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" <hpa...@fredhutch.org> > To: "cstrato" <cstr...@aon.at>, "Dan Tenenbaum" <dtene

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

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]

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"

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: >>

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:

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

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:

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

at\Documents\MSPC" >> > * checking for file 'C:\Users\jvrat\Documents\MSPC/DESCRIPTION' ... OK >> > * preparing 'MSPC': >> > * checking DESCRIPTION meta-information ... OK >> > * installing the package to build vignettes >> > * creating vignettes ...Warnin

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" <juratb...@gmail.com> > To:

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

atb...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Friday, December 2, 2016 9:11:29 AM > Subject: Re: [Bioc-devel] package vignette error : external data can't be > captured when compili

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

See below. - Original Message - > From: "Jurat Shayidin" <juratb...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Friday, December 2, 2016 8:32:35 AM > Subject

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

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

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

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

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

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

ot;Jurat Shayidin" <juratb...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Friday, November 11, 2016 1:59:32 PM > Subject: Re: [Bioc-devel] Fwd: can't install CRAN Packages after insta

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"

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 >

Re: [Bioc-devel] Question about InteractionSet package

- > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Ioannis Vardaxis" <ioannis.varda...@math.ntnu.no> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Friday, October 21, 2016 10:44:26 AM > Subject: Re: [Bioc-devel] Question

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

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

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

rom: "Martin Morgan" <martin.mor...@roswellpark.org> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Tuesday, October 18, 2016 3:25:16 PM > Subject: staging.bioconductor.org not responsive

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:

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

Re: [Bioc-devel] Automatic build failure notifications

- Original Message - > From: "Hervé Pagès" <hpa...@fredhutch.org> > To: "Emma Schymanski" <emma.schyman...@eawag.ch>, "bioc-devel" > <bioc-devel@r-project.org> > Cc: "Dan Tenenbaum" <dtene...@fredhutch.org>

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] 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

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

- Original Message - > From: "Hervé Pagès" <hpa...@fredhutch.org> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Philipp Angerer" <philipp.ange...@helmholtz-muenchen.de>, "bioc-devel" > <bioc-devel@r-proje

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

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"

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] 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 >

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

- Original Message - > From: "Karim Mezhoud" <kmezh...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Tuesday, August 16, 2016 8:33:39 AM > Subject: Re: [Bioc-d

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

- Original Message - > From: "Martin Morgan" <martin.mor...@roswellpark.org> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "lcollado" <lcoll...@jhu.edu> > Cc: "Jeff Leek" <jtl...@gmail.com>, "bioc-devel&q

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" <lcoll...@jhu.edu> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Jeff Leek" <jtl...@gmail.com>, "bioc-devel" <bioc-devel@r-project.or

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

- > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "lcollado" <lcoll...@jhu.edu> > Cc: "Jeff Leek" <jtl...@gmail.com>, "bioc-devel" <bioc-devel@r-project.org>, > "Andrew Jaffe" <andreweja...@gmail.com>

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

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 >

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

- Original Message - > From: "Steffen Neumann" <sneum...@ipb-halle.de> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Wednesday, July 27, 2016 5:02:22 AM > Subject: bioc

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" <anand...@hotmail.com> > To: "Dan Tenenba

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

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

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

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"

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" <lcoll...@jhu.edu> > To: "Antti Honkela" <antti.honk...@hiit.fi> > Cc: "Dan Tenenbaum" <dtene...@fre

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" <lcoll...@jhu.edu> > To: "Antti Honkela" <antti.honk...@hiit.fi> > Cc: "Dan Tenenbaum" <dtene...@fre

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

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

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

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

- Original Message - > From: "Yu, Guangchuang" > To: "bioc-devel" > Sent: Wednesday, June 8, 2016 1:44:12 AM > Subject: [Bioc-devel] notify out-dated branches > Dear all, > > I found many peoples still using (and asking questions of)

Re: [Bioc-devel] Permission denied warning when building vignette

I can't reproduce this. One thing you can do is try and reproduce it in an interactive session in order to get more information. So install your package: R CMD INSTALL ASAFE Then do the following: cd ASAFE/vignettes R CMD Stangle ASAFE.Rmd This will produce a file called ASAFE.R containing

Re: [Bioc-devel] New Package Submission Process

I put the wrong link in my announcement--the instructions for submitting a new package are at: https://github.com/Bioconductor/Contributions Dan - Original Message - > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "bioc-devel" <bioc-devel@r-

Re: [Bioc-devel] New Package Submission Process

The new GitHub-based new package contribution system is up and running. To contribute a Bioconductor package, file a new issue at https://github.com/Bioconductor/Contributions/issues/new Read the full instructions here: https://github.com/Bioconductor/Contributions/issues/new as well as the

Re: [Bioc-devel] Cannot update the release in svn

- Original Message - > From: "Tiphaine Martin" <tiphaine.mar...@kcl.ac.uk> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <Bioc-devel@r-project.org> > Sent: Thursday, June 2, 2016 2:28:44 PM > Subj

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

It's a problem on the server itself. It will not be present in today's build report which should be up in half an hour or so. This is an intermittent problem, not a continuous one. Dan - Original Message - > From: "Hartley, Stephen (NIH/NHGRI) [F]" <stephen.hart...@nih

Re: [Bioc-devel] Cannot update the release in svn

- Original Message - > From: "Tiphaine Martin" > To: "bioc-devel" > Sent: Sunday, May 29, 2016 2:54:20 PM > Subject: [Bioc-devel] Cannot update the release in svn > Hi, > > > I cleaned my gitHub repository to have now the

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

It's an as yet unknown problem with the build system. It's very likely that it will resolve itself in tonight's builds. Dan On May 26, 2016 5:04:43 PM PDT, Monther Alhamdoosh wrote: >​Hi developers, > >Our package named EGSEA seems to fail to be built on Windows​ as it

Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

- Original Message - > From: "Aaron Lun" <a...@wehi.edu.au> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Tuesday, May 24, 2016 11:04:59 AM > Subject: Re: [Bioc-de

[Bioc-devel] building packages that depend on openssl (was Re: problems linking to Rhtslib on Mac OSX)

[renamed the thread] - Original Message - > From: "Jason Serviss" <jason.serv...@ki.se> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Aaron Lun" <a...@wehi.edu.au>, "bioc-devel" <bioc-devel@r-project.org

Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

- Original Message - > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Aaron Lun" <a...@wehi.edu.au> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Tuesday, May 24, 2016 9:38:01 AM > Subject: Re: [Bioc-devel] p

Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

- Original Message - > From: "Aaron Lun" > To: "bioc-devel" > Sent: Tuesday, May 24, 2016 8:06:13 AM > Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX > Dear Martin and List, > > I have a problem with linking to Rhtslib on

Re: [Bioc-devel] workflow builds on windows but not on mac and linux

Hi, The problem on linux has been fixed, but now there's another problem. It is running out of memory when building your workflow. The problem on mac is that R-3.2.x is not compatible with the newest knitr (1.13), so the recommendation is to downgrade to knitr 1.12 or upgrade to R-3.3.0. The

Re: [Bioc-devel] test coverage not shown

It looks like something has changed at codecov. I have contacted them and asked them for guidance about the issue. Thanks, Dan - Original Message - > From: "Ramon Diaz-Uriarte" > To: "bioc-devel" > Cc: "ramon diaz" >

Re: [Bioc-devel] New package submission warning

You can ignore these warnings. Those build machines need to be updated to the devel version of Bioconductor but there are several other things that need to happen before we can do that. Dan - Original Message - > From: "Brad Nelms" > To: "bioc-devel"

Re: [Bioc-devel] Version numbers incremented?

For the record, here is the log message: Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R

Re: [Bioc-devel] \donttest and the "80% of man pages documenting exported objects must have runnable examples" rule

- Original Message - > From: "Richard Cotton" > To: "bioc-devel" > Sent: Sunday, May 15, 2016 4:45:09 AM > Subject: [Bioc-devel] \donttest and the "80% of man pages documenting > exported objects must have runnable examples" rule > I

Re: [Bioc-devel] new download stats

- Original Message - > From: "bioc-devel" > To: "bioc-devel" , "Hervé Pagès" > > Sent: Thursday, May 12, 2016 5:27:17 PM > Subject: Re: [Bioc-devel] new download stats > Hervé, > Thanks for the update, it looks

Re: [Bioc-devel] GEOquery for Bioc devel

uot;Sean Davis" <seand...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Vincent Carey" <st...@channing.harvard.edu>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Sunday, May 8, 2016 5:00:41 PM > Subje

[Bioc-devel] Mac builds in bioconductor devel

Hi all, You may have noticed that there are no Mac builds in the new devel (Bioconductor 3.4) build report. One of the build macs died. We have ordered replacement hardware and we hope it will arrive soon. Then after it is configured, we aim to get Mac builds going again as soon as

Re: [Bioc-devel] GEOquery for Bioc devel

If the package does not build for many days on end, it's more than > flakiness and one wonders if the service is usable at all. > Tests that indicate this seem appropriate to me, though I agree false > positives > can be annoying. > Dan > > > ----- Original Message

Re: [Bioc-devel] GEOquery for Bioc devel

rey" <st...@channing.harvard.edu> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Sunday, May 8, 2016 8:46:57 AM &g

Re: [Bioc-devel] GEOquery for Bioc devel

It has not built since the devel (3.4) builds started. Apparently GEO has been pretty flaky. Dan - Original Message - > From: "Kasper Daniel Hansen" > To: "bioc-devel" > Sent: Sunday, May 8, 2016 5:54:59 AM > Subject:

Re: [Bioc-devel] New package version and BiocCheck

The package builder attached to the tracker is running on release, not devel. It will be like that for a while so just ignore that warning. Dan - Original Message - > From: "Peng Ni" > To: "bioc-devel" > Sent: Friday, May 6, 2016 7:48:50 PM

Re: [Bioc-devel] how to declare vignette processing properly

Yeah, this was because pandoc-citeproc was not installed. So it should go away Dan - Original Message - > From: "lcollado" <lcoll...@jhu.edu> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Vincent Carey" <st...@channing.h

Re: [Bioc-devel] error message - package GSAR

This is an issue that was reported 3 years ago (http://thr3ads.net/r-devel/2013/04/2193760-Failed-to-locate-the-texi2pdf-output-file) and has not been fixed, probably because it is extremely hard to reproduce. It tends to happen on random packages from one day to the next. In fact, in today's

[Bioc-devel] Bioconductor 3.3 is released

April 4, 2016 Bioconductors: We are pleased to announce Bioconductor 3.3, consisting of 1211 software packages, 293 experiment data packages, and 916 up-to-date annotation packages. There are 107 new software packages, and many updates and improvements to existing packages; Bioconductor 3.3 is

Re: [Bioc-devel] svn co with username and password

Never mind, I found it. Please try the checkout again now. Dan - Original Message - > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Billy Chang" <billyheungw...@gmail.com> > Cc: "bioc-devel" <bioc-devel@r-project.org>

Re: [Bioc-devel] svn co with username and password

Whst is your svn username? Dan - Original Message - > From: "Billy Chang" > To: "bioc-devel" > Sent: Wednesday, May 4, 2016 11:58:23 AM > Subject: [Bioc-devel] svn co with username and password > Dear All, > > I recently submitted a

Re: [Bioc-devel] 3.3 branch created

- Original Message - > From: "lcollado" <lcoll...@jhu.edu> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Tuesday, May 3, 2016 7:52:50 PM > Subject: Re: [Bioc-devel] 3.

[Bioc-devel] 3.3 branch created

The BioC 3.3 branch is now ready. Remember, you always have access to 2 versions of your package: the "release" and the "devel" versions. Right now the "release" version of your package (which is not officially released yet but will be tomorrow if everything goes well) is in the 3.3 branch and

[Bioc-devel] Bioconductor 3.3 branch to be created today - do not commit during this time

Hello BioC developers, We will be creating the Bioconductor 3.3 branch today at 2:15 PM Seattle time. (21:15 UTC). This is about an hour from now. Please stop all commits to trunk before 2:15PM and do not resume until further notice. We will send another email when it is OK to resume commits.

Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

- > From: "Jianhong Ou" <jianhong...@umassmed.edu> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Monday, May 2, 2016 12:34:47 PM > Subject: Re: [Bioc-devel] could not install S4Vector

Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

This question should probably go on the support site as it is not about package development. You should update to Mavericks or higher. Earlier versions of Mac OS X are no longer officially supported by R or Bioconductor (that's why a binary is not available). Dan - Original Message

Re: [Bioc-devel] can't find an annotation package

Annotation packages are not in a public repository. You can get the tarball from the package landing page. Here's the devel (soon to be release) version: https://www.bioconductor.org/packages/devel/data/annotation/html/LowMACAAnnotation.html Dan - Original Message - > From: "Giorgio

[Bioc-devel] Updating package NEWS files for Bioconductor 3.3 release announcement (and biocViews)

Package developers -- Each Bioconductor release is accompanied by release notes that mention new packages and other significant project developments. For the forthcoming release we will include release notes for individual packages, so that users have an easy way to survey changes in their

Re: [Bioc-devel] prebs failing in devel

t;valerie.obench...@roswellpark.org>, "bioc-devel" > <bioc-devel@r-project.org> > Cc: "Dan Tenenbaum" <dtene...@fredhutch.org> > Sent: Monday, April 25, 2016 1:02:02 AM > Subject: Re: prebs failing in devel > Hi, > > Now the problem with R

Re: [Bioc-devel] gage fails to build on Windows in devel

Seems like a hiccup in the build system. In the report that will come out today, gage installs OK. Dan - Original Message - > From: "Monther Alhamdoosh" > To: "bioc-devel" > Sent: Monday, April 25, 2016 2:08:54 AM > Subject: [Bioc-devel]

Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)

- Original Message - > From: "Thomas Lawson" <thomas.nigel.law...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Steffen Neumann" <sneum...@ipb-halle.de>, "bioc-devel" > <Bioc-devel@r-project.or

Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)

- Original Message - > From: "Steffen Neumann" > To: "Thomas Lawson" , "bioc-devel" > > Sent: Thursday, April 21, 2016 7:29:50 AM > Subject: Re: [Bioc-devel] linking stage excessive runtime issue on

Re: [Bioc-devel] git-svn-mirror problem committing

- Original Message - > From: "Hector Corrada Bravo" > To: "bioc-devel" > Sent: Monday, April 18, 2016 7:56:06 AM > Subject: [Bioc-devel] git-svn-mirror problem committing > I am having issues committing to new package 'epivizrServer'. The

Re: [Bioc-devel] SVN and GitHub mirror out-of-sync

Should be caught up now. Dan - Original Message - > From: "Peter Hickey" > To: "bioc-devel" > Sent: Monday, April 18, 2016 7:00:29 AM > Subject: Re: [Bioc-devel] SVN and GitHub mirror out-of-sync > Typo - github version is 1.5.23 > >

Re: [Bioc-devel] update versions for 3.3 with to deal with new testthat

The build system will automatically pick up new versions from CRAN when they are available. So yes, packages (in both release and devel) need to be compatible with the changes in the new testthat. Dan - Original Message - > From: "Ramon Diaz-Uriarte" > To:

Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

I upgraded to r70462 and I cannot reproduce it now either. I guess it was an issue in R-alpha, since fixed. Sorry for the trouble. Dan - Original Message - > From: "Henrik Bengtsson" <henrik.bengts...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhu

Re: [Bioc-devel] Using Git with Bioconductor SVN repositories

>From your git log excerpt it looks like there has been some non-linear commit >history. svn does not like this. You may need to follow the instructions here: https://www.bioconductor.org/developers/how-to/git-mirrors/#dealing-with-prior-history--merge-conflicts Dan - Original Message

Re: [Bioc-devel] import except on Window Machine

this: import(S4Vectors, except=c(fold, values)) import(IRanges, except=values) So maybe make sure the objects to be excepted are not quoted? Dan - Original Message - > From: "Karim Mezhoud" <kmezh...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fred

Re: [Bioc-devel] import except on Window Machine

roxygen2 does not support the new syntax. Do you still get the same error if you write your NAMESPACE manually? - Original Message - > From: "Karim Mezhoud" <kmezh...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Lihua Zh

Re: [Bioc-devel] import except on Window Machine

Karim, What is the sessionInfo() in your R-3.3? It might be too old to have the new feature. It needs to be at svn rev r70426 or newer. Dan - Original Message - > From: "Karim Mezhoud" <kmezh...@gmail.com> > To: "Lihua Zhu" <julie@umassme

Re: [Bioc-devel] package submission - problem with vignette

It means that when you run R CMD build YourPackageName, the vignette is not built. It simply looks in the output of R CMD build for a line that starts: * creating vignettes ... If this line is present, it means `R` has not detected that a vignette needs to be built. It's `REQUIRED` that

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