Re: [Bioc-devel] Problem for Biostrings?

Hi Hai, Looks you added CRAN ggforce recently (in February) to the Suggests field of Pi. ggforce depends on CRAN package udunits2, which itself requires system library libudunits2 in order to compile on Linux, which itself can be installed with sudo apt-get install libudunits2-dev on

Re: [Bioc-devel] pc algorithm library missing on linux builder

Hi Martin, Not sure what happened during automatic installation of CRAN package pcalg by the build system on malbec2 but it seems that the installed package ended up being in a broken state. I just went on malbec2 and re-installed the package by hand so normally epiNEM should look all green on

Re: [Bioc-devel] Problem for Biostrings?

Thanks for the clarification. Now everything is ok except the check in Linux (http://bioconductor.org/checkResults/devel/bioc-LATEST/Pi/malbec2-checksrc.html). The package 'ggforce' is not preinstalled in Linux (others seem fine). Best, Hai Sent from my iPhone > On 29 Mar 2017, at 17:17,

Re: [Bioc-devel] condition tests on vectors with length greater than 1

Hi Martin, On 03/29/2017 02:37 PM, Martin Morgan wrote: Bioc developers, R emits a warning when a condition test has length > 1 $ R --vanilla if (letters == "a") TRUE [1] TRUE Warning message: In if (letters == "a") TRUE : the condition has length > 1 and only the first element will be

Re: [Bioc-devel] condition tests on vectors with length greater than 1

On 03/29/2017 05:37 PM, Martin Morgan wrote: Bioc developers, R emits a warning when a condition test has length > 1 $ R --vanilla if (letters == "a") TRUE [1] TRUE Warning message: In if (letters == "a") TRUE : the condition has length > 1 and only the first element will be used These

[Bioc-devel] Bioconductor 3.5 release: contributed annotation packages

Dear annotation contributors, Just a reminder the deadline to update annotation packages is Friday April 7. Please make updated packages available via dropbox or another location that allows wget. Indicate if the old version should be included in the upcoming release or if the new package should

Re: [Bioc-devel] Git Transition Plan

Thanks. I have a few thoughts and questions in order to plan ahead: > - Our plan is to make a 'clean' transition from SVN to git, approximately one > month after the next Bioconductor release. Developers or users will not have > access to the SVN system after the date of transition. In order

Re: [Bioc-devel] Recommendations for Shiny app on Bioconductor

On Wed, Mar 29, 2017, at 11:23 AM, Martin Morgan wrote: > On 03/29/2017 09:32 AM, Vladimir Kiselev wrote: > > Hi Wellinton, > > > > As far as I know if you wrap you shiny stuff into an R function that should > > be enough. Then you can provide both non-interactive and interactive > > functions and

Re: [Bioc-devel] Trouble checking out svn with username and password

Hello all, I think that I'm running into a similar problam as Brad: If I try the link https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/IPO/ for my package IPO, I'm prompted to insert my login-data. Readonly works as expected. But with my username t.riebenbauer (and

[Bioc-devel] Git Transition Plan

Dear Bioconductor Developers, More news about the Git transition plan. We are coming close to our transition date and have made significant progress in getting our new server ready for the Bioconductor community. 1. Overall plan: - Bioconductor hosts each package as a distinct repository at

Re: [Bioc-devel] Error loading rtracklayer

For the single package builder: Once the issue is resolved you could kick off a new build by bumping the version number; it is probably the fastest way. I will also try to check and manually build packages that encountered this error and haven't kicked off a new build. Lori Shepherd

Re: [Bioc-devel] Error loading rtracklayer

Thanks for the quick reply. Will i need to bump the version to trigger a rebuild once the changes are made? On 29 Mar 2017 5:17 pm, "Jurat Shayidin" wrote: > Hi: > > This happened to me several times, and I figured out the issue. I tried to > remove `rtracklayer` package

Re: [Bioc-devel] Problem for Biostrings?

It's actually an error in rtracklayer. On Wed, Mar 29, 2017 at 8:28 AM, Shepherd, Lori wrote: > That is correct. When the Biostrings package is corrected this ERROR in your > package should resolve automatically. > > > Lori Shepherd > > Bioconductor Core Team > >

Re: [Bioc-devel] Problem for Biostrings?

That is correct. When the Biostrings package is corrected this ERROR in your package should resolve automatically. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] Recommendations for Shiny app on Bioconductor

On 03/29/2017 09:32 AM, Vladimir Kiselev wrote: Hi Wellinton, As far as I know if you wrap you shiny stuff into an R function that should be enough. Then you can provide both non-interactive and interactive functions and the user can choose what to run. You can have a look at my SC3 package

Re: [Bioc-devel] Error loading rtracklayer

This is an ERROR with rtracklayer until the ERROR is resolved in rtracklayer you will continue to see this ERROR in your package. We are in the processes of resolving and should be correctly shortly. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of

Re: [Bioc-devel] Error loading rtracklayer

Hi: This happened to me several times, and I figured out the issue. I tried to remove `rtracklayer` package completely from `R` home directory; you can try: remove.packages("rtracklayer"). Don't be panic, if this problem still bumps up again, try to reboot your PC (you may need to restart your

[Bioc-devel] Problem for Biostrings?

Hi, I got the error “object ‘inverted’ is not exported by 'namespace:Biostrings” at http://bioconductor.org/checkResults/devel/bioc-LATEST/Pi/. It seems due to the package “Biostrings” which failed to pass the check (http://bioconductor.org/checkResults/devel/bioc-LATEST/Biostrings/). Is it

Re: [Bioc-devel] Error loading rtracklayer

It looks like things got out of sync with some recent shuffling. A change to Biostrings made it through to the latest builds, but not the change to rtracklayer. There should be a fixed version of rtracklayer available soon, or you could grab it from svn. On Wed, Mar 29, 2017 at 7:49 AM, Malcolm

[Bioc-devel] Error loading rtracklayer

Hi all, I receive this error when loading rtracklayer in my vignette which is stopping my package from building: Loading required package: IRanges Loading required package: GenomeInfoDb Quitting from lines 39-50 (heatmaps.Rmd) Error: processing vignette 'heatmaps.Rmd' failed with diagnostics:

Re: [Bioc-devel] Recommendations for Shiny app on Bioconductor

Hi Wellinton, As far as I know if you wrap you shiny stuff into an R function that should be enough. Then you can provide both non-interactive and interactive functions and the user can choose what to run. You can have a look at my SC3 package where I implemented a strategy above:

[Bioc-devel] Recommendations for Shiny app on Bioconductor

I am developing a web application using Shiny to be distributed as Bioconductor package. I would like to know if there are some recommendations for better integration with Bioconductor ecosystem. Best regards, Welliton [[alternative HTML version deleted]]

[Bioc-devel] pc algorithm library missing on linux builder

Hi, our package epiNEM produces an error on the linux builder, due to some missing pcalg library. This seems to be an error on the builder’s end, because the packages ddgraph and miRLAB suffer the same error, also exclusively for the linux builder. Does that problem go hand in hand with the

Re: [Bioc-devel] Problem to install bioconductor for R devel (3.5)

On 03/29/2017 12:57 AM, Dan Tenenbaum wrote: Don't install R-3.5; install R-3.4 from https://cran.rstudio.com/bin/windows/base/rtest.html Expanding a little -- R has a yearly release cycle, Bioc a 6 month release cycle Bioc-devel tries to use the R that will be used when Bioc-devel becomes