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] 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] 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] 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] mzR build failure on Windows: missing HDF5 libraries

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 missing HDF5 libs: https://github.com/sneumann/mzR/issues/143 I am looking for some hints how to fix this. The

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] 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

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] '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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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.

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.

-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] 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] 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] 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] 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] 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] 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] "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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] EXTERNAL: Re: Cannot move 'xps' to GIT

s/rabbitus/.ssh/id_rsa': Everything up-to-date I hope that I could commit my changes and my development version on    https://github.com/cstrato/xps will be updated to 'xps_1.37.2' (PS: my repository https://github.com/cstrato/xps is still empty) Thank you very much for your help. Best regards, Chr

Re: [Bioc-devel] Bioconductor 3.6 release: update NEWS

On 10/14/2017 11:05 AM, Stian Lågstad wrote: Hi, What should the NEWS file look like? Are there guidelines somewhere? the basic requirement is that it be parsed by util::news(); using an 'Rd' format is most robust. A couple of examples include

Re: [Bioc-devel] EXTERNAL: BioC 3.6: timeouts on veracruz1 (OS X)

On 10/12/2017 07:08 AM, Ramon Diaz-Uriarte wrote: Dear All, I have noticed that on the latest build report, a package I maintain, OncoSimulR (http://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/veracruz1-buildsrc.html), I wonder if it is this issue

Re: [Bioc-devel] EXTERNAL: git push problem to bioconductor

On 10/13/2017 04:35 AM, Riccardo Romoli wrote: Hi bioc-devel, I am unable to push to g...@git.bioconductor.org to may package called "flagme". Please try again -- your public key was associated with the incorrect svn identifier. Martin ### $ git push upstream master X11 forwarding

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] 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] 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] 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: 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: 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] EXTERNAL: Increase timeout for mzR on Windows?

On 10/11/2017 08:29 AM, Laurent Gatto wrote: On 11 October 2017 11:14, Rainer Johannes wrote: Dear Martin, On 11 Oct 2017, at 13:05, Martin Morgan <martin.mor...@roswellpark.org> wrote: On 10/11/2017 03:48 AM, Rainer Johannes wrote: Hi, would it be possible to increase the allowed

Re: [Bioc-devel] EXTERNAL: Doscheda package edit

On 10/11/2017 09:06 AM, Piero Ricchiuto wrote: Hello, I am a developer of Doscheda package and I have noticed that the citation is incorrect. Specifically my name should be changed from Ricchiuto DP to Ricchiuto P Here is the page I am referring to:

Re: [Bioc-devel] EXTERNAL: Increase timeout for mzR on Windows?

On 10/11/2017 03:48 AM, Rainer Johannes wrote: Hi, would it be possible to increase the allowed build and check times for mzR on Windows? Building mzR takes very long due to the compilation of the included proteowizard (and boost?) code so there is not much we can do to speed that up.

Re: [Bioc-devel] EXTERNAL: git push to devel versions

On 10/11/2017 02:02 AM, Samuel Wieczorek wrote: Hi all, The new release of Bioconductor is coming soon and I would like to be sure that I am doing the right things with Git. I am a bit confused with the Git commands to use in order to update the devel versions of my packages Prostar and DAPAR

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: 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: Re: Git permission denied (publickey)

On 10/10/2017 04:43 PM, Sebastian Gibb wrote: Dear Biocondcutor admins, I am the maintainer of the cleaver package (and a co-maintainer of MSnbase, Pbase, synapter). As many other user mentioned here I got the same "permission denied (publickey)" error message. I already submit my mail address,

Re: [Bioc-devel] clarification of the BiocParallel vignette for SnowParam() usage

On 10/10/2017 04:56 AM, Aaron Lun wrote: Dear list; Currently the vignette for the BiocParallel package states that the functions to be executed should contain the necessary library() calls if bplapply is used with SnowParam(). Now, I use bplapply in several of my packages with internal

Re: [Bioc-devel] EXTERNAL: can not fetch git upstream repository

On 10/10/2017 12:06 PM, Yu Kong wrote: Dear Bioc-devel group, Sorry for the disrupt here, I got the same errors many people had these days. I can not fetch remote upstream repository using github. I've already submitted my git ID through google form. Is there anything that I missed? Thanks a

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] 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] Query regarding size limit and including external datasets

The data definitely does not belong in the software package. We are a little schizophrenic about Experiment Data at the moment; my own feeling is that ExperimentHub is the right place, especially for data over say 10 Mb. This is more labor intensive and harder to version, but potentially

Re: [Bioc-devel] Several ssh keys ?

On 10/02/2017 10:50 AM, Bernat Gel wrote: Don't want to be alarmist, but is there anything in place to prevent a "malicious agent" inserting a new ssh key to the form and gaining access to our git repo? Maybe it would be sufficient to send an email to the maintainer whenever a new key is added

[Bioc-devel] Changes in 'digest' mode

Bioc-devel subscribers! The 'digest' mode was previously configured to send mail daily, or whenever the size of the digest exceeded a threshold, whichever came first. It is now configured to send the digest on a daily basis, hopefully reducing frequency for those preferring this form of

Re: [Bioc-devel] write access to RTNduals and RTNsurvival

On 10/02/2017 09:57 AM, m castro wrote: Hi Nitesh, Thank you. In the submission of these packages, Vinicius and Clarice had included all the team as maintainers (I can confirm in the packages' homepages, below), not sure why it did not work at that occasion. We encourage just a single

Re: [Bioc-devel] external dependencies

I want to add, though, that OS-specific functionality and system requirements greatly limit the utility of your package and, like the OS-specific dependencies your package depends on, serves as a kind of virus that makes any other package that uses yours also not operable on the unsupported

Re: [Bioc-devel] Problem building package with devtools+Rcpp

On 09/27/2017 08:11 AM, sergi.pic...@upc.edu wrote: Dear developers, Sorry if the e-mail is duplicated, I had an issue sending it. I have been struggling with problems building my package DIFFUSTATS a The problem is related to the usage of Rcpp. In my current machine, I am unable

Re: [Bioc-devel] biocLite and automatic installing of packages Imports packages

On 09/25/2017 09:40 PM, Stefan Mutter wrote: Hi, we are currently developing a package that we want to submit to Bioconductor and I am working on the documentation part at the moment. Our packages requires Rcpp and we have added this dependency under Imports into the DESCRIPTION file. What

Re: [Bioc-devel] [Untrusted Server]Re: [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow

:* Hervé Pagès <hpa...@fredhutch.org> *Sent:* Thursday, 21 September 2017 3:06:18 PM *To:* Aaron Lun; Martin Morgan; bioc-devel@r-project.org *Subject:* Re: [Bioc-devel] [Untrusted Server]Re: [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow Hi, @Martin: It's goo

Re: [Bioc-devel] Change push privileges on MotifDb

On 09/22/2017 04:29 PM, Matt Richards wrote: Hi all, I've been working with Paul Shannon to update the MotifDb package, of which he is currently maintainer. Going forward, we have agreed that I should take over the responsibility of pushing package changes to the upstream branch. I assume this

Re: [Bioc-devel] Need write permission for CNPBayes

On 09/23/2017 08:28 AM, Rob Scharpf wrote: Dear Bioc- Please add me to the list of maintainers for the package CNPBayes. You should have write access now. Martin Thanks- Rob WARNING: E-mail sent over the Internet is not secure. Information sent by e-mail may not remain confidential.

Re: [Bioc-devel] R: Errors updating DaMiRseq package

On 09/23/2017 08:44 AM, Mattia Chiesa wrote: Dear Nitesh, thank you! Now it seems to work perfectly. I will check the effect tomorrow after the nighty build. Just another little question, related with my issue: I solve it using git merge --allow-unrelated-histories upstream/master And then

Re: [Bioc-devel] Vignette figures are wrong size

On 09/22/2017 03:27 AM, Christopher John wrote: Dear Bioconductor I checked my vignette using the knit option to biocstyle on my PC and the figure sizes were all fine after some tweaking. However, in the online vignette they have come out crazy small sizes. Previously I was resizing them so

Re: [Bioc-devel] Cannot clone PhenStat

Fill out this form https://goo.gl/forms/eg36vcBkIUjfZfLe2 using the id I will forward to you separately. The form is processed daily, so there will be short delay before access is available. See http://bioconductor.org/developers/how-to/git/ for additional instructions. Martin On

Re: [Bioc-devel] Support site question can't be edited: Language "ca" is not one of the supported languages ['en']!

On 09/19/2017 10:30 PM, Gordon K Smyth wrote: As a Bioc support site moderator, I tried to edit the following post to fix the tags in the original question: https://support.bioconductor.org/p/edit/100572/ However any attempt by me to edit the question elicits the error message: "Language

Re: [Bioc-devel] [Untrusted Server]Re: [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow

to have some formal support for splitting up the workflow into modules that can be independently installed. -Aaron From: Vincent Carey <st...@channing.harvard.edu> Sent: Saturday, 16 September 2017 10:08:13 PM To: Aaron Lun Cc: Martin Morgan; bioc-devel@

Re: [Bioc-devel] [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow

On 09/16/2017 01:53 AM, Aaron Lun wrote: Bumping this rather old thread. To re-iterate, I'm updating my simpleSingleCell workflow and I'm running into R's DLL limit. I've added a code block halfway through the workflow that unloads all DLLs and cleans them out, and this works fine during

Re: [Bioc-devel] TLS error in vignette on all devel builds

On 09/15/2017 10:01 AM, Nan Xiao wrote: Hi Vladimir, - it looks like the same issue as reported here a few days ago: https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011540.html Probably due to the hs-tls bug which caused the communication errors between pandoc and Google servers. so

Re: [Bioc-devel] denied access to git

On 09/11/2017 07:20 AM, Karim Mezhoud wrote: 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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

.4.0 [10] GenomeInfoDbData_0.99.1 On Mon, Sep 22, 2014 at 1:54 AM, Hervé Pagès <hpa...@fhcrc.org> wrote: Hi, On 09/20/2014 11:14 AM, Martin Morgan wrote: On 09/20/2014 10:43 AM, Sean Davis wrote: Hi, Vince. Looks like a good start. I'd probably pull all the assays from ExpressionSet

Re: [Bioc-devel] denied access to git

On 09/11/2017 04:43 AM, Karim Mezhoud wrote: 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 origin

Re: [Bioc-devel] COHCAP GitHub Update

AM, Charles Warden < cwarde...@gmail.com> wrote: Hi Martin and Nitesh, Thanks for your help. I created a public ssh-key, I added it as a deploy key for the Bioconductor package, and I provided that key in the git/svn transition Google Doc file. I was trying to provide a key what wo

Re: [Bioc-devel] NEWS, inst/NEWS, NEWS.md

On 09/09/2017 06:11 PM, Levi Waldron wrote: What's the currently recommended location for package NEWS? At https://www.bioconductor.org/developers/package-submission/ it says inst/NEWS, and I feel like I heard somewhere that NEWS.md was supported. But in a scan of the first page of

Re: [Bioc-devel] How can I remove limit of row numbers that can be printed on console?

the user to navigate through some kind of work flow that involves selection of options through a series of function calls. Martin Sincerely, Arman *From: *Martin Morgan <mailto:martin.mor...@roswellpark.org> *Sent: *Saturday, September 9, 2017 01:17 *To: *Arman Shahrisa <mailto:sh

Re: [Bioc-devel] How can I remove limit of row numbers that can be printed on console?

= ... head(x) ``` To explore this object interactively, try ```{r, eval=FALSE} View(x) ``` Martin Best regards, Arman *From: *Martin Morgan <mailto:martin.mor...@roswellpark.org> *Sent: *Saturday, September 9, 2017 00:34 *To: *Arman Shahrisa <mailto:shahrisa.ar...@hotmail.c

Re: [Bioc-devel] How can I remove limit of row numbers that can be printed on console?

> mystudies = queryStudies(url, "brca")) > dim(mystudies) [1] 9 3 which is very easy to work with, e.g., View() Martin Best wishes, Arman *From: *Martin Morgan <mailto:martin.mor...@roswellpark.org> *Sent: *Friday, September 8, 2017 23:48 *To: *Arman Shahrisa

Re: [Bioc-devel] How can I remove limit of row numbers that can be printed on console?

On 09/08/2017 02:11 PM, Arman Shahrisa wrote: Hi everyone, How can I prevent the R from truncating the printed result on console? I have to print the output on console and I can�t use options(max.print = 1) in my function. What else I can do? this isn't really the right forum for base R

Re: [Bioc-devel] Duplicate commit error on and off

On 09/08/2017 09:34 AM, Turaga, Nitesh wrote: Hi Thomas, So, you do actually have a “duplicate” commit and you should NOT be pushing this to the bioc-git server. Notice that the body of both those commits is the same. If you want to check the rest of your commit history, please try `git log

Re: [Bioc-devel] pandoc SSL error on malbec2 and tokay2

On 09/05/2017 10:35 AM, Nan Xiao wrote: Hey Kasper, - I really appreciate your help. Although it didn't help answer the question directly, I think it would still be necessary to clarify some facts: 1. I agree that using "non-standard fonts" could bring better aesthetics for a

Re: [Bioc-devel] Bioconductor-mirror permanently removed August 25th

On 09/06/2017 11:28 AM, Robert M. Flight wrote: I agree with Jim. It has been very useful to have the Bioconductor GitHub mirror to examine code, and the CRAN mirror as well. A post-hook to push there would be very useful. The mirror causes tremendous confusion on several fronts. The updates

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] Package changes not merging with upstream

Thanks Martin, I retried the push to upstream and it works just fine now. Thanks Matt On Fri, Aug 25, 2017 at 10:27 AM, Martin Morgan < martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>> wrote: > On 08/25/2017 01:17 PM, Matt

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] 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:

<    1   2   3   4   5   6   7   8   9   10   >