Re: [Bioc-devel] Warning for Matrix during R CMD Check

Likely you or one of your dependent packages makes use of Matrix without using import() in the NAMESPACE file. Email formatting makes it hard to tell exactly what is going on; make sure you are sending email in plain text, and that the build / check steps are done at the command line rather

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

positories not to regenerate? Martin thanks, Stephanie On 8/21/17 9:00 AM, Martin Morgan wrote: Hi git transitioners -- We'd like to regenerate git repositories from svn. This is because some svn user ids were mapped to 'unknown' git users, so that contributors would not be credited

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

really was no known user... Biobase$ git log --all --committer="unknown" |grep -B 3 cvs2svn Author: unknown <unknown@email> Date: Mon Aug 23 17:00:07 2004 + This commit was manufactured by cvs2svn to create branch 'RELEASE_1_4'. Martin thanks, Stephanie On 8/21/17

Re: [Bioc-devel] Trying to clone my repo but my key is not recognized.

On 08/22/2017 04:59 AM, Joris Meys wrote: Hi, I sent my public key as registered in my github account to you a while ago, but when I tried to clone my repository, I get the following error message after git fetch upstream: - The authenticity of host 'git.bioconductor.org (34.192.48.227)'

[Bioc-devel] Git transition -- regenerating repositories from svn

Hi git transitioners -- We'd like to regenerate git repositories from svn. This is because some svn user ids were mapped to 'unknown' git users, so that contributors would not be credited accurately. This will invalidate any local clones made from git.bioconductor.org. Our plan is to

Re: [Bioc-devel] Odd version in release

On 08/21/2017 09:22 AM, Bernat Gel wrote: Hi, It seems like a couple of months ago I fixed a bug in release version of karyoploteR and pushed a DESCRIPTION with the wrong version number, going from 1.0.1 to 1.1.6 (the one in devel at the moment). So now both devel and release are in 1.1.*

Re: [Bioc-devel] Package not updated in build system from github

On 08/25/2017 03:36 AM, Panagiotis Moulos wrote: Dear all, For some time now, my package metaseqR fails to pass the checks at the build system http://bioconductor.org/checkResults/3.6/bioc-LATEST/metaseqR/ Although I am not sure I understand the source of the problem (all is well in my local

Re: [Bioc-devel] Package changes not merging with upstream

On 08/25/2017 01:17 PM, Matt Richards wrote: Hi all, I maintain the "trena" package and I'm attempting to sync the changes from my in-house Github repo with the Bioconductor version. I submitted my ssh keys last week, so essentially I'm following these instructions:

Re: [Bioc-devel] Git transition is happening August 16th.

it worked. yes, but to solve this for other people generally can you tell me what you did to see the message? git clone g...@git.bioconductor.org:pacakges/TCGAbiolinks ? git status ? ... ? Thanks Best regards, Tiago Chedraoui Silva On Fri, Aug 18, 2017 at 8:35 AM, Martin Morgan &

Re: [Bioc-devel] Error following post acceptance instructions: permission denied

On 08/29/2017 02:49 AM, Christopher John wrote: Hi I have had my package accepted to the bioconductor (M3C). I then followed the instructions in the email to add a ssh key to my account, then summited this to the bioconductor. I tested the key using the github instructions and it seemed to work

Re: [Bioc-devel] Canot push to git.biocondutor.org

On 08/31/2017 03:08 PM, Javier Iserte wrote: Hi, I'm Javier Iserte, a collaborator to ASpli package (http://bioconductor.org/checkResults/3.5/bioc-LATEST/ASpli/). I'm am unable to push my local repository to git.bioconductor.org. I

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

On 10/05/2017 01:50 PM, Henrik Bengtsson wrote: Is there an easily accessible archive for Bioconductor packages similar to what is provided on CRAN where you can find all released versions of a package, e.g. https://cran.r-project.org/src/contrib/Archive/PSCBS/? Say I want to access the source

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

On 10/05/2017 05:14 PM, Henrik Bengtsson wrote: On Thu, Oct 5, 2017 at 1:46 PM, Martin Morgan <martin.mor...@roswellpark.org> wrote: On 10/05/2017 01:50 PM, Henrik Bengtsson wrote: Is there an easily accessible archive for Bioconductor packages similar to what is provided on CRAN whe

Re: [Bioc-devel] EXTERNAL: Fetuching Upstream Permission Denied

On 10/11/2017 08:00 PM, Dario Strbenac wrote: Good day, I have submitted my public key a couple of months ago and am now trying to do some maintenance. The code I used is: git clone https://github.com/DarioS/ClassifyR.git cd ClassifyR git remote add upstream

Re: [Bioc-devel] EXTERNAL: Re: Difficulty obtaining access to BioC git repository

On 10/11/2017 10:54 AM, Raborn, R. Taylor wrote: Hi Nitesh: Thank you for the message. In my previous email I should have mentioned that I have matched each VM public key with their respective private keys, which are in both of the respective .ssh folders. It’s puzzling, but it’s something

Re: [Bioc-devel] EXTERNAL: Fetuching Upstream Permission Denied

On 10/11/2017 08:30 PM, Dario Strbenac wrote: Good day, Yes, that's the end of the key digiOcean.pub. I also copied the private key to /tmp and re-generated the public key. The newly made public key is exactly the same as the one in ~/SSHkeys/ so the key pair matches. if you say ssh -v

Re: [Bioc-devel] EXTERNAL: error: Could not fetch upstream

On 10/10/2017 01:56 PM, greg gloor wrote: I too am having problems with this. I checked to make sure I had an ssh public key on github, I submitted my svn id (gloor.g) and re-submitted the form last Friday. Today I did the following, and am still not able to access the upstream repository:

Re: [Bioc-devel] EXTERNAL: change maintainer of a package

Sorry for the oversight; I responded to the mail at packages@ just now. Martin On 10/10/2017 02:44 PM, Christoph Bernau wrote: Hi, I would like to appoint a new maintainer for my package and could not find any documentation on this topic. I was told to send an email mentioning both new and

Re: [Bioc-devel] EXTERNAL: Can't push to git

Actually, 'tjh48' was used to map your public key to package permissions, but that was not your svn id. I updated your public key / package access mapping, and you should have success now. Martin On 10/11/2017 10:09 AM, Shepherd, Lori wrote: When did you submit the new svnid and key? It

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

Tomas Kalibera on R-core says that in R-devel I've increased the number of DLLs... Now it is 614 on systems where the soft limit on open files allows, but R now attempts to increase the limit when needed. If this is not possible, the maximum will be smaller. R will fail to start if the maximum

Re: [Bioc-devel] Cannot move 'xps' to GIT

On 10/08/2017 01:37 PM, cstrato wrote: Dear all, I wanted to update my package 'xps' and realized that I can no longer use 'svn commit' In order to use GIT I did the following: 1, I created a public key '~/.ssh/id_rsa.pub' 2, I did submit my 'SSH public key or github id to Bioconductor',

Re: [Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT

. It sounds like, now that you have access to git.bioconductor.org, you could follow https://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Martin I am not sure what I need to do next? Thank you. Best regards, Christian On 10/12/17 19:40, Martin Morgan wrote: On 10/08

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

On 10/19/2017 07:04 AM, jmason wrote: Hi bioc-devel, I am maintainer of the IMPCdata package.  I can clone the package, but when I push I get: ➜  IMPCdata git:(master) ✗ git push FATAL: W any packages/IMPCdata jmason DENIED by fallthru (or you mis-spelled the reponame) fatal: Could not read

Re: [Bioc-devel] ShortRead readFasta UniProt Incorrect Import

On 10/18/2017 01:00 AM, Dario Strbenac wrote: Good day, If I have a FASTA file that contains sp|Q9NYW0|T2R10_HUMAN Taste receptor type 2 member 10 OS=Homo sapiens GN=TAS2R10 PE=1 SV=3 MLRVVEGIFIFVVVSESVFGVLGNGFIGLVNCIDCAKNKLSTIGFILTGLAISRIFLIWI

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

Re: [Bioc-devel] Updating Rsamtools to support BAMs with >65535 CIGAR operators

On 10/18/2017 04:32 PM, Heng Li wrote: Hi, I am not sure whether I should send the request to this mailing list in this case, but I am not sure what is the best place to ask. Anyway, an alignment with >65535 operators can't be encoded in the current BAM format. Unfortunately, a tiny fraction

Re: [Bioc-devel] DOI for packages

On 10/19/2017 03:10 PM, Laurent Gatto wrote: On 19 October 2017 13:22, Shepherd, Lori wrote: Hello Bioconductor, We have added DOI's for packages on Bioconductor package landing pages. The DOI will get generated automatically when a package is accepted to Bioconductor. This is the

Re: [Bioc-devel] write access to git repos for two packages maintained

On 11/10/2017 02:14 AM, Alicia Schep wrote: I have two new packages in latest release of Bioconductor, and am having issues pushing to the git repo for one. One was accepted when BioC was still using SVN, and the other after transition to git. I first entered my ssh key info into the form with

Re: [Bioc-devel] R: DaMiRseq in ERROR in the stable release

lso that 1:opt.comp causes problems, much like omitting drop=FALSE, when opt.comp == 0 and it is always better to use seq_len() (or its compatriot seq_along()). > 1:opt.comp [1] 1 0 > seq_len(opt.comp) integer(0) Martin Mattia --------

Re: [Bioc-devel] Build failing for MutationalPatterns

On 11/30/2017 10:01 AM, Janssen-10, R.R.E. wrote: Dear Martin, Martin writes: On 11/29/2017 11:14 AM, Janssen-10, R.R.E. wrote: Hi Martin, Thanks for your reply! Martin Morgan writes: On 11/29/2017 09:58 AM, Janssen-10, R.R.E. wrote: Dear Bioconductor, The build for MutationalPatterns

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

On 11/24/2017 01:25 PM, Ioannis Vardaxis wrote: Hei, Both kalliston and salmon er for RNA data, I have DNA data. Is there any other solution rather than Rsubread which is extremely slow? I am making an algorithm where one of its steps should be to map the DNA reads to the reference genome. So I

Re: [Bioc-devel] Data package timeouts

On 11/30/2017 06:05 AM, Mike Smith wrote: Thanks for the speedy response Sean. I'll switch back to the version using a file name shortly. Is there a use case for BiocFileCache in here -- check if the file is in the cache bfcquery(), if so, check whether it needs updating bfcneedsupdate()

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

On 11/17/2017 04:08 AM, Neumann, Steffen wrote: Hi, I would like to have a URL to individual files we have in BioC packages. This is useful e.g. if I need test data from, say, the msdata package, in another context. In the SVN days, I was able to point directly into the SVN repo with

Re: [Bioc-devel] How much does it takes for a package to appear at Bioconductor.org after a push?

How come you guys are so secretive about what package you're talking about? ;) Check the 'nightly' builds to see that your package has been built. http://bioconductor.org/checkResults/3.7/bioc-LATEST/ Note that the nightly builds do sometimes fail, so check the date at the top center of

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

27 <tel:(502)%20509-1827> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. - Ronald Fisher On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan <martin.m

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

-11-17 at 04:31 -0500, Martin Morgan wrote: On 11/17/2017 04:08 AM, Neumann, Steffen wrote: Hi, I would like to have a URL to individual files we have in BioC packages. This is useful e.g. if I need test data from, say, the msdata package, in another context. In the SVN days, I was able to point

Re: [Bioc-devel] DaMiRseq in ERROR in the stable release

On 11/20/2017 08:54 AM, Shepherd, Lori wrote: It is quite possible that it could be because of a dependent package. Unfortunately the only way to tell would be to see if any of those packages are producing a similar ERROR on the build report or to investigate your code to see where and how

Re: [Bioc-devel] batchtools support in BiocParallel

On 11/16/2017 11:41 AM, Steve Lianoglou wrote: Hi all, Given BatchJobs' end-of-life status, has there been any thought/discussion about adding support for its successor batchtools (https://github.com/mllg/batchtools) to BiocParallel? I skimmed the bioc-devel list but haven't seen any mention

Re: [Bioc-devel] Build error on windows (devel)

On Windows and Mac, we install binary versions of CRAN packages from CRAN, rather than building them from source; this is what users would do. For unknown reasons, the CRAN packages for R-devel (hence Bioc-devel, where your package is not building) are built against R-3.4.2, and are not

Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

now. The following is the Command-line output: > Arman@Arman-VAIO MINGW64 /z/cbaf/Source/cbaf (master) > $ git branch -a > * master >   remotes/origin/HEAD -> origin/master >   remotes/origin/RELEASE_3_6 >   remotes/origin/master >   remotes/upstream/RELEASE_3_6

Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

On 11/01/2017 04:42 PM, Gabe Becker wrote: Arman, Not on the Bioc team per se, but I would say only have a checkout of the release branch when you need it, ie a bug is reported, you have fixed it in devel, and you are ready to push the very narrow bugfix to release. I only keep "master"

Re: [Bioc-devel] any interest in a BiocMatrix core package?

On 11/01/2017 05:15 PM, Bemis, Kylie wrote: Yes, the ideal solution seems rather unlikely, but I feel like there must be a solution better than the current situation. I’d like to implement some more of the functionality from matrixStats for ‘matter’ matrices, but importing DelayedArray and

Re: [Bioc-devel] any interest in a BiocMatrix core package?

h.ethz.ch wrote: Martin Morgan <martin.mor...@roswellpark.org> on Thu, 2 Nov 2017 06:17:19 -0400 writes: > On 11/02/2017 05:00 AM, Martin Maechler wrote: >>>>>>> "ML" == Michael Lawrence <lawrence.mich...@gene.com>

Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

On 11/01/2017 07:53 PM, Arman Shahrisa wrote: I cloned the package into a clean directory. It helps to be more precise here. Were did you clone the package from? In the simplest case it would be git clone g...@git.bioconductor.org:packages/your-package and you'd have a single remote

Re: [Bioc-devel] Package additional maintainers

: of the package has asked that additional individuals have write access. Martin Best regards, Fatemeh From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Martin Morgan <martin.mor...@roswellpark.org> Sent: Wednesday, November 1, 2

Re: [Bioc-devel] any interest in a BiocMatrix core package?

ny prospect for factoring out the definition of the generics from implementation of the methods? Re-purposing stats4 ? Martin Morgan Best, Martin Maechler ETH Zurich (and R core team) > On Wed, Nov 1, 2017 at 1:59 PM, Hervé Pagès > <hpa...@fredhutch.org> wrote:

Re: [Bioc-devel] Confusion with how to maintain release/devel files on local computer.

-package (push) and so on. Martin Best regards, Arman *From: *Martin Morgan <mailto:martin.mor...@roswellpark.org> *Sent: *Thursday, November 2, 2017 05:00 *To: *Arman Shahrisa <mailto:shahrisa.ar...@hotmail.com>; Stephanie M. Gogarten <mailto:sdmor...@uw.edu>; bioc-devel &l

Re: [Bioc-devel] 'IlluminaHumanMethylation450k.db' package installation

On 12/07/2017 10:48 AM, Maryam Hosseini Asanjan wrote: Hi, I am trying to install the 'IlluminaHumanMethylation450k.db' package the way it is described at the bioconductor website (https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450k.db.html) but it

Re: [Bioc-devel] parallel processing in R?

On 12/11/2017 12:19 PM, Dwivedi, Bhakti wrote: Hi, Is there a way to parallelize ConsensusClusterPlus package? Consider https://bioconductor.org/packages/BiocParallel https://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html We are developing a R shiny tool that

Re: [Bioc-devel] Pigengene problems reported due to partykit::as.party

Remember that Bioconductor uses the current (3.4.3) or devel version of R, and the corresponding versions of packages enforced by BiocInstaller::biocValid(). Below you are using 3.3.3, which is not current. The first step then is to get a current installation of R and Bioconductor. Also >

Re: [Bioc-devel] BiocFileCache for developers

On 12/01/2017 11:23 AM, Sean Davis wrote: On Fri, Dec 1, 2017 at 11:16 AM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: So having a user argument might be best. Or defining a unique cache location for your package would be another option. The R package development policies

Re: [Bioc-devel] Bioconductor Git: Online interface

There has been previous discussion about this. https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html It is not in our short-term plans to offer a full on-line solution, but not impossible in a longer context. Martin On 10/26/2017 03:01 AM, Stian Lågstad wrote: I would very

Re: [Bioc-devel] "extra" unit tests

There is currently some capacity in the build system to support 'extended' builds. One possibility would be to provide facilities for packages to 'opt in' to a distinct 'extended' build, with a (weekly?) build report. One could also just increase the timeouts of the current builds. I think

Re: [Bioc-devel] how can I contribute to the success of great packages?

On 10/20/2017 07:00 PM, Dario Strbenac wrote: Hello, I noticed that October 24 is "Deadline for packages passing ‘‘R CMD build’’ and ‘‘R CMD check’’ without errors or warnings." and "Identify packages to be ‘deprecated’ in the new devel, Bioconductor 3.7." and "... or those with errors and

Re: [Bioc-devel] how can I contribute to the success of great packages?

On 10/20/2017 09:00 PM, Dario Strbenac wrote: Good day, Thanks for the clarification. I appreciate your regular insights on the support forum over the years. It seems that Gviz will be stable enough to use, although the same maintainer's domainsignatures package has strikethrough across its

Re: [Bioc-devel] Incrimental writing to HDF5 / DelayedMatrix

On 12/21/2017 06:22 AM, Francesco Napolitano wrote: Hi, I need to deal with very large matrices and I was thinking of using HDF5-based data models. However, from the documentation and examples that I have been looking at, I'm not quite sure how to do this. My use case is as follows. I want to

[Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

17, see http://bioc2018.bioconductor.org/call-for-abstracts http://bioc2018.bioconductor.org/scholarships Martin Morgan Bioconductor This email message may contain legally privileged and/or...{{dropped:2}} ___ Bioc-devel@r-project.org mailing

Re: [Bioc-devel] Switch to SSH protocol for git clone instructions on package landing pages?

On 04/30/2018 08:17 AM, Kasper Daniel Hansen wrote: Still, it is convenient for some of us to have copy+paste code on the landing page. How about having both https and ssh? Supporting https:// would require account and password management. I guess we have moved closer to that than

Re: [Bioc-devel] BiocInstaller: next generation

Installer (I removed BiocInstaller from my library) for either the release or devel version of Bioconductor. Please post issues / pull requests / etc to the github repository https://github.com/Bioconductor/BiocManager Martin On 05/09/2018 06:11 PM, Martin Morgan wrote: Developers -- A

Re: [Bioc-devel] Package download when using functions from affy and oligo

One of your cell files is funky > colSums(exprs(alldata) == 0) GSM907854.CEL.gz GSM907866.CEL.gz GSM907857.CEL.gz GSM907863.CEL.gz 000 686388 GSM907856.CEL.gz GSM907862.CEL.gz GSM907855.CEL.gz GSM907861.CEL.gz 0

Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

The scholarships support up to $500 travel. The scholarship also covers accommodation and registration. A letter inviting you to the conference will be sent separately. Martin On 05/09/2018 01:13 AM, Pijush Das wrote: Dear Martin Morgan, Thank you Morgan for informing me to join your

Re: [Bioc-devel] build machines

For what it's worth, BiocParallel implemented as outlined in it's vignette limits the number of cores via if (nzchar(Sys.getenv("BBS_HOME"))) cores <- min(4L, cores) i.e., checking an environment variable set on the build system. This is highly fragile and I wouldn't necessarily

Re: [Bioc-devel] BiocInstaller: next generation

ager seems the most sober of the lot. And thematically appropriate - you might have an orchestra and conductor, but you still need a manager to get everyone paid, fed and on the stage. -Aaron Martin Morgan wrote: Developers -- A preliminary heads-up and request for comments. Almost since project

Re: [Bioc-devel] BiocInstaller: next generation

or current and past versions of Bioconductor. Going forward, it would go through a cycle of deprecated and defunct. Martin -Ryan On Wed, May 9, 2018 at 3:29 PM Martin Morgan <martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>> wrote: Developers --

[Bioc-devel] BiocInstaller: next generation

Developers -- A preliminary heads-up and request for comments. Almost since project inception, we've used the commands source("https://bioconductor.org/biocLite.R;) biocLite(pkgs) to install packages. This poses security risks (e.g., typos in the url) and deviates from standard R package

Re: [Bioc-devel] Unexpected Warning About Cross-Reference Without Package Specification

Thank you, the reproducible example helps one think through things. For what it's worth the warning can be generated via > tools:::.check_Rd_xrefs(dir = "~/Downloads/Tester") Looking at the code and reflecting on the issue, since limma is in the Suggests: field, it is not guaranteed to be

Re: [Bioc-devel] Unexpected Warning About Cross-Reference Without Package Specification

On 05/11/2018 01:00 AM, Dario Strbenac wrote: Good day, I have documented a parameter that is linked to lmFit's documentation. \item{...}{Optional settings that are passed to \code{\link{lmFit}}.} The package checking process displays a warning. * checking Rd cross-references ... WARNING

Re: [Bioc-devel] BiocInstaller: next generation

Bioconductor, so there can only be one BiocInstaller. BiocInstaller as it exists in Bioconductor supports two different interfaces to package management already ('legacy' biocLite, plus more recent BiocInstaller::biocLite()) and has 15 years of code; it is better to start with a clean implementat

Re: [Bioc-devel] Unexpected Warning About Cross-Reference Without Package Specification

I'm not really sure about this, but Writing R Extensions says about these forms of \link that they are seldom needed, except when linking to "not-yet-installed packages". I think if you were to have installed limma without first building it (e.g., R CMD INSTALL limma rather than R CMD INSTALL

Re: [Bioc-devel] Vignette warnings/errors

On 05/11/2018 01:37 PM, Kenneth Condon wrote: Hi all, I'm hoping to submit my package soon. But I am having issues with the vignette. R CMD check results0 errors | 1 warning | 0 noteschecking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc':

Re: [Bioc-devel] Unexpected Warning About Cross-Reference Without Package Specification

On 05/11/2018 06:00 PM, Dario Strbenac wrote: Good day, limma was installed using biocLite, so it would be built before R CMD check was run. I could summarise all of the relevant information and send to R-package-devel mailing list to check if it is a bug. the 'relevant information' needs

Re: [Bioc-devel] proc.time error

On 05/08/2018 02:58 AM, Anand MT wrote: Hi Developers, I maintain Bioconductor package maftools, which has been failing to build on WIndows platform since it the new release. Error seems to be originating while running examples with the below error. base::assign(".ptime", proc.time(), pos

Re: [Bioc-devel] BiocInstaller: next generation

On 05/16/2018 10:23 AM, Nicolas Descostes wrote: Dear Martin, I am starting using BiocInstaller. Regarding the BiocManager::valid(), would it be possible to retrieve a list with one element being a vector of the packages to update? or to run BiocManager() as we do with biocLite()? Running

Re: [Bioc-devel] Build error in tokay2: cannot reserve space for vector

Remember that 32-bit Windows can only address vectors that are less than 2^32 - 1 elements long -- it looks like your example is trying to do more than this, and the solution is to implement a more modest example. Martin On 05/18/2018 04:05 AM, Sergio Picart Armada wrote: Dear Bioconductor

Re: [Bioc-devel] Update existing packages and change name

On 05/22/2018 05:46 AM, Sokratis Kariotis wrote: Hi all, After lots of tries we decided to follow your second suggestion. How can we stop the support for 32-bit windows? An obvious place to start is with a less comprehensive example data set; > geo_sum_data class: SummarizedExperiment dim:

Re: [Bioc-devel] Examples of reading files of not allowed type

Save these under a folder inst/, conventionally inst/extdata/. Access them using system.file(package="YourPackage", "extdata", "") Martin On 05/23/2018 06:44 PM, Jordan Bisanz wrote: Hello, I have a developed a package called qiime2R which serves to facilitate the analysis of files from

Re: [Bioc-devel] BiocInstaller: next generation

On 05/18/2018 03:28 AM, Neumann, Steffen wrote: Hi, On Wed, 2018-05-09 at 18:11 -0400, Martin Morgan wrote: ... - version() version of Bioconductor in use - valid() are all Bioconductor packages from the same Bioconductor version? I'd like to challenge the concept of the release

Re: [Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?

You can create a plain text file in the root directory of your package .BBSoptions with the line UnsupportedPlatform: win Your package will not be available on Windows, losing about 1/2 your potential audience. A better strategy is to figure out why you are Suggests:'ing Rsubread, and find

Re: [Bioc-devel] Action for Uncompressed Data Warning

My general approach is to make the build report as clean as possible, so that (a) it's easy to see true positives and (b) I'm not provoked by notes / warnings that I think of as irritating more than useful each time I look at the build report :) . So yes, I'd recompress the data. Martin On

Re: [Bioc-devel] BiocParallel on Windows Never Ends

yes it would be useful to post this to R-devel as a 'using parallel::makeCluster() question, removing BiocParallel from the equation, where some general insight might be had... Martin On 06/13/2018 05:00 PM, Dario Strbenac wrote: Good day, I couldn't get a working param object. It never

Re: [Bioc-devel] BiocParallel on Windows Never Ends

It's more likely that it never starts, probably because it tries to create socket connections on ports that are not available, or perhaps because the file path to the installed location of the BiocParallel package is on a network share, or the 'master' node needs to be specified with an IP

Re: [Bioc-devel] eval() and evalq() of BiocGenerics used in Rcpp causes segfault in some cases

On 06/07/2018 04:56 AM, Joris Meys wrote: Dear all, the following issue drew my attention. The new package "conflicted" manipulates the search path and by doing so, highlighted that Rcpp is using the BiocGenerics version of evalq() in case BiocGenerics is loaded. Otherwise it uses the base

Re: [Bioc-devel] build cache on bioconductor build system?

There is no cache; like users you get the 'current' version of the package from the relevant repository. If your package used concatenateObjects, then it needs to be updated. If your package is broken through a third package, it needs to be fixed (perhaps it has been but did not propagate, see

Re: [Bioc-devel] installed, system.file(package="RCyjs") is "/Users/biocbuild/bbs-3.8-bioc/meat/RCyjs.buildbin-libdir/RCyjs"

On 06/29/2018 06:44 PM, Paul Shannon wrote: My package RCyjs reads an html/js/css file when the constructor is called, then sends that file to the user’s browser. The actual path to that file is calculated at global scope in RCyjs-class.R: cyjsBrowserFile <-

Re: [Bioc-devel] Bioconductor package update

(cc'ing bioc-devel, where questions like this should be posted so other developers can benefit / contribute) I see commit 5fea2c1f2e0f3407cb6804db638b565e0a2ea5dd Author: Ahrim Youn Date: Fri Jun 22 16:34:02 2018 -0400 update version number DESCRIPTION | 2 +-

Re: [Bioc-devel] About Adding SSH Keys to GitHub Account

butions/issues/787 ). Thanks, Koki *差出人:* Bioc-devel が 露崎 弘毅 の代理で送信 *送信日時:* 2018年6月28日 20:56 *宛先:* Martin Morgan; Bioc-devel@r-project.org *件名:* Re: [Bioc-devel] About Adding SSH Keys to GitHub Account Hi, Martin

Re: [Bioc-devel] Need some help to submit a R package.

of changes in the original code. So should we submit our package (sigFeature) as a new submission or replace the contents of existing git repository with version increment. regards Pijush On Mon, Apr 16, 2018 at 5:01 PM, Martin Morgan <

Re: [Bioc-devel] Need some help to submit a R package.

b.com/Bioconductor/Contributions/issues/713 <https://github.com/Bioconductor/Contributions/issues/713> The link is not opening. Is there any problem in github repository? Please check it. Thank you regards Pijush On Thu, A

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

But that issue will be fixed, so Tim's advice is inappropriate. On 04/30/2018 10:42 AM, Tim Triche, Jr. wrote: Don't do that. Seriously, just don't. https://github.com/Bioconductor/DelayedArray/issues/16 --t On Mon, Apr 30, 2018 at 10:02 AM, Elizabeth Purdom < epur...@stat.berkeley.edu>

Re: [Bioc-devel] Unable to reproduce error!

On 10/20/2017 03:43 AM, Paolo Martini wrote: Dear all, I am the clipper package maintainer. According to the "Build/check report" for BioC 3.6, the clipper package has an error while compiling the vignette. I try to reproduce the error in my computer using the devel version but the R CMD check

Re: [Bioc-devel] R6 class v.s. S4 class

On 10/19/2017 09:24 PM, Charles Plessy wrote: (Just sharing my thoughts as those days I am spending quite some time preparing the upgrade of a Bioconductor package). Le Fri, Oct 20, 2017 at 12:50:48AM +, Ryan Thompson a écrit : gene_client <- BioThingsClient("gene") query("CDK2",

Re: [Bioc-devel] Gviz Abandonware

On 10/20/2017 03:00 AM, Dario Strbenac wrote: Hello, Gviz hasn't been updated for the past two months but has a CHECK warning and there are almost no answered questions on the support website in the past three months. Is it worthwhile developing plotting functions based on Gviz if it is

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

On 10/23/2017 09:22 AM, Raymond Cavalcante wrote: 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

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 <martin.mor...@roswellpark.org <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 gett

Re: [Bioc-devel] BiocParallel: fine-grained progress bar

On 12/30/2017 04:08 PM, Ludwig Geistlinger wrote: Hi, I'm currently playing around with progress bars in BiocParallel - which is a great package! ;-) For demonstration, I'm using the example code from DESeq2::DESeq. library(DESeq2) library(BiocParallel) f <- function(mu) { cnts <-

Re: [Bioc-devel] mzR build failure on Windows: missing HDF5 libraries

to help try and get mzR working with it. On 2 January 2018 at 21:31, Martin Morgan <martin.mor...@roswellpark.org> wrote: On 01/02/2018 03:16 PM, Neumann, Steffen wrote: Dear BioC team, a happy new year to you as well ;-) for a while we have a build error for mzR on windows due to m

Re: [Bioc-devel] search - was: differential expression tools for proteins

On 01/07/2018 08:13 AM, Wolfgang Huber wrote: 7.1.18 12:46, Wolfgang Huber scripsit: Thank you for your question. It would however be more appropriate for the support forum, not for the developer mailing list. Would you mind moving it there, perhaps also the responses so far? I just saw

Re: [Bioc-devel] I cannot reproduce the error my package raises in production

On 01/15/2018 03:31 AM, Carles Hernandez-Ferrer wrote: Dear all, During the package verification step I got the following error: Quitting from lines 112-115 (batch_query.Rmd) Error: processing vignette 'batch_query.Rmd' failed with diagnostics: subscript out of bounds Execution halted

Re: [Bioc-devel] Missing link files in Windows (release and devel)

On 01/16/2018 10:37 AM, Leonardo Collado Torres wrote: Hi, I have been seen warnings in several of my packages on both release and devel only in the Windows build machines in relation to missing link files. Is this something that I can address from my side or a more widespread issue? If it

Re: [Bioc-devel] Question regarding potential package

On 01/16/2018 04:44 PM, Rupji, Manali wrote: Hello, I have recently developed a shiny R package to perform clustering analysis. It is currently in publication and under review. I wish to also create a bio-conductor package for the same. Does bio-conductor allow a shiny tool to be created as

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