Re: [Bioc-devel] notify out-dated branches

- Original Message - > From: "Yinming Jiao" <20907...@zju.edu.cn> > To: "Dan Tenenbaum" > Cc: "Yu, Guangchuang" , "bioc-devel" > > Sent: Sunday, June 12, 2016 7:33:02 PM > Subject: Re: Re: [Bioc-devel] notify out-dated b

Re: [Bioc-devel] submitting annotation and data package

For annotation packages, see this: https://bioconductor.org/developers/package-submission/#annotation-packages For experiment packages, I'm not sure. Dan - Original Message - > From: "Kasper Daniel Hansen" > To: "bioc-devel" > Sent: Tuesday, June 14, 2016 6:28:06 PM > Subject: Re: [

Re: [Bioc-devel] submitting annotation and data package

Maybe it belongs in ExperimentHub instead? Dan - Original Message - > From: "Dan Tenenbaum" > To: "Kasper Daniel Hansen" > Cc: "bioc-devel" > Sent: Tuesday, June 14, 2016 7:02:25 PM > Subject: Re: [Bioc-devel] submitting annotation and data pac

Re: [Bioc-devel] git svn dcommit

My understanding is that this happens if you ever had non-linear commit history in your github repository (i.e. more than one branch changed and then were merged together), or if you used the old git/svn bridge. As far as I understand it, the only solution (in the near term) is to cherry pick th

Re: [Bioc-devel] Confusion on biocLite() with github and annotation data repo

I think you need to add the dependencies=TRUE argument which gets passed to devtools::install_github() and thence to devtools::install(). Dan - Original Message - > From: "Martin Morgan" > To: "James W. MacDonald" , "Sean Davis" > > Cc: "bioc-devel" > Sent: Tuesday, June 28, 2016

Re: [Bioc-devel] NotNeeded in build report RSS feeds

Hi Antti, I'm not sure I follow. NotNeeded is a status seen in the INSTALL phase of the build, and it means your package did not need to be installed because no other package built by the build system depends on it. This status should not change from one day to the next. (It would change if s

Re: [Bioc-devel] NotNeeded in build report RSS feeds

We didn't (intentionally anyway) change anything with the RSS feeds. We'll look into it. Dan - Original Message - > From: "lcollado" > To: "Antti Honkela" > Cc: "Dan Tenenbaum" , "bioc-devel" > > Sent: Wednesday,

Re: [Bioc-devel] NotNeeded in build report RSS feeds

We didn't (intentionally anyway) change anything with the RSS feeds. We'll look into it. Dan - Original Message - > From: "lcollado" > To: "Antti Honkela" > Cc: "Dan Tenenbaum" , "bioc-devel" > > Sent: Wednesday,

Re: [Bioc-devel] NotNeeded in build report RSS feeds

> To: "Antti Honkela" > Cc: "Dan Tenenbaum" , "bioc-devel" > > Sent: Wednesday, June 29, 2016 7:19:26 AM > Subject: Re: [Bioc-devel] NotNeeded in build report RSS feeds > Hi, > > I don't think this has anything to do with "NotNeeded&q

Re: [Bioc-devel] build error only occurs in window system

Don't bother. The issue is a long-standing one and very difficult to reproduce which is why it has not been fixed. It happens sporadically so the solution is to wait for the next day's build and it will clear itself up. Dan On July 7, 2016 11:05:22 AM PDT, "Ou, Jianhong" wrote: >Hi Julie, >

Re: [Bioc-devel] GenRank package build error 0.99.4

- Original Message - > From: "Chakravarthi Kanduri" > To: "bioc-devel" > Sent: Tuesday, July 12, 2016 12:37:29 PM > Subject: Re: [Bioc-devel] GenRank package build error 0.99.4 > Dear Bioconductor developers, > > The latest build of GenRank package (development version) shows error >

Re: [Bioc-devel] BioC check error for flowClust on windows

When you don't see a specific error message, it's often a hint that R actually crashed (popped up a dialog box that you can't see in the build report. And indeed that is the case here. I can reproduce it easily as follows: R --arch i386 library(flowClust) example(flowClust) It works fin

Re: [Bioc-devel] shrunken vignette

Also note that the build system does not use devtools to build vignettes, it uses R CMD build. - Original Message - > From: "Kasper Daniel Hansen" > To: "Anand MT" > Cc: "bioc-devel" > Sent: Friday, July 15, 2016 8:43:00 PM > Subject: Re: [Bioc-devel] shrunken vignette > If you add a

Re: [Bioc-devel] shrunken vignette

It can be changed if we can identify the problem. Bioconductor package developers should be using the devel version of Bioconductor in order to identify problems like this. Dan - Original Message - > From: "Anand MT" > To: "Dan Tenenbaum" , "Kasper

Re: [Bioc-devel] Submission of a revision of a package

Packages that were submitted to the old tracker should continue to use the old tracker. It looks like your review is in progress in the old tracker: you have been assigned a reviewer who has sent you comments about your package. Dan - Original Message - > From: "Mathieu EMILY" > To:

Re: [Bioc-devel] "platforms" information not updated

Hi Ramon, Thanks for letting us know about this. We've identified and fixed the problem. Dan - Original Message - > From: "Ramon Diaz-Uriarte" > To: "bioc-devel" > Cc: "ramon diaz" > Sent: Monday, July 25, 2016 11:30:39 AM > Subject: [Bioc-devel] "platforms" information not updated

Re: [Bioc-devel] bioconductor/metabolomics Docker image available

- Original Message - > From: "Steffen Neumann" > To: "Dan Tenenbaum" > Cc: "bioc-devel" > Sent: Wednesday, July 27, 2016 5:02:22 AM > Subject: bioconductor/metabolomics Docker image available > Hi Dan and BioC community! > > I n

Re: [Bioc-devel] commit changes with scenario 1

- Original Message - > From: "Karim Mezhoud" > To: "bioc-devel" > Sent: Tuesday, August 2, 2016 2:53:53 PM > Subject: [Bioc-devel] commit changes with scenario 1 > I am trying to commit some changes to bioCancer > . the issue is no chan

Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

1.33.11 is the latest version in svn. https://www.bioconductor.org/checkResults/3.4/bioc-LATEST/zin1-R-instpkgs.html will tell you (with a reasonable degree of accuracy) which version of which package is installed on zin1, it reports that it has version 1.33.11 installed. The issue with recount

Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

--- Original Message - > From: "Dan Tenenbaum" > To: "lcollado" > Cc: "Jeff Leek" , "bioc-devel" , > "Andrew Jaffe" , > "Ben Langmead" , "Abhi Nellore" > Sent: Tuesday, August 9, 2016 11:46:32 AM > Subject: Re

Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

never come up again. Dan - Original Message - > From: "lcollado" > To: "Dan Tenenbaum" > Cc: "Jeff Leek" , "bioc-devel" , > "Andrew Jaffe" , > "Ben Langmead" , "Abhi Nellore" > Sent: Friday, August

Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

- Original Message - > From: "Martin Morgan" > To: "Dan Tenenbaum" , "lcollado" > Cc: "Jeff Leek" , "bioc-devel" , > "Andrew Jaffe" , > "Ben Langmead" , "Abhi Nellore" > Sent: Friday, Au

Re: [Bioc-devel] commit changes with scenario 1

- Original Message - > From: "Karim Mezhoud" > To: "Dan Tenenbaum" > Cc: "bioc-devel" > Sent: Tuesday, August 16, 2016 8:33:39 AM > Subject: Re: [Bioc-devel] commit changes with scenario 1 > Thanks Dr Dan, > I have multiple file

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

Your username is b.nelms (note the dot). Dan - Original Message - > From: "Brad Nelms" > To: "bioc-devel" > Sent: Saturday, September 3, 2016 1:23:18 PM > Subject: [Bioc-devel] Trouble checking out svn with username and password > Hi all, > > I'm trying to checkout a package that wa

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", echo=

Re: [Bioc-devel] SSL connect error on package build machine

Seems like that was a transient error. I was able to kick off another build that did not have this problem. https://github.com/Bioconductor/Contributions/issues/155#issuecomment-250036650 Dan - Original Message - > From: "Tyler Smith" > To: "bioc-devel" > Sent: Tuesday, September 27,

Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

- Original Message - > From: "Hervé Pagès" > To: "Philipp Angerer" , "bioc-devel" > > Sent: Tuesday, October 4, 2016 9:23:29 AM > Subject: Re: [Bioc-devel] tokay1 (windows) build server cannot use the > nbconvertR vignette engine > Hi Philipp, > > On 10/04/2016 12:13 AM, Angerer, Ph

Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

- Original Message - > From: "Hervé Pagès" > To: "Dan Tenenbaum" > Cc: "Philipp Angerer" , "bioc-devel" > > Sent: Tuesday, October 4, 2016 10:16:34 AM > Subject: Re: [Bioc-devel] tokay1 (windows) build server cannot use the &

Re: [Bioc-devel] Why can't NAMESPACE be a strict subset of DESCRIPTION Imports?

- Original Message - > From: "Martin Morgan" > To: "McDavid, Andrew" , "bioc-devel" > > Sent: Tuesday, October 4, 2016 2:09:27 PM > Subject: Re: [Bioc-devel] Why can't NAMESPACE be a strict subset of > DESCRIPTION Imports? > On 10/04/2016 05:07 PM, McDavid, Andrew wrote: >> BiocCheck

Re: [Bioc-devel] unable to install/download IRanges, Biobase, GenomeInfoDb

Have you tried to install those packages? Note that errors (or warnings) in the build report does NOT mean that you cannot install the packages. Installing them works for me in the devel version of bioconductor. If you have tried to install the packages, please share the command you used to do

Re: [Bioc-devel] Automatic build failure notifications

- Original Message - > From: "Hervé Pagès" > To: "Emma Schymanski" , "bioc-devel" > > Cc: "Dan Tenenbaum" > Sent: Tuesday, October 11, 2016 10:55:20 AM > Subject: Re: Automatic build failure notifications > OK, will do. Th

Re: [Bioc-devel] flowCore fails with GCC 4.4.7 on RHEL 6.0

- Original Message - > From: "Kasper Daniel Hansen" > To: "Mike" > Cc: "bioc-devel" > Sent: Tuesday, October 11, 2016 5:57:02 PM > Subject: Re: [Bioc-devel] flowCore fails with GCC 4.4.7 on RHEL 6.0 > Two things. > > 1. You might be surprised how many HPC facilities uses older versio

Re: [Bioc-devel] biocLite and useDevel

Probably related to: https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009897.html Dan - Original Message - > From: "Kasper Daniel Hansen" > To: "bioc-devel" > Sent: Friday, October 14, 2016 9:07:34 AM > Subject: [Bioc-devel] biocLite and useDevel > This is unexpected, to me at

Re: [Bioc-devel] staging.bioconductor.org not responsive

gt; From: "Martin Morgan" > To: "Dan Tenenbaum" , "bioc-devel" > > Sent: Tuesday, October 18, 2016 3:25:16 PM > Subject: staging.bioconductor.org not responsive > Hi Dan, et al., > > When I try to ssh I get > > $ ssh ubu...@staging.biocondu

Re: [Bioc-devel] Package "not supported" on some platforms, and dependent packages

- Original Message - > From: "Kevin RUE" > To: "bioc-devel" > Sent: Tuesday, October 18, 2016 3:28:23 PM > Subject: [Bioc-devel] Package "not supported" on some platforms, and > dependent packages > Hi all, > > Heartless logic works as follows: > > - ensemblVEP is "not suppor

Re: [Bioc-devel] Question about InteractionSet package

You need to tell us the command that produced that error. InteractionSet is a Bioconductor package, not a CRAN package. Maybe you tried to install it with install.packages() instead of biocLite()? See the "Installlation" section of https://bioconductor.org/packages/release/bioc/html/Interaction

Re: [Bioc-devel] Question about InteractionSet package

- > From: "Dan Tenenbaum" > To: "Ioannis Vardaxis" > Cc: "bioc-devel" > Sent: Friday, October 21, 2016 10:44:26 AM > Subject: Re: [Bioc-devel] Question about InteractionSet package > You need to tell us the command that produced that error. > >

Re: [Bioc-devel] No release svn repository for proFIA/plasFIA maintainer

The same credentials work for release. - Original Message - > From: "DELABRIÈRE Alexis" > To: "bioc-devel" > Sent: Tuesday, October 25, 2016 4:43:17 AM > Subject: [Bioc-devel] No release svn repository for proFIA/plasFIA maintainer > Hello, > > > My packages (proFIA, plasFIA) have bee

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

Don't do this in RStudio, do it at the command line/terminal. Type in R --vanilla. You won't get the same interface as RStudio but you can see if the problem persists. Dan - Original Message - > From: "Jurat Shayidin" > To: "Kasper Daniel Hansen" , "bioc-devel" > > Sent: Friday, Nov

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

ot;Jurat Shayidin" > To: "Dan Tenenbaum" , "bioc-devel" > > Sent: Friday, November 11, 2016 1:59:32 PM > Subject: Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed > devel version of R and Bioc 3.4 > Dear Dan : > I tried same command i

Re: [Bioc-devel] stuck in setting up Bioconductor GitHub

Did you fork the repository first? - Original Message - > From: "Leif Väremo" > To: "bioc-devel" > Sent: Tuesday, November 15, 2016 1:50:37 AM > Subject: [Bioc-devel] stuck in setting up Bioconductor GitHub > Hi, > > I am trying to setup up my pre-existing Bioconductor package piano in

Re: [Bioc-devel] GSL on Windows

You need to make sure both i386 and x64 versions of GSL are installed under c:\GnuWin32, for a directory structure like this: c:\GnuWin32\i386 c:\GnuWin32\x64 (Also I would recommend using a more descriptive name than c:\GnuWin32, perhaps call it c:\GSL?) And then notice how the DirichletMulti

Re: [Bioc-devel] svn permissions

You have full permissions on minfiDataEPIC, but not for minfiData; I added those. Make sure you are committing as user khansen. Dan - Original Message - > From: "Kasper Daniel Hansen" > To: "bioc-devel" > Sent: Sunday, November 20, 2016 6:11:09 PM > Subject: [Bioc-devel] svn permissio

Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

- Original Message - > From: "Sean Davis" > To: "Martin Morgan" > Cc: "bioc-devel" > Sent: Wednesday, November 30, 2016 1:20:58 PM > Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC > devel in mac >> On Nov 30, 2016, at 4:13 PM, Martin Morgan >> wrote: >> >

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

If your package is in github at https://github.com/julaiti/MSPC , it looks like there is no inst or extdata folder in that repository. Maybe it has not yet been added/committed/pushed to git? Note that everything _under_ inst gets installed when you install the package, but the inst directory i

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

See below. - Original Message - > From: "Jurat Shayidin" > To: "Dan Tenenbaum" , "bioc-devel" > > Sent: Friday, December 2, 2016 8:32:35 AM > Subject: Re: [Bioc-devel] package vignette error : external data can't be > captured when

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

permission in, such as your home directory. R CMD check will alert you about various problems, including referring to packages in NAMESPACE but not DESCRIPTION, relying on BiocStyle but not mentioning it in DESCRIPTION, etc. Dan - Original Message - > From: "Jurat Shayidin

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

I don't really understand your question. But, create an inst/extdata directory: md inst md inst\extdata ... add your files to inst\extdata ... git add inst\extdata git commit git push Dan - Original Message - > From: "Jurat Shayidin" > To: "Dan Tenenbaum&

Re: [Bioc-devel] biconductor build error and warning

- Original Message - > From: "Bhakti Dwivedi" > To: "bioc-devel" > Sent: Sunday, December 4, 2016 6:29:22 AM > Subject: [Bioc-devel] biconductor build error and warning > Could anyone please help me with the below two bioconductor build error and > warnings? > > > I am getting the be

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

te dir 'C:\Program Files\R\R-devel\bin\x64\MSPC.Rcheck', >> > reason 'Permission denied' >> > ERROR: cannot create check dir 'C:/Program >> > Files/R/R-devel/bin/x64/MSPC.Rcheck' >> > >> > C:\Program Files\R\R-devel\bin\

Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)

Actually it looks like the version of java installed on morelia is 1.6. So it appears that 1.7 (or higher) needs to be installed. Dan - Original Message - > From: "Zach Charlop-Powers" > To: "Nan Xiao" > Cc: "bioc-devel" > Sent: Monday, December 5, 2016 1:02:52 PM > Subject: Re: [Bio

Re: [Bioc-devel] Bioconductor package license: dependency on work under non-commercial license

I can't speak to the license question (I'd guess the answer is no) but I am pretty sure that any dependencies of a Bioconductor package have to be available on CRAN or in Bioconductor itself. So you can't depend on packages that are only in GitHub. Dan - Original Message - > From: "Da

Re: [Bioc-devel] Package not being built on Windows or Mac

As I recall, there were issues building RCytoscape (and packages that depend on it) on Mac and Windows. Mostly because this requires a running instance of Cytoscape for each platform (and double that for release + devel). That used too much infrastructure so we disabled building on those platfor

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

- Original Message - > From: "Hervé Pagès" > To: "Martin Morgan" , "lcollado" > , "bioc-devel" > > Cc: "Jeff Leek" , "Andrew Jaffe" > Sent: Wednesday, March 22, 2017 10:21:43 AM > Subject: Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that > sometimes popped up, someti

Re: [Bioc-devel] xps build problem on veracruz2

- Original Message - > From: "Hervé Pagès" > To: "cstrato" , "bioc-devel" > Sent: Thursday, March 23, 2017 12:14:38 PM > Subject: Re: [Bioc-devel] xps build problem on veracruz2 > On 03/23/2017 11:09 AM, cstrato wrote: >> Dear Herve, >> >> Thank you for your explanation. >> >> The reas

Re: [Bioc-devel] Unit tests

Here's what BiocCheck says: Consider adding unit tests. We strongly encourage them. See http://bioconductor.org/developers/how-to/unitTesting-guidelines/ So, unit tests are encouraged but not required. Dan - Original Message - > From: "张腾" <2573552...@qq.com> > To: "bioc-devel" > Sent:

Re: [Bioc-devel] Something about time out errors

- Original Message - > From: "Martin Morgan" > To: "Rainer Johannes" > Cc: "Aimin Yan" , "bioc-devel" > > Sent: Monday, March 27, 2017 12:29:49 PM > Subject: Re: [Bioc-devel] Something about time out errors > On 03/27/2017 12:57 PM, Rainer Johannes wrote: >> Do you have code fetching

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

Don't install R-3.5; install R-3.4 from https://cran.rstudio.com/bin/windows/base/rtest.html Dan - Original Message - > From: "bioc-devel" > To: "bioc-devel" > Sent: Tuesday, March 28, 2017 7:59:57 PM > Subject: [Bioc-devel] Problem to install bioconductor for R devel (3.5) > Hi, > >

Re: [Bioc-devel] xps build problem on veracruz2

Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - > From: "Hervé Pagès" > To: "cstrato" , "Dan Tenenbaum" > Cc: "bioc-devel" > Sent: Thursday,

[Bioc-devel] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14

Hi all, Bioconductor 2.14 (release) packages are now available for the Mavericks (Mac OS X 10.9) build of R. If you install this version of R, you can install Mavericks packages by typing: source("http://bioconductor.org/biocLite.R";) ...and then using biocLite() to install the package(s) you

Re: [Bioc-devel] [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14

3 > > [4] GenomeInfoDb_1.0.2 IRanges_1.22.6 > > BiocGenerics_0.10.0 > > [7] BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > > [1] Biobase_2.24.0 RColorBrewer_1.0-5 stats4_3.1.0 > > tools_3.1.0 > > > > [

Re: [Bioc-devel] Is roxygen2 version 4.0.0 supported on the devel build system?

- Original Message - > From: "Nicolas Delhomme" > To: bioc-devel@r-project.org > Sent: Tuesday, May 6, 2014 7:24:08 AM > Subject: [Bioc-devel] Is roxygen2 version 4.0.0 supported on the devel build > system? > > Hej! > > I was wondering if the version 4.0.0 of roxygen2 is supported o

Re: [Bioc-devel] Is roxygen2 version 4.0.0 supported on the devel build system?

- Original Message - > From: "Nicolas Delhomme" > To: bioc-devel@r-project.org > Sent: Tuesday, May 6, 2014 7:24:08 AM > Subject: [Bioc-devel] Is roxygen2 version 4.0.0 supported on the devel build > system? > > Hej! > > I was wondering if the version 4.0.0 of roxygen2 is supported o

Re: [Bioc-devel] [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14

- Original Message - > From: "Dan Tenenbaum" > To: "Tom Harrop" > Cc: "bioc-devel" , "Bioconductor mailing list" > > Sent: Tuesday, May 6, 2014 7:33:01 AM > Subject: Re: [Bioc-devel] [BioC] Mavericks (Mac OS X 10.

Re: [Bioc-devel] Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14)

- Original Message - > From: "Martin Morgan" > To: bioc-devel@r-project.org > Sent: Wednesday, May 7, 2014 10:07:10 PM > Subject: Re: [Bioc-devel] Tracking Current release > (http://www.bioconductor.org/packages/current redirect to > http://www.bioconductor.org/packages/2.14) > > Hi Do

Re: [Bioc-devel] Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14)

- Original Message - > From: "Don Armstrong" > To: bioc-devel@r-project.org > Sent: Thursday, May 8, 2014 11:27:13 AM > Subject: Re: [Bioc-devel] Tracking Current release > (http://www.bioconductor.org/packages/current redirect to > http://www.bioconductor.org/packages/2.14) > > On Wed

Re: [Bioc-devel] error when creating gitsvn bridge

Hi Jonathon, - Original Message - > From: "Jonathon Hill" > To: bioc-devel@r-project.org > Sent: Friday, May 9, 2014 8:45:28 AM > Subject: [Bioc-devel] error when creating gitsvn bridge > > Hi am trying to recreate my gitsvn bridge. However, it simply says > > An error occurred creating

Re: [Bioc-devel] larger BioC AMI EBS volume

I think this should cover it: http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/ebs-expand-volume.html Dan - Original Message - > From: "Vincent Carey" > To: "Robert Castelo" > Cc: bioc-devel@r-project.org > Sent: Friday, May 9, 2014 1:32:22 PM > Subject: Re: [Bioc-devel] larger BioC

Re: [Bioc-devel] Bioconductor git-svn bridge is available

Hi Moritz, - Original Message - > From: "Moritz Gerstung" > To: "Kasper Daniel Hansen" > Cc: "Dan Tenenbaum" , bioc-devel@r-project.org, "Sean > Davis" > Sent: Monday, May 12, 2014 1:32:38 AM > Subject: Re: [Bioc-d

Re: [Bioc-devel] Bioconductor git-svn bridge is available

> > I'm not a git guru, so maybe I'm missing something here, but it > > seems feasible. > > > > Cheers, > > > > Moritz > > > > PS. Resent as it bounced from list before. > > > > > > On 21 Feb 2014, at 17:00, Kaspe

Re: [Bioc-devel] R CMD CHECK options

Hi Siddartha, - Original Message - > From: "Siddhartha Bagaria" > To: bioc-devel@r-project.org > Cc: "Craig Citro" > Sent: Monday, May 12, 2014 9:00:04 PM > Subject: [Bioc-devel] R CMD CHECK options > > Hello! > > This is my first time posting to the community. I am working on a new >

Re: [Bioc-devel] R CMD CHECK options

- Original Message - > From: "Siddhartha Bagaria" > To: "Dan Tenenbaum" > Cc: "Craig Citro" , bioc-devel@r-project.org > Sent: Tuesday, May 13, 2014 12:02:37 AM > Subject: Re: [Bioc-devel] R CMD CHECK options > > Hi Dan, thanks. Ju

Re: [Bioc-devel] git-svn bridge: Track devel and release in different branches of same repo

- Original Message - > From: "Julian Gehring" > To: bioc-devel@r-project.org > Sent: Wednesday, May 14, 2014 6:26:12 AM > Subject: [Bioc-devel] git-svn bridge: Track devel and release in different > branches of same repo > > Hi, > > Are there plans for the awesome git-svn bridge to al

Re: [Bioc-devel] bioconductor AMI & shiny app

Hi Robert, - Original Message - > From: "Robert Castelo" > To: bioc-devel@r-project.org > Sent: Wednesday, May 21, 2014 7:37:31 AM > Subject: [Bioc-devel] bioconductor AMI & shiny app > > hi, > > i'm trying to use a shiny app through AWS and the bioconductor AMI, > but > i cannot make i

Re: [Bioc-devel] Bioconductor git-svn bridge is available

Hi Kasper, - Original Message - > From: "Kasper Daniel Hansen" > To: "Hector Corrada Bravo" > Cc: "Dan Tenenbaum" , bioc-devel@r-project.org, "Sean > Davis" > Sent: Wednesday, May 21, 2014 4:50:59 PM > Subject: Re: [Bioc-de

Re: [Bioc-devel] Bioconductor git-svn bridge is available

- Original Message - > From: "Kasper Daniel Hansen" > To: "Dan Tenenbaum" > Cc: bioc-devel@r-project.org, "Sean Davis" , "Hector > Corrada Bravo" > Sent: Wednesday, May 21, 2014 6:15:50 PM > Subject: Re: [Bioc-devel] Bioco

Re: [Bioc-devel] bioconductor AMI & shiny app

- Original Message - > From: "Robert Castelo" > To: "Dan Tenenbaum" > Cc: bioc-devel@r-project.org > Sent: Thursday, May 22, 2014 7:47:53 AM > Subject: Re: [Bioc-devel] bioconductor AMI & shiny app > > hi Dan, > > On 05/21/2014 10:2

Re: [Bioc-devel] Namespace issues with ggbio 1.13.6 from AnnotationDbi 1.27.6 not exporting 'cols'

OrganismDbi 1.7.2 (available via biocLite()) has already fixed this so you shouldn't have to change anything. Dan - Original Message - > From: "Tengfei Yin" > To: "Leonardo Collado Torres" > Cc: bioc-devel@r-project.org > Sent: Thursday, May 22, 2014 12:10:29 PM > Subject: Re: [Bioc-d

Re: [Bioc-devel] Bioconductor git-svn bridge is available

ick on "...") the deliveries corresponding to your recent git commits, then click "Redeliver", this will send the message to the bridge that there is a new commit, and this time the bridge should handle it properly. I'll update the documentation with the changed verbi

Re: [Bioc-devel] Bug tracker for Bioconductor?

- Original Message - > From: "Michael Lawrence" > To: "Kasper Daniel Hansen" > Cc: "Michael Lawrence" , bioc-devel@r-project.org > Sent: Friday, May 23, 2014 12:48:55 PM > Subject: Re: [Bioc-devel] Bug tracker for Bioconductor? > > To support the decentralized model, it would be nice t

Re: [Bioc-devel] can't create git-svn bridge

Hi Doug, - Original Message - > From: "Doug H. Phanstiel" > To: bioc-devel@r-project.org > Sent: Monday, May 26, 2014 6:34:30 PM > Subject: [Bioc-devel] can't create git-svn bridge > > My apologies if you receive this email multiple times. This is my > first email to the list and I have

Re: [Bioc-devel] BiocCheck

Hi Kasper, - Original Message - > From: "Kasper Daniel Hansen" > To: bioc-devel@r-project.org > Sent: Wednesday, May 28, 2014 7:20:00 AM > Subject: [Bioc-devel] BiocCheck > > 1) The hash bang in the BiocCheck script currently requires > intervention at > install time. > Only if you don

Re: [Bioc-devel] BiocCheck

- Original Message - > From: "Kasper Daniel Hansen" > To: "Dan Tenenbaum" > Cc: bioc-devel@r-project.org > Sent: Thursday, May 29, 2014 10:51:56 AM > Subject: Re: [Bioc-devel] BiocCheck > > > This is the content of the Sweave script in

Re: [Bioc-devel] evaluation of C post-increments changed in GCC 4.8.2

Hi Robert, - Original Message - > From: "Robert Castelo" > To: bioc-devel@r-project.org > Sent: Thursday, June 12, 2014 5:45:28 AM > Subject: [Bioc-devel] evaluation of C post-increments changed in GCC 4.8.2 > > hi, > > this is just a warning to developers who may have C code in their >

Re: [Bioc-devel] BiocCheck

- Original Message - > From: "Kasper Daniel Hansen" > To: bioc-devel@r-project.org > Sent: Wednesday, May 28, 2014 7:20:00 AM > Subject: [Bioc-devel] BiocCheck > > 1) The hash bang in the BiocCheck script currently requires > intervention at > install time. > > It would be much more co

Re: [Bioc-devel] differences between petty and perceval (OS X 10.6.8 build machines for release/devel)

Hi Michael, - Original Message - > From: "Michael Stadler" > To: "Dan Tenenbaum" , bioc-devel@r-project.org > Sent: Friday, June 13, 2014 12:32:52 AM > Subject: differences between petty and perceval (OS X 10.6.8 build machines > for release/deve

Re: [Bioc-devel] BiocCheck

- Original Message - > From: "Dan Tenenbaum" > To: "Kasper Daniel Hansen" > Cc: bioc-devel@r-project.org > Sent: Friday, June 13, 2014 4:24:27 PM > Subject: Re: [Bioc-devel] BiocCheck > > > > - Original Message - > &g

Re: [Bioc-devel] New package submission process

- Original Message - > From: "Xiaobei Zhao" > To: bioc-devel@r-project.org > Sent: Thursday, June 26, 2014 5:20:31 AM > Subject: [Bioc-devel] New package submission process > > Hi everyone, > > I am about to submit a new package at Bioconductor. I have followed > the > instructions lin

Re: [Bioc-devel] Distinction between release and devel package websites

Seems like there are two problems, first that the release and devel pages look similar, but more importantly that people are downloading and installing from the package pages when they should be using biocLite(). I am open to the suggestions for making the release/devel pages look more differen

Re: [Bioc-devel] Distinction between release and devel package websites

- Original Message - > From: "James W. MacDonald" > To: "Dan Tenenbaum" , "Julian Gehring" > > Cc: "Michael Lawrence" , bioc-devel@r-project.org > Sent: Tuesday, July 22, 2014 9:26:13 AM > Subject: Re: [Bioc-devel] Distinctio

Re: [Bioc-devel] Distinction between release and devel package websites

- Original Message - > From: "Andrzej Oleś" > To: "James W. MacDonald" > Cc: "Dan Tenenbaum" , "Julian Gehring" > , "Michael Lawrence" > , bioc-devel@r-project.org > Sent: Tuesday, July 22, 2014 10:14:05 AM >

Re: [Bioc-devel] Distinction between release and devel package websites

people inadvisedly > > > clicking > > and > > > installing things, is there a good rationale for allowing them to > > > do so? > > > > > > Perhaps the landing page for each package should be stripped of > > > links and > > >

Re: [Bioc-devel] Distinction between release and devel package websites

- Original Message - > From: "James W. MacDonald" > To: "Andrzej Oleś" > Cc: "Dan Tenenbaum" , "Julian Gehring" > , "Michael Lawrence" > , bioc-devel@r-project.org > Sent: Tuesday, July 22, 2014 10:51:35 AM >

Re: [Bioc-devel] NAMESPACE problem in MacOS with VariantFiltering

Hi Robert, I just installed VariantFiltering on my system (using the Snow Leopard build of R) and had no trouble loading it. Here's my sessionInfo(): R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF

Re: [Bioc-devel] Distinction between release and devel package websites

Hi Andrzej, - Original Message - > From: "Andrzej Oleś" > To: "Dan Tenenbaum" > Cc: "James W. MacDonald" , "Julian Gehring" > , "Michael Lawrence" > , bioc-devel@r-project.org > Sent: Tuesday, July 22, 2014 2:06:25

Re: [Bioc-devel] Distinction between release and devel package websites

- Original Message - > From: "Leonardo Collado Torres" > To: bioc-devel@r-project.org > Sent: Wednesday, July 23, 2014 6:41:06 PM > Subject: Re: [Bioc-devel] Distinction between release and devel package > websites > > > Date: Wed, 23 Jul 2014 11:33:44 -0700 > > From: Martin Morg

Re: [Bioc-devel] affycoretools in devel failed to install

- Original Message - > From: "Vojtech Kulvait" > To: bioc-devel@r-project.org > Sent: Friday, July 25, 2014 4:32:43 AM > Subject: [Bioc-devel] affycoretools in devel failed to install > > Hello, > when I try to install affycoretools in devel i get an error: > > * installing *source* pa

Re: [Bioc-devel] affycoretools in devel failed to install

- Original Message - > From: "Vojtech Kulvait" > To: bioc-devel@r-project.org > Sent: Tuesday, July 29, 2014 4:40:36 AM > Subject: Re: [Bioc-devel] affycoretools in devel failed to install > > Looks like I was right :) > > > 2014-07-29 13:15 GMT+02:00 Martin Morgan : > > > Looks like

Re: [Bioc-devel] svn commit problem

You can't commit to release 2.13 since we are no longer building it. You can commit to the current release branch (2.14) and to trunk (devel). Dan - Original Message - > From: "Chen Meng" > To: bioc-devel@r-project.org > Sent: Friday, August 1, 2014 3:41:21 AM > Subject: [Bioc-devel] sv

Re: [Bioc-devel] Contradicting descriptions of "Enhances"

- Original Message - > From: "Jonathan Rosenblatt" > To: bioc-devel@r-project.org > Sent: Sunday, August 3, 2014 10:39:57 PM > Subject: [Bioc-devel] Contradicting descriptions of "Enhances" > > At the time of writing: > > *Writing R Extensions:* > "...the ‘Enhances’ field lists packag

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