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

2017-09-19 Thread Gordon K Smyth
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 "ca" is not one of the supported languages

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

2017-09-19 Thread Aaron Lun
Thanks Martin. I think I will stick to one workflow for now, until the BioC-workflows page provides some formal support for multiple workflows representing different components of the same workflow (i.e., other than me manually writing in the abstract that "This workflow is based on the

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

2017-09-19 Thread Wolfgang Huber
19.9.17 18:16, Martin Morgan scripsit: On 09/19/2017 09:50 AM, Wolfgang Huber wrote: My 3 cents: - I think this is a more and more common problem that I'm also encountering in everyday work and that asks for a general solution. - I agree with Martin that setting R_MAX_NUM_DLLS is better than

Re: [Bioc-devel] VIGNETTES IN DEVEL

2017-09-19 Thread Rodriguez Martinez, Andrea
Thanks very much. Best wishes, Andrea From: Shepherd, Lori Sent: 19 September 2017 12:17:12 To: Rodriguez Martinez, Andrea; bioc-devel@r-project.org Subject: Re: VIGNETTES IN DEVEL There were changes to BiocStyle in devel

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

2017-09-19 Thread Martin Morgan
On 09/19/2017 09:50 AM, Wolfgang Huber wrote: My 3 cents: - I think this is a more and more common problem that I'm also encountering in everyday work and that asks for a general solution. - I agree with Martin that setting R_MAX_NUM_DLLS is better than unloading. AfaIk it is not even

[Bioc-devel] Cannot clone PhenStat

2017-09-19 Thread jmason
Hi all, We're trying to get access to a repository that we maintain PhenStat for the first time since the transition to git. Unfortunately, the original maintainer has left the project and so we don't have access to her email. How do we go about getting the right credentials to clone and

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

2017-09-19 Thread Wolfgang Huber
My 3 cents: - I think this is a more and more common problem that I'm also encountering in everyday work and that asks for a general solution. - I agree with Martin that setting R_MAX_NUM_DLLS is better than unloading. AfaIk it is not even possible to cleanly unload every package ('as if it

Re: [Bioc-devel] VIGNETTES IN DEVEL

2017-09-19 Thread Shepherd, Lori
There were changes to BiocStyle in devel which might account for some of the different The changes can be found in the BiocStyle NEWS file https://github.com/Bioconductor/BiocStyle/blob/master/NEWS There also was some previous discussion in this thread:

[Bioc-devel] VIGNETTES IN DEVEL

2017-09-19 Thread Rodriguez Martinez, Andrea
Hello, I think there is something weird with the html vignettes in the devel branch. For some reason, they've less width and the some images appear misaligned, compared to the release version. See below for example:

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

2017-09-19 Thread Aaron Lun
The simplest approach is to try unloading each package in turn (it will fail if there are dependencies) and repeat until all desired packages are unloaded. After this, you can call gcDLLs() from the R.utils package. There is a code chunk in my workflow.Rmd file from lines 1588 to 1605 to do

Re: [Bioc-devel] Generic for write to BiocGenerics

2017-09-19 Thread Laurent Gatto
Out of curiosity, do you also have an import() function? On 18 September 2017 22:22, Michael Lawrence wrote: > I was also about to suggest that we converge on export() but held back > because I was obviously biased. I also agree with making the target > explicit in the function name. It makes

Re: [Bioc-devel] Generic for write to BiocGenerics

2017-09-19 Thread Rainer Johannes
Thanks for the suggestions! Yes, writeMSData was my first go - but we have already a writeMSData function in mzR. I didn't want to make that a generic and implement it for the MS data objects in MSnbase, because I thought that calling a method `writeMSData,MSnExp` on an object the user knows to