Re: [Bioc-devel] Updating author/maintainer info

Hi Kylie, It seems that we somehow forgot to grant you write access to your CardinalWorkflows package. This should work now. Please try again. Sorry for the inconvenience, H. On 09/21/2016 07:16 PM, Kyle Dwayne Bemis wrote: Hello, My personal information has changed and I need to update my

Re: [Bioc-devel] Updating author/maintainer info

Did you add --username xxx --password to the svn co command? On Thu, Sep 22, 2016 at 1:42 PM, Bemis, Kylie wrote: > Thanks, but when I follow the directions, it doesn’t work: > > svn: E175013: Commit failed (details follow): > svn: E175013: Unable to connect to a

Re: [Bioc-devel] Updating author/maintainer info

Thanks, but when I follow the directions, it doesn’t work: svn: E175013: Commit failed (details follow): svn: E175013: Unable to connect to a repository at URL 'https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/CardinalWorkflows' svn: E175013: Access to

[Bioc-devel] Updating author/maintainer info

Hello, My personal information has changed and I need to update my author/maintainer name and email address on my packages. For Cardinal, this is easy, but CardinalWorkflows is a data package, so I cannot update it myself. How can I update the data package info? Besides subscribing to the

Re: [Bioc-devel] New package deadline for this release: 26 September

Dear Martin and core members, We have a package named uSORT submitted to Bioconductor through GitHub half a month ago, FYI * Github Link: * Bioconductor submission track: Now the

Re: [Bioc-devel] lpsymphony - BiocParallel crash

On 09/21/2016 10:42 AM, Christian Arnold wrote: Dear Bioconductor developers, I am having a somewhat mysterious and challenging problem which we believe is a bug in either (1) BiocParallel or (2) the lpsymphony library from either Bioconductor or the SYMPHONY backend. Thank you for the clear

[Bioc-devel] Package pages: Link to NEWS gone?

I've noticed this for a while and thought it was a temporary glitch, or maybe I missed some announcement about it, but it appears that NEWS files are no longed listed on the Bioc package pages, e.g. https://bioconductor.org/packages/devel/bioc/html/Biobase.html. A mistake? /Henrik

Re: [Bioc-devel] msPurity build fail on Mac OS X (morelia)

So this seems like a bug in mzR which is the main backend / parser for proteomics and metabolomics data. Someone should try to fix this. Unfortunately, mzR depends on several pieces of software which are written by other people, but bundled with the package. Martin's traceback suggests that

Re: [Bioc-devel] msPurity build fail on Mac OS X (morelia)

One thing I notice is that the crash does not happen every time. I have successfully built the package on morelia by hand with "R CMD build". Similarly I can source the stangled vignette without a crash sometimes. But when it does crash, this is what I see: > source("msPurity-vignette.R",

Re: [Bioc-devel] msPurity build fail on Mac OS X (morelia)

Thanks for reply. Some of those errors are a bit cryptic for me also. I have not heard of the valgrind functionality before in R. I will test a few things out with valgrind and hopefully I can pinpoint the error a bit more. Thanks again. Tom On Wed, Sep 21, 2016 at 12:50 PM, Martin Morgan <

[Bioc-devel] lpsymphony - BiocParallel crash

Dear Bioconductor developers, I am having a somewhat mysterious and challenging problem which we believe is a bug in either (1) BiocParallel or (2) the lpsymphony library from either Bioconductor or the SYMPHONY backend. The problem is, in a nutshell, that R silently crashes or, to be more

Re: [Bioc-devel] github mirror and svn out of sync

thanks Martin! Now everything is in sync again. You're right, the git commits were commited as separate svn commits; an alternative would be to use `git-merge --squash`, but I didn't try that one; so far I used `git cherry-pick` to merge a selected range of git commits into the devel branch

Re: [Bioc-devel] msPurity build fail on Mac OS X (morelia)

On 09/20/2016 05:18 AM, Thomas Lawson wrote: Hi BioConductor community, My package (msPurity) is passing the build on the Linux (*zin1*) and Windows servers (*moscato1*) but failing on the Mac OS X server (*morelia*). Also I cannot seem to replicate the failure either on a local installation of

[Bioc-devel] new biocView

A new biocView has been added to the list of terms: SingleCell Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or

Re: [Bioc-devel] github mirror and svn out of sync

On 09/21/2016 12:01 AM, Rainer Johannes wrote: Dear all, I recently observed that the svn and the github mirror of `ensembldb` is out of sync. Is this something specific to `ensembldb` or is this a general problem? Is there anything I could do to fix this? I think it is up-to-date now? I

Re: [Bioc-devel] there is no package called 'zlibbioc' on WINDOWS

On 09/21/2016 06:06 AM, Moritz Gerstung wrote: Hi Dan Has this problem problem resurrected? I see many packages depending on zlibbioc fail, including gage, Rhtslib and deepSNV. http://bioconductor.org/checkResults/devel/bioc-LATEST/gage/moscato1-install.html The situation has improved but

Re: [Bioc-devel] there is no package called 'zlibbioc' on WINDOWS

Hi Dan Has this problem problem resurrected? I see many packages depending on zlibbioc fail, including gage, Rhtslib and deepSNV. http://bioconductor.org/checkResults/devel/bioc-LATEST/gage/moscato1-install.html Cheers Moritz > On 1 Jun 2016, at 20:40, Dan Tenenbaum