Re: [Bioc-devel] BiocStyle not acknowledging fig.wide=TRUE in knitr

Hi Aaron, thanks fo reporting this! I've fixed it in BiocStyle 2.5.38. Best, Andrzej On Fri, Sep 15, 2017 at 9:23 AM, Aaron Lun wrote: > Dear list, > > > I'm playing around with the BiocStyle aesthetics for my csaw user's guide, > and it looks pretty good in general.

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

Hi, In my package's (scmap) vignette I plot a Sankey digram using gvisSankey function from googleVis package. It used to work and the digram was plotted, but now there is this error (on devel branch - http://bioconductor.org/checkResults/devel/bioc-LATEST/scmap/malbec1-buildsrc.html ): pandoc:

Re: [Bioc-devel] Unable to create a remote branch

It is trying to push to git.bioconductor.org. You probably don’t have your remotes set up right. Try `git remote -v` and paste the result. > On Sep 15, 2017, at 4:23 AM, Samuel Wieczorek wrote: > > Hi all, > > I try to create a remote branch but it fails. The

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

[Bioc-devel] Question about inclusion in upcoming bioconductor

Dear Bioconductor Team, I had a couple of quick questions 1) Is our package set to go into the next Bioconductor if it’s made it through the submission process and we have access to the Bioconductor git repository? Is the master branch for that properly staged for the upcoming release, or do

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

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. Best, -Nan On Fri, Sep 15, 2017 at 5:40 AM,

[Bioc-devel] Unable to create a remote branch

Hi all, I try to create a remote branch but it fails. The branch is named tes3. I used the following command : > git push origin tes3 and here is the error message I received : Total 0 (delta 0), reused 0 (delta 0) remote: FATAL: W refs/heads/tes3 packages/Prostar s.wieczorek DENIED by

Re: [Bioc-devel] [PROVENANCE INTERNET] Unable to create a remote branch

Fixed ! the address for my git repositories was wrong ;-) Le 15/09/2017 à 10:23, Samuel Wieczorek a écrit : > Hi all, > > I try to create a remote branch but it fails. The branch is named tes3. > I used the following command : > > > git push origin tes3 > > > and here is the error message I

Re: [Bioc-devel] BiocStyle not acknowledging fig.wide=TRUE in knitr

Dear list, I'm playing around with the BiocStyle aesthetics for my csaw user's guide, and it looks pretty good in general. However, setting fig.wide=TRUE doesn't seem to be respected by knitr during compilation. To give an example: %%% Latex code start %%% \documentclass{article}

Re: [Bioc-devel] Bioconductor failing package MEAL

Hi Nitesh, I have checked my mail and I have 3 different SVN ids, one for each package I have submitted: - r.carlos: MEAL - c.ruiz-arenas: MultiDataSet - c.ruiz: scoreInvHap When I submitted MultiDataSet, I asked Bioc to consolidate my svn user. From then, I used c.ruiz-arenas for MEAL and

Re: [Bioc-devel] Bioconductor failing package MEAL

Hi Carlos Your ID is standardized across all your packages now to “c.ruiz”. Your key is the one your submitted most recently ssh-rsa B3NzaC1yc2EDAQABAAABAQDEMdup9kYuv4KO5MO1lctLXl4Griu571wbbDZU+ueZHhtuEm2WBqWTC0Zp6V+rszWORQkDGcM2ym+pVMNapSbFFbCJPDG1kxXpJI+2 ….. Please use that key

Re: [Bioc-devel] Bioconductor failing package MEAL

Hi Carlos, Do you by any chance have 2 separate SVN id’s? 1. c.ruiz 2. c.ruiz-arenas Best, Nitesh > On Sep 14, 2017, at 12:17 PM, Carlos Ruiz wrote: > > Hi, > Today I definitely was able to fetch from the Bioc git. However, I cannot > push. Here, the commands

Re: [Bioc-devel] Bioconductor failing package MEAL

Hi Carlos, Give me a till tomorrow to solve this. Good news is r.carlos isn’t used anywhere yet. I think this is mostly on our end, and not on your end. Best, Nitesh > On Sep 14, 2017, at 1:30 PM, Carlos Ruiz wrote: > > Hi Nitesh, > > I have checked my mail and

Re: [Bioc-devel] Bioconductor failing package MEAL

Bioc-git server* (git.bioconductor.org). Ignore the typo. > On Sep 14, 2017, at 2:20 PM, ni41435_ca wrote: > > Hi Carlos > > Your ID is standardized across all your packages now to “c.ruiz”. Your key is > the one your submitted most recently > > ssh-rsa >

Re: [Bioc-devel] assay dimnames in SingleCellExperiment / SummarizedExperiment

I'll leave the first point to the SummarizedExperiment maintainers, though I note that your code seems to be about the names of the dimnames rather than the dimnames themselves. (I'm under the impression that consistency in the actual dimnames is enforced somehow by the SE constructor.) As

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

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 compilation on my local machine. However, it

[Bioc-devel] ggplot error Error in grid.Call.graphics

Hi Everyone, One of my colleagues is creating an R package to submit to bioconductor. In one of his functions he is creating a plot with ggplot2. I tested out the function for him and occasionally I get the error below. It happens sporadically using the exact same input as when it works

[Bioc-devel] Problems with vignette and makeovers file

Hi, I am trying to build a package (called MACPET) and I am struggling to solve some problems. First of all, I am using c++ code through the Rcpp package. I have read that there is no need of a makeovers file in the package anymore. Is that true? Or should I include a makevars file somewhere?