report for the checking of a package I submitted to Bioconductor skipped both the Mac and Windows builds. The Mac build was skipped because of a known issue with another R package dependency, gmp, and this can be ignored. However, the Windows build being skipped is a mystery to

Re: [Bioc-devel] Help with setting up a build environment to match

package, it successfully runs all the examples in the vignette without error. From: Fan, Jean Sent: April 24, 2020 12:51 PM To: Kieran O'Neill Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Help with setting up a build environment to match Hi Kieran,

Re: [Bioc-devel] Help with setting up a build environment to match

?Thanks Stephanie, that's also a very helpful suggestion! I hadn't thought of using Docker containers. From: Stephanie Gogarten Sent: April 24, 2020 4:34 PM To: Kieran O'Neill Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Help with set

Re: [Bioc-devel] Help with setting up a build environment to match

__ From: Andris Jankevics Sent: April 24, 2020 2:01 PM To: Kieran O'Neill Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Help with setting up a build environment to match Hi, Are you using R 4.00 on Ubuntu? Travis error indicates that you are using class(), output of this command

Re: [Bioc-devel] Help with setting up a build environment to match

I have found the BIocnductor docker images very helpful in reproducing the build environment: https://www.bioconductor.org/help/docker/ I used a combination of the examples under "modifying the images" to get a version of the docker images that would build my vignettes, and also install all depend

Re: [Bioc-devel] Help with setting up a build environment to match

Hi, Are you using R 4.00 on Ubuntu? Travis error indicates that you are using class(), output of this command has changed. https://www.bioconductor.org/developers/how-to/troubleshoot-build-report/#classEq BW, Andris On 24 Apr 2020 20:40, kone...@bcgsc.ca wrote: A package I maintain, contiBAI

Re: [Bioc-devel] Help with setting up a build environment to match

Hi Kieran, It looks like your Travis build is failing because of your vignettes: Error: processing vignette 'contiBAIT.Rnw' failed with diagnostics: 6542 chunk 13 (label = orderAllLinkageGroupsExampleb) 6543Error in if (spearmanCor < 0) { : missing value where TRUE/FALSE needed 6544 6545 The

[Bioc-devel] Help with setting up a build environment to match

A package I maintain, contiBAIT, is failing to build on the BioC test servers. https://bioconductor.org/checkResults/3.11/bioc-LATEST/contiBAIT/malbec2-buildsrc.htmlv It's also failing on my Travis build set up on GitHub https://travis-ci.org/github/oneillkza/ContiBAIT/builds/674999114 But

Re: [Bioc-devel] Help with tokay2 errors

, March 28, 2020 4:22 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Help with tokay2 errors Hi, Recently I've been having several examples fail on the tokay2 test machine, specifically the i386 examples. Unfortunately I don't have access to a windows machine to diagnose these fa

[Bioc-devel] Help with tokay2 errors

Hi, Recently I've been having several examples fail on the tokay2 test machine, specifically the i386 examples. Unfortunately I don't have access to a windows machine to diagnose these failures right now, and the output that I can see shows no errors; the examples just end abruptly. I don't see th

Re: [Bioc-devel] Help needed on BioC Git credential for package maintainer

Hi I've created the account for you. I'll send you your login details in a private email. Nitesh > On Mar 24, 2020, at 12:20 PM, Huang, Lei [CRI] > wrote: > > Dear Bioconductor team, > > I am one of the maintainers of BioC packages Lumi > (https://bioconductor.org/packages/release/bioc/h

[Bioc-devel] Help needed on BioC Git credential for package maintainer

Dear Bioconductor team, I am one of the maintainers of BioC packages Lumi (https://bioconductor.org/packages/release/bioc/html/lumi.html) and methyAnalysis (https://bioconductor.org/packages/release/bioc/html/methyAnalysis.html); and would like to sync the bug-fix with the bioc-devel repositor

Re: [Bioc-devel] help with Win10 TLS problem?

Did it work? On 3/18/20 15:41, Egon Willighagen wrote: Thanks, in going to try your suggestion tomorrow! On Wed, Mar 18, 2020, 23:22 Hervé Pagès > wrote: mmh.. for some reason the original post in this thread is only showing up now in my mailbox i.e. way a

Re: [Bioc-devel] help with Win10 TLS problem?

mmh.. for some reason the original post in this thread is only showing up now in my mailbox i.e. way after Steffen's answer (and even if Steffen's answer includes the original post, I must confess that I didn't really pay attention to it) Anyway, based on that original post I see now that Egon

Re: [Bioc-devel] help with Win10 TLS problem?

The getBridgeNames() function in BridgeDbR uses the following code to download the HTML page at https://bridgedb.github.io/data/gene_database/ url <- "https://bridgedb.github.io/data/gene_database/"; library(RCurl) CURL_SSLVERSION_TLSv1_2 <- 6L opts <- curlOptions(sslversion=CURL_SSLVERS

Re: [Bioc-devel] help with Win10 TLS problem?

Hi, can you get me the URL that wants to be downloaded ? The "tlsv1 alert protocol version" indicates that the proper solution might be to notify the server to reconfigure the web server supported TLS versions. Yours, Steffen On Wed, 2020-03-18 at 19:55 +0100, Egon Willighagen wrote: > Hi

[Bioc-devel] help with Win10 TSL problem?

Hi all, in the BridgeDbR package I have a TSL issue, just on Windows10 [0]: > location <- getDatabase("Bacillus subtilis") Error in function (type, msg, asError = TRUE) : error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version Calls: getDatabase ... getBridgeNames -> cu

Re: [Bioc-devel] help: Adding a new branch with latest R version to package repository

ject.org Subject: [Bioc-devel] help: Adding a new branch with latest R version to package repository Hi, We try to publish a paper that based on ceRNAnetsim <https://www.bioconductor.org/packages/devel/bioc/html/ceRNAnetsim.html> package (i am also developer of it) in development version o

[Bioc-devel] help: Adding a new branch with latest R version to package repository

Hi, We try to publish a paper that based on ceRNAnetsim package (i am also developer of it) in development version of Bioconductor. But actually reviewers want to test our result via this package. Unfortunately, they could't

Re: [Bioc-devel] help

It's a NOTE, you can't change the affiliation of the authors, so ignore it. The purpose of the note is to improve readability by enabling display in fixed-width windows (e.g., in github!) so make changes that are consistent with improving readability without degrading information. Martin On 2

Re: [Bioc-devel] help

`sapply()` implies that you expect the result to be _s_implified, which implies that all your elements are the same length. Sounds like you want to use `lapply()` instead, to signal that it will *not* be simplified, even if by chance the elements are the same length. Martin On 2/11/20, 3:51 P

[Bioc-devel] help

" Avoid sapply(); use vapply()" Hi, This is a Note I received from BiocCheck() I tried to change my sapply functions to vapply; however, vapply requires knowing the exact length of the vector(list), however, my vector length are not static and variable. Therefore, vapply may not be of use for me

[Bioc-devel] help

Greetings, I am developing a Bioconductor package. After runningBiocCheck:::checkFormatting("CommunityAMARETTO", nlines=Inf) I receive * NOTE: Consider multiples of 4 spaces for line indents, 114 lines(3%) are not. The majority of the lines being shown are manual pages (pages in man f

[Bioc-devel] help

Hi , I am developing a Bioconductor package. By runningBiocCheck:::checkFormatting("CommunityAMARETTO", nlines=Inf) I receive *NOTE: Consider shorter lines; 10 lines (0%) are > 80* * characters long.* However, all these 10 lines belong to Vignette and affiliation part and you can not pu

Re: [Bioc-devel] Help git package maintaining

Thank you all seems in order. * cf86353 (upstream/master, origin/master, master) bump x.y.z version to odd y after creation of RELEASE_3_10 branch * a724b95 (HEAD -> RELEASE_3_10, upstream/RELEASE_3_10, origin/RELEASE_3_10) bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Re: [Bioc-devel] Help git package maintaining

Alright, last try git checkout master git branch -D RELEASE_3_10 git checkout -b RELEASE_3_10 upstream/RELEASE_3_10 git push -f origin RELEASE_3_10 This has to work. Otherwise add me as a collaborator to https://github.com/Peyronlab/MACSQuantifyR. I'll force

Re: [Bioc-devel] Help git package maintaining

It shows fatal: 'RELEASE_3_10' branch already exist Le 22/01/2020 à 16:28, Turaga, Nitesh a écrit : Ok, try this instead git checkout -b RELEASE_3_10 origin/RELEASE_3_10 git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd git push. -f origin RELEASE_3_10 On J

Re: [Bioc-devel] Help git package maintaining

Ok, try this instead git checkout -b RELEASE_3_10 origin/RELEASE_3_10 git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd git push. -f origin RELEASE_3_10 > On Jan 22, 2020, at 10:26 AM, Raphael Bonnet > wrote: > > Hi Nitesh, > > This is what I previously tri

Re: [Bioc-devel] Help git package maintaining

Hi Nitesh, This is what I previously tried but it does not affect (origin/RELEASE_3_10), here are the outputs I get : > git checkout origin/RELEASE_3_10 Note: checking out 'origin/RELEASE_3_10'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them,

Re: [Bioc-devel] Help git package maintaining

Hi Rafael, Please try the following git checkout origin/RELEASE_3_10 git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd This is the cleanest way to achieve what you need. Please also keep in mind to back up your entire folder in another directory should something go

[Bioc-devel] Help git package maintaining

Hi everyone, I'm struggling to understand how to maintain the two version of the my package through git. This is my first package and you will probably guess that I'm not very used to working with multiple branches and remotes. I've read the documentation and understood that the master branch

Re: [Bioc-devel] Help with merida1 R CMD install error

Fantastic! Thank you. Ben > Le 1 janv. 2020 à 20:38, Martin Morgan a écrit : > > This is from the bibtex package > > https://github.com/romainfrancois/bibtex/issues/23 > > And the solution is to either not use that package (settling for base R > functionality) or wait for the upstream fix.

Re: [Bioc-devel] Help with merida1 R CMD install error

This is from the bibtex package https://github.com/romainfrancois/bibtex/issues/23 And the solution is to either not use that package (settling for base R functionality) or wait for the upstream fix. Martin On 1/2/20, 7:06 AM, "Bioc-devel on behalf of Benjamin Jean-Marie Tremblay" wrote

[Bioc-devel] Help with merida1 R CMD install error

Dear bioc-devel, My package has been getting a strange error on merida1 (also celaya2) during the initial install phase. I've pasted it at the bottom of this message. My question is: what can I do to figure out what the problem is? I already work on a Mac currently, and R CMD check runs fine. I'v

Re: [Bioc-devel] help with accessing CRISPRseek

Never mind, I recovered my key and that fixed it. Thanks! Best regards, Julie On 6/18/19, 5:39 PM, "Bioc-devel on behalf of Zhu, Lihua (Julie)" wrote: Hi, I am trying to use git to access CRISPRseek. However, it asks for passphrase. I was able to do this without entering the pa

[Bioc-devel] help with accessing CRISPRseek

Hi, I am trying to use git to access CRISPRseek. However, it asks for passphrase. I was able to do this without entering the passphrase a couple of months ago. Could you please help? Thanks! git clone g...@git.bioconductor.org:packages/CRISPRseek Cloning into 'CRISPRseek'... Enter passphrase

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

Hi, thanks everyone for the input, I now have a few more leads to follow. It would be great to have a general single package builder even for existing packages to check if one has no direct access to the failing architecture. https://win-builder.r-project.org/ is discouraging BioC package upl

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

I second the idea of reproducing with the Windows build commands, which have to do more than 'just' build for a particular architecture. One might test the hypothesis that it is staged install that is causing the problem with StagedInstalll: no in the DESCRIPTION file. Makevars is evaluated

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

I can reproduce the error using R-3.6.0beta and running the following two steps to replicate the Bioc builder commands: R CMD build --keep-empty-dirs --no-resave-data Rdisop rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --m

[Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

Hi, with the next release coming up, I am out of wits regarding the failure at http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/tokay2-buildbin.html which exists since before April this year, when we committed some changes to get rid of the RcppClassic dependency. Max Helf succeede

Re: [Bioc-devel] Help with installing netReg

On Sun, Apr 14, 2019 at 6:30 PM Spencer Brackett < spbracket...@saintjosephhs.com> wrote: > Good evening, > > I am having problems with downloading the package used to generate > regression models on R. The following is the error message I received. I > tried installing BiocManager instead as sug

[Bioc-devel] Help with installing netReg

Good evening, I am having problems with downloading the package used to generate regression models on R. The following is the error message I received. I tried installing BiocManager instead as suggested, but this too did not work. Any ideas? The downloaded binary packages are in C:\Users\Spence

Re: [Bioc-devel] Help with Building Package in Rstudio

Subject: [Bioc-devel] Help with Building Package in Rstudio Hi � I am trying to build an Bioconductor package and I am using the latest version of RStudio (version info): > version _ platform x86_64-w64-mingw32 arch x86_64 os mingw32 system x86_

[Bioc-devel] Help with Building Package in Rstudio

Hi – I am trying to build an Bioconductor package and I am using the latest version of RStudio (version info): > version _ platform x86_64-w64-mingw32 arch x86_64

Re: [Bioc-devel] Help with class lost after subsetting.

On 08/28/2018 11:46 AM, Hervé Pagès wrote: On 08/27/2018 11:01 PM, Martin Morgan wrote: On 08/28/2018 12:19 AM, Charles Plessy wrote: Dear Bioconductor developers, In the CAGEr package, I created a "CAGEexp" class that extends "MultiAssayExperiment" without adding new slots, in order to defi

Re: [Bioc-devel] Help with class lost after subsetting.

On 08/27/2018 11:01 PM, Martin Morgan wrote: On 08/28/2018 12:19 AM, Charles Plessy wrote: Dear Bioconductor developers, In the CAGEr package, I created a "CAGEexp" class that extends "MultiAssayExperiment" without adding new slots, in order to define generic functions that require CAGEr-sp

Re: [Bioc-devel] Help with class lost after subsetting.

On 08/28/2018 12:19 AM, Charles Plessy wrote: Dear Bioconductor developers, In the CAGEr package, I created a "CAGEexp" class that extends "MultiAssayExperiment" without adding new slots, in order to define generic functions that require CAGEr-specific contents in the colData slot. Unfortuna

[Bioc-devel] Help with class lost after subsetting.

Dear Bioconductor developers, In the CAGEr package, I created a "CAGEexp" class that extends "MultiAssayExperiment" without adding new slots, in order to define generic functions that require CAGEr-specific contents in the colData slot. Unfortunately, when run in the development branch of Biocond

Re: [Bioc-devel] Help with version numbering

Hi Rhonda, You can fix your version in your local repo. Just try to amend your commit if your version bump is in the most recent commit. You can try, "git commit --amend" This will allow you to fix your version number and try to push again. It hasn’t changed on the server side (git.bi

[Bioc-devel] Help with version numbering

Hi, For the Trendy package I wanted to bump the version from 1.2.0 to 1.2.1 but accidentally pushed with the wrong version number. I want to fix it but I get the error below. How can I fix this? remote: Error: Illegal version bump from '1.3.1' to '1.2.1'. Check remote: http://bioconductor.org/dev

[Bioc-devel] Help: git push complains non-existing files being too big

Martin, A while ago, Jim suggested to replace two big data files with two smaller ones, which I did. Oddly, when I tried to import the package GUIDEseq to github today, it still mentions these two files being too big, although I do not see these two files in my local repository, checked out fr

Re: [Bioc-devel] Help for Error "Maximal Number of DLLs reached..."

Thanks guys for your kind help! I would follow your tips and try to fix these issues. It's indeed quite hard to maintain it, luckily in past two years I made it. It's indeed the right time to cut down some unnecessary packages and make it easier to be maintained. Thanks for your help! ^_^ Best Y

Re: [Bioc-devel] Help for Error "Maximal Number of DLLs reached..."

Hi, On 03/21/2018 07:32 AM, Martin Morgan wrote: On 03/21/2018 10:14 AM, Henrik Bengtsson wrote: A few quick comments: * I don't think the limit was hardened in R 3.4.0; maybe you started to experience it sound then because more dependent packages started to rely on more DLLs? * The limit

Re: [Bioc-devel] Help for Error "Maximal Number of DLLs reached..."

On 03/21/2018 10:14 AM, Henrik Bengtsson wrote: A few quick comments: * I don't think the limit was hardened in R 3.4.0; maybe you started to experience it sound then because more dependent packages started to rely on more DLLs? * The limit is OS/platform specific so it's not that R core is u

Re: [Bioc-devel] Help for Error "Maximal Number of DLLs reached..."

A few quick comments: * I don't think the limit was hardened in R 3.4.0; maybe you started to experience it sound then because more dependent packages started to rely on more DLLs? * The limit is OS/platform specific so it's not that R core is unwilling to fix this - I think they havejust tried t

[Bioc-devel] Help for Error "Maximal Number of DLLs reached..."

Hello Guys: I encountered an error like "maximal number of dlls reached...". I am maintaining ChAMP package now, which integrated many other packages in my research field. I have not updated this package in past 2 months but suddenly this error happens. Currently, I think I know the reason is sin

Re: [Bioc-devel] Help with GWASTools

Hi, Try the following. Just print "bed.fn" to see if they are imported correctly. And use "snpgdsBED2GDS(... verbose=TRUE)" to print more detailed information or error log. Qian Liu Bioconductor Core Team Roswell Park Cancer Institute library(SNPRelate) (bed.fn <- system.file("extdata", "plinkh

[Bioc-devel] Help with GWASTools

Hi, I am a graduate student at University of Texas School of Public health, and I am using GWASTools for the first time. I am trying to upload PLINK files to use, but I am getting an error which I cannot understand. I would appreciate if you could help me with the same. Code: bed.fn <- sys

Re: [Bioc-devel] Help with a Gviz-plot that differs on a Mac and on an Ubuntu machine

Thank you for testing, Dario! There seems to be something wrong with those 5' and 3' markers. I'll look into it, thanks! On Mon, Oct 23, 2017 at 3:00 AM, Dario Strbenac wrote: > Good day, > > I can't reproduce the problem on Windows, so it seems specific to MacOS. > > Is having 5' and 3' labels

Re: [Bioc-devel] Help with a Gviz-plot that differs on a Mac and on an Ubuntu machine

Good day, I can't reproduce the problem on Windows, so it seems specific to MacOS. Is having 5' and 3' labels at the same ends of both DNA strands biologically incorrect? DNA strands are anti-parallel. See http://www.phschool.com/science/biology_place/biocoach/dnarep/strands.html Perhaps makin

[Bioc-devel] Help with a Gviz-plot that differs on a Mac and on an Ubuntu machine

Hi, I hope it is ok that I ask for help here. I have a mac-specific problem with one of the plot chimeraviz produces. This Github issue has code that p

Re: [Bioc-devel] Help with R CMD check NOTEs

Hi Anusha, On Wed, Oct 18, 2017 at 2:30 PM, Anusha Nagari < anusha.nag...@utsouthwestern.edu> wrote: > > Can you please let me know how to go about the following NOTE. Or if this is something that should be really taken care of for a successful package build and install: > > * checking re-building

Re: [Bioc-devel] Help with R CMD check NOTEs

Hi Herve, Thank you for your response. >In other words putting everything in Imports can hurt >usability/friendliness. The approach should be more nuanced. It's >good that the 'R CMD check' NOTE reminds us about the Depends vs >Imports trade-off but for Bioconductor packages the choices made >by

Re: [Bioc-devel] Help with R CMD check NOTEs

Hi, On 10/18/2017 09:19 AM, Pariksheet Nanda wrote: Hi Anusha On Wed, Oct 18, 2017 at 12:04 PM, Anusha Nagari wrote: Depends: includes the non-default packages: ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’ Adding so many packa

Re: [Bioc-devel] Help with R CMD check NOTEs

Hi Anusha On Wed, Oct 18, 2017 at 12:04 PM, Anusha Nagari wrote: > > Depends: includes the non-default packages: > ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ > ‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’ > Adding so many packages to the search path is excessive and importing

[Bioc-devel] Help with R CMD check NOTEs

Hello, I am getting the following NOTES at R CMD check step: NOTE1: * checking package dependencies ... NOTE Depends: includes the non-default packages: ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’ Adding so many packages to the sear

Re: [Bioc-devel] Help understanding an R performance issue

66 Sent from my MetroPCS 4G LTE Android deviceOn Jun 30, 2017 5:32 AM, Bernat Gel wrote: > > Ok, so it seems more like a bug somewhere than something I falied to > understand, then. One of the surprises for me is that shuffling the data so > the misses do not happen one after the other seems t

Re: [Bioc-devel] Help understanding an R performance issue

Ok, that makes sense In my current use case I think I'll be able to filter out first the elements that will miss, so this behaviour is not triggered. But it's good to know this happens so I can try to avoid it in the future. Thanks. Bernat *Bernat Gel Moreno* Bioinformatician Hereditary C

Re: [Bioc-devel] Help understanding an R performance issue

The reason it's faster when shuffled vs. all that end is that when a miss happens R compares the string to all strings before it in the subscript. So it's a lot worse to have a miss towards the end. As Martin wrote, there are basically two possible improvements that are somewhat complementary: 1)

Re: [Bioc-devel] Help understanding an R performance issue

Ok, so it seems more like a bug somewhere than something I falied to understand, then. One of the surprises for me is that shuffling the data so the misses do not happen one after the other seems to solve the issue... Thanks, Bernat *Bernat Gel Moreno* Bioinformatician Hereditary Cancer Pr

Re: [Bioc-devel] Help understanding an R performance issue

Hi Bernat, Michael, FWIW I reported this issue on R-devel a couple of times. Last time was in 2013: https://stat.ethz.ch/pipermail/r-devel/2013-May/066616.html Cheers, H. On 06/29/2017 11:58 PM, Bernat Gel wrote: Yes, that would explain part of the situation. But example cc5 shows that hash

Re: [Bioc-devel] Help understanding an R performance issue

Yes, that would explain part of the situation. But example cc5 shows that hash misses would account only for part of the time. Thanks for taking a look into it Bernat *Bernat Gel Moreno* Bioinformatician Hereditary Cancer Program Program of Predictive and Personalized Medicine of Cancer (PMPP

Re: [Bioc-devel] Help understanding an R performance issue

Preliminary analysis suggests that this is due to hash misses. When that happens, R ends up doing costly string comparisons that are on the order of n^2 where 'n' is the length of the subscript. Looking into it. On Thu, Jun 29, 2017 at 10:43 AM, Bernat Gel wrote: > Hi all, > > This is not strictl

[Bioc-devel] Help understanding an R performance issue

Hi all, This is not strictly a Bioconductor question, but I hope some of the experts here can help me understand what's going on with a performance issue I've found working on a package. It has to do with selecting elements from a named vector. If we have a vector with the names of the chrom

Re: [Bioc-devel] Help needed to reproduce my crash report

On 11/16/2016 02:44 AM, Ted Wong wrote: Hi, I need help to reproduce a crash in my crash report. The crash report is: http://master.bioconductor.org/checkResults/3.4/bioc-LATEST/Anaquin/malbec1-buildsrc.html This is what I did: 1. svn co --username ... --password https://hedgehog.fhcrc

[Bioc-devel] Help needed to reproduce my crash report

Hi, I need help to reproduce a crash in my crash report. The crash report is: http://master.bioconductor.org/checkResults/3.4/bioc-LATEST/Anaquin/malbec1-buildsrc.html This is what I did: 1. svn co --username ... --password https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Anaq

Re: [Bioc-devel] Help using Git with Bioconductor SVN repositories

Hi, I recommend using git cherry-pick as Jim described in other threads. You might also want to check out Mike's instructions. You'll find all the links at https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008141.html Cheers, Leo On Mon, Oct 19, 2015 at 5:35 AM, Elena Grassi wrote: >> Then

Re: [Bioc-devel] Help using Git with Bioconductor SVN repositories

> Then I tried forking the repo available from bioconductor-mirror > (https://github.com/Bioconductor-mirror/GenomicTuples). This resulted > in an error due to a non-existent devel branch. Yep, same here. I disabilited the git-svn bridge forked the Bioconductor-mirror/REPO and cloned it, used upda

[Bioc-devel] Help using Git with Bioconductor SVN repositories

I used to use the git-svn bridge for my GenomicTuples package, which I develop on GitHub. Several months ago I attempted to switch to the new method described at http://bioconductor.org/developers/how-to/git-mirrors/ but made a complete mess of it. This wasn't so important at the time since I didn'

Re: [Bioc-devel] help with imports for new package and other questions

oh! that's cool! super nice, will try it. thanks a lot! On 08/20/2015 12:46 PM, Adrienne Stilp wrote: Hi Lorena, For your last question about coding style, you could look into the lintr package: https://github.com/jimhester/lintr You can run it either as an R function, or add it as a plugin

Re: [Bioc-devel] help with imports for new package and other questions

Hi Lorena, For your last question about coding style, you could look into the lintr package: https://github.com/jimhester/lintr You can run it either as an R function, or add it as a plugin to some editors. The developer, Jim Hester, is also part of the Bioconductor team! Adrienne > On Aug 14

Re: [Bioc-devel] help with imports for new package and other questions

Thanks a lot Hervé. Your suggestions are perfect. I fully imported these classes because I realized that it would be less chances of errors, as you say here. I used that, and it is true that I am using these functions for dplyr. The reason I tried to do with dplyr is was to summarize quicker.

Re: [Bioc-devel] help with imports for new package and other questions

Hi Lorena, In your particular case it seems to me that you're using dplyr internally for convenient data frame transformations (nothing that couldn't be done with plain R BTW), and that you're only using a few dplyr symbols for this. The codetoolsBioC package could be useful to help you identify

Re: [Bioc-devel] help with imports for new package and other questions

As I understand it, the function sometimes gives false positives (I have never experience it myself though - Michael Lawrence has, but perhaps his use cases are more complicated). My guess is that this is a showstopper for including it in codetools (where it would be great to go, in my opinion).

Re: [Bioc-devel] help with imports for new package and other questions

Hi, thanks a lot for the link!, I would definitely try that one...you save me a lot of time! On 08/14/2015 10:03 AM, Kasper Daniel Hansen wrote: > Indeed, you need to use importFrom to selectively import. > > In this process you'll realize how great it would be to have a > function called > i

Re: [Bioc-devel] help with imports for new package and other questions

On Fri, Aug 14, 2015 at 10:03 AM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > Indeed, you need to use importFrom to selectively import. > > In this process you'll realize how great it would be to have a function > called > importEverythingFromExcept( PACKAGE, NOT_THESE_FUNCTIO

Re: [Bioc-devel] help with imports for new package and other questions

Indeed, you need to use importFrom to selectively import. In this process you'll realize how great it would be to have a function called importEverythingFromExcept( PACKAGE, NOT_THESE_FUNCTIONS) but last time I raised this issue on R-devel, I was gently shut down. In the meantime you should us

[Bioc-devel] help with imports for new package and other questions

Hi, I am trying to get right my new package (http://github.com/lpantano/isomiRs). But I am having some problems with the packages I import. The main problem is that I get warnings while loading my packages because some dplyr replaces functions in others packages like S4Vectors and others.

Re: [Bioc-devel] Help with creating first Bioconductor package

On 11/15/2014 12:04 PM, January Weiner wrote: Dear Martin, thanks for your description, just a question mkdir -p ~/src/R-devel cd ~/src/R-devel svn co https://svn.r-project.org/R/trunk tools/rsync-recommended I think this should be trunk/tools/rsync-recommended mkdir -p ~/bin/R-devel cd

Re: [Bioc-devel] Help with creating first Bioconductor package

Dear Martin, thanks for your description, just a question > mkdir -p ~/src/R-devel > cd ~/src/R-devel > svn co https://svn.r-project.org/R/trunk > tools/rsync-recommended I think this should be trunk/tools/rsync-recommended > mkdir -p ~/bin/R-devel > cd ~/bin/R-devel > ~/src/R-devel/configure

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