Re: [Bioc-devel] Using non-CRAN/Bioc package

You cannot. All dependencies of Bioconductor packages must be available in CRAN or Bioconductor. You could ask the maintainer of that package to submit it to CRAN or Bioconductor. Alternatively you could minimize the dependence on it so that code that depends on it is only run if

Re: [Bioc-devel] workflows running Bioc-devel

Hi, This has come up before and probably should be done at some point. I can be virtually certain that it will not happen before the upcoming (3.3) release though. Thanks. Dan - Original Message - > From: "Michael Love" > To: "Aaron Lun"

Re: [Bioc-devel] package build : Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE

- Original Message - > From: "Diana LOW" > To: "bioc-devel" > Sent: Sunday, February 28, 2016 9:25:43 PM > Subject: [Bioc-devel] package build : Warning: 'rgl_init' failed, running > with rgl.useNULL = TRUE > Hi, > > I've been

Re: [Bioc-devel] R CMD check problems

A Bioconductor package cannot depend on act version of a package that is not available in Bioconductor or CRAN. So he needs to make sure this new version if available in CRAN ASAP. On February 25, 2016 8:48:49 AM PST, Luca De Sano wrote: >I think that the answer

Re: [Bioc-devel] Bioconductor 3.3 release schedule

April 6 and pay lots of attention to March 25! I'm updating the support site version of this post. Dan - Original Message - > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "bioc-devel" <bioc-devel@r-project.org> > Sent: Friday, February 19,

Re: [Bioc-devel] git svn mirrors

OK, the scater repos exists now, so try again. Dan - Original Message - > From: "Davis McCarthy" > To: "bioc-devel" > Sent: Monday, February 29, 2016 3:21:53 AM > Subject: [Bioc-devel] git svn mirrors > Hi develers > > My new package

Re: [Bioc-devel] GenVisR vignette build issues

- Original Message - > From: "Zach Skidmore" > To: "bioc-devel" > Sent: Saturday, February 27, 2016 10:04:19 AM > Subject: [Bioc-devel] GenVisR vignette build issues > Hi All, > > Recently the vignette in the GenVisR package has

[Bioc-devel] Fwd: Git-Svn bridge will be removed permanently on January 29, 2016

Reminder, this will happen this coming Friday, January 29th. Dan - Forwarded Message - From: "Dan Tenenbaum" <dtene...@fredhutch.org> To: "bioc-devel" <bioc-devel@r-project.org> Sent: Monday, December 28, 2015 11:08:29 AM Subject: [Bioc-devel] Git-Svn br

Re: [Bioc-devel] C library or C package API for regular expressions

R requires PCRE to build, therefore perhaps it is available for use within packages? Dan - Original Message - > From: "Jiří Hon" > To: "bioc-devel" > Sent: Saturday, January 23, 2016 1:56:52 AM > Subject: [Bioc-devel] C library or

Re: [Bioc-devel] package citation and version is not updated

OK, I looked into this a bit. The citation is there now and I will continue to look into this. Dan - Original Message - > From: "Michael Love" <michaelisaiahl...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-de

Re: [Bioc-devel] BiocGenerics attaches when methods package is imported

I have answered your email in the tracker, twice. Please do not reply all to random threads on bioc-devel. On February 16, 2016 8:41:25 AM PST, Yuande Tan wrote: >Dear all: >Today I resubmit the revised version of MBttest with fix error >occurring in >building windows.

Re: [Bioc-devel] github mirror

tes/origin/master remotes/origin/vignette So if you want to work on release-3.2, all you have to do is: git checkout release-3.2 Dan - Original Message - > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Kasper Daniel Hansen" <kasperdanielhan...@gma

[Bioc-devel] Bioconductor 3.3 release schedule

The Bioconductor 3.3 release schedule is now available: http://bioconductor.org/developers/release-schedule/ One important deadline is April 6, after which we will not accept any new packages into the release. Also, all packages must pass R CMD build and R CMD check without error by April 1,

Re: [Bioc-devel] workflow builder "Failed to check repository revision..."

Thanks, there was a password change and some things had to be tweaked as a result. Should be building now: http://docbuilder.bioconductor.org:8080/job/rnaseqGene/6/label=master/console Dan - Original Message - > From: "Michael Love" > To: "bioc-devel"

Re: [Bioc-devel] Your branch and 'bioc/master' have diverged

- Original Message - > From: "Luca De Sano" <l.des...@campus.unimib.it> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Thursday, March 10, 2016 10:21:38 AM > Subjec

Re: [Bioc-devel] Odd behavior by R CMD check

- Original Message - > From: "Hartley, Stephen (NIH/NHGRI) [F]" > To: "Henrik Bengtsson" > Cc: "bioc-devel" > Sent: Monday, March 14, 2016 6:58:04 AM > Subject: Re: [Bioc-devel] Odd behavior by R CMD check

Re: [Bioc-devel] BUILD error on moscato2: package not installed for 'arch=x64'

- Original Message - > From: "THEVENOT Etienne 207099" > To: "bioc-devel" > Sent: Thursday, March 10, 2016 10:57:05 PM > Subject: [Bioc-devel] BUILD error on moscato2: package not installed for > 'arch=x64' > Dear Bioconductor

Re: [Bioc-devel] best practice for storing long error message in R package

Staying out of the debate as to whether to emit a long error message or direct the user to the relevant man page, I will say that whether the error message is long or short, it should still direct the user to the relevant man page, where the way to avoid the error should be discussed in full.

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

- Original Message - > From: "Karim Mezhoud" <kmezh...@gmail.com> > To: "bioc-devel" <bioc-devel@r-project.org> > Cc: "Dan Tenenbaum" <dtene...@fredhutch.org> > Sent: Tuesday, March 29, 2016 6:11:15 AM > Subject:

Re: [Bioc-devel] No report from automated single package builder

I've resubmitted it. Dan - Original Message - > From: "Monther Alhamdoosh" > To: "bioc-devel" > Sent: Wednesday, March 30, 2016 3:22:27 PM > Subject: [Bioc-devel] No report from automated single package builder > Hi, > > I submitted a

Re: [Bioc-devel] R-beta, windows, and Rtools version

There will be an answer tomorrow (Thursday Seattle time). Dan - Original Message - > From: "Ramon Diaz-Uriarte" > To: "bioc-devel" > Cc: "ramon diaz" > Sent: Wednesday, March 30, 2016 11:17:17 PM > Subject:

Re: [Bioc-devel] No report from automated single package builder

Yes. There will be an announcement about this new toolchain tomorrow (Thursday). Dan - Original Message - > From: "Steffen Neumann" <sneum...@ipb-halle.de> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-dev

Re: [Bioc-devel] Build error on Moscato2

The mzR maintainers are aware of the issue, which has to do with the new windows toolchain. They are working on it. Dan - Original Message - > From: "Samuel Wieczorek" > To: "bioc-devel" > Sent: Thursday, April 7, 2016 1:28:00 AM >

Re: [Bioc-devel] namespace question

Michael, do you know if this change will be (or has already been) backported into R-3.3.0? Thanks. Dan - Original Message - > From: "Lihua Zhu" <julie@umassmed.edu> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "Michael Lawrence"

Re: [Bioc-devel] need advice on how to fix build error in windows

It's fine in today's build report. Dan On April 8, 2016 1:31:24 PM PDT, Krithika Bhuvaneshwar wrote: >Dear Biconductor team, > >We are developers of newly accepted Bioconductor package CINdex. Our >package is meant for DNA copy number data analysis, and the example >data

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] 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

Re: [Bioc-devel] mascato2 check error

- Original Message - > From: "Karim Mezhoud" > To: "bioc-devel" > Sent: Monday, April 11, 2016 5:52:43 AM > Subject: [Bioc-devel] mascato2 check error > Dear BioC devel, > I did not understand the following error check message. >

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

The problem seems to have to do with illuminaio and possibly minfiData; it can be reduced to / reproduced by the following: library(illuminaio) file <- "e:/biocbld/bbs-3.3-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat" illuminaio:::readIDAT_nonenc(file) Specifically

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

The windows machine is still running an older version of R that does not support this NAMESPACE syntax. I will update it this week. Dan - Original Message - > From: "Lihua Zhu" > To: "bioc-devel" > Cc: "Michael Lawrence"

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] 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] 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] Announcing Docker containers for Bioconductor

Sure, send a pull request. Pushing is done automatically. https://github.com/Bioconductor/bioc_docker/blob/master/Rakefile#L98-L102 Dan - Original Message - > From: "Steffen Neumann" > To: "bioc-devel" > Sent: Friday, March 18, 2016

Re: [Bioc-devel] package 'splineTCDiffExpr'

This has been done, in tomorrow's (Thursday's) builds this should be reflected. Dan - Original Message - > From: "Herbert Braselmann" > To: "bioc-devel" , "Michna, Agata Anna" > > Sent:

[Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

Attention package maintainers, When building an R package, if R thinks there is a vignette, it will emit this line during R CMD build: * creating vignettes ... OK If there is either no vignette, or in the case of non-sweave vignettes, something is not set up correctly (there are many things

Re: [Bioc-devel] svn branching

You can work in git (https://bioconductor.org/developers/how-to/git-mirrors/) and create as many local branches as you want. You can't create any branches in svn. You have access only to your package, in devel (trunk) and the release branch. If working in git, be wary of creating a non-linear

Re: [Bioc-devel] NAMESPACE issue in bumphunter

Please make the change yourself using the git mirrors. https://bioconductor.org/developers/how-to/git-mirrors/ Dan - Original Message - > From: "lcollado" > To: "bioc-devel" > Cc: "Rafael Irizarry" > Sent: Thursday,

Re: [Bioc-devel] Identify Bioc build machines

There are a number of variables defined. You could check to see if the variable BBS_HOME is defined (it does not matter what the value is in your case, just whether it is defined or not). Dan - Original Message - > From: "Thomas Dybdal Pedersen" > To:

Re: [Bioc-devel] spliceSites Vignette build error

Are you using R-devel on your computer? - Original Message - > From: "Wolfgang Kaisers" > To: "bioc-devel" > Sent: Friday, March 4, 2016 12:41:30 AM > Subject: [Bioc-devel] spliceSites Vignette build error > Dear All, > >

Re: [Bioc-devel] spliceSites Vignette build error

2-4splines_3.3.0 seqLogo_1.37.0 > Dan - Original Message - > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Wolfgang Kaisers" <wolfgang.kais...@uni-duesseldorf.de> > Cc: "bioc-devel" <bioc-devel@r-project.org> >

Re: [Bioc-devel] Imports, depends and warnings

Can you be more specific about which docker image you pulled? Dan - Original Message - > From: "Federico Marini" > To: "Martin Morgan" , "bioc-devel" > > Sent: Thursday, March 3, 2016 1:20:46 AM > Subject:

[Bioc-devel] C++ header changes in R-devel

Hi, I contacted some of you yesterday because your packages are breaking in R-devel. Specifically these packages MAY have this issue: AffyTiling bgx CALIB Cardinal flipflop Ringo rMAT seqbias I may have said something like this: "Probably due to changes in R headers in recent R-devel.

Re: [Bioc-devel] Noticed change of version for some packages in BioC 3.2

Have a look at http://blog.revolutionanalytics.com/2014/08/gran-and-switchr-cant-send-you-back-in-time-but-they-can-send-r-sort-of.html https://cran.r-project.org/web/packages/packrat/index.html Dan - Original Message - > From: "Stefano Berri" <sbe...@illumina.com> &

Re: [Bioc-devel] SVN Commit - Problem with the Version Number

You can merge from devel into release (as long as it's only bug fixes), but make sure you don't overwrite the version number. If the version number in release was 1.0.0 before the merge, make sure it is 1.0.1 before committing. See

Re: [Bioc-devel] Imports, depends and warnings

/devel_base is now up to date. Of course this only includes one Bioconductor package (BiocInstaller) and fewer system dependencies, but it might be a helpful stopgap for you. Dan - Original Message - > From: "Federico Marini" <mari...@uni-mainz.de> > To: "Dan Tenenba

Re: [Bioc-devel] Noticed change of version for some packages in BioC 3.2

The main reason for packages to change in release is because of bug fixes, also documentation enhancements. You should not expect the versions in release to be frozen. Dan - Original Message - > From: "Bernd Klaus" > To: "Stefano Berri" ,

Re: [Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available: II

- Original Message - > From: "Ramon Diaz-Uriarte" <rdia...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Ramon Diaz-Uriarte" <rdia...@gmail.com>, "Luca De Sano" > <l.des...@campus.unimib.it>,

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

- > From: "Karim Mezhoud" <kmezh...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Friday, April 1, 2016 5:17:32 AM > Subject: Re: [Bioc-devel] 49 software packages either

Re: [Bioc-devel] Package Without a Vignette

- Original Message - > From: "Zhilong Jia" <zhilong...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Stefan Haunsberger" <stefan.haunsber...@gmail.com>, "bioc-devel" > <bioc-devel@r-project.or

Re: [Bioc-devel] Package Without a Vignette

; <zhilong...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Stefan Haunsberger" <stefan.haunsber...@gmail.com>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Saturday, April 2, 2016 7:23:14 PM > Subject: Re: [Bioc-deve

Re: [Bioc-devel] Package Without a Vignette

In DESCRIPTION change VignetteBuilder: rmarkdown to VignetteBuilder: knitr Dan - Original Message - > From: "Zhilong Jia" > To: "Stefan Haunsberger" > Cc: "bioc-devel" > Sent: Saturday, April 2, 2016

Re: [Bioc-devel] R CMD CHECK error in examples

Can we see the code to your package? Hi Karl, It might be good to first fix the issue preventing vignette build in devel: https://bioconductor.org/checkResults/devel/bioc-LATEST/rgsepd/zin2-buildsrc.html Then we can take a look at the R CMD check issue. Note that Bioconductor does not run

Re: [Bioc-devel] BiocCheck Local and Single Package Builder Discrepancy

- Original Message - > From: "David Kuo" > To: "bioc-devel" > Sent: Friday, April 1, 2016 1:13:47 PM > Subject: [Bioc-devel] BiocCheck Local and Single Package Builder Discrepancy > Hi, > > I'm observing different results from executing

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

- Original Message - > From: "Karim Mezhoud" <kmezh...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Tuesday, March 29, 2016 12:05:03 PM > Subject:

Re: [Bioc-devel] Vignette name not appearing on bioconductor package page

You have two titles in the vignette and the second one is blank: dtenenba@Dans-Air:~/devel/CINdex/vignettes$ grep VignetteIndexEntry CINdex.Rnw %\VignetteIndexEntry{CINTutorial} %\VignetteIndexEntry{} Remove the second one. Dan - Original Message - > From: "Krithika Bhuvaneshwar"

Re: [Bioc-devel] not yet updated package sources/binaries in devel

There were no windows build results yesterday, and Snow Leopard builds stopped some time ago. So nothing needs to be done. Dan - Original Message - > From: "Maarten van Iterson" > To: "bioc-devel" > Sent: Thursday, March 31, 2016 12:01:04

[Bioc-devel] Change to scheduling of devel builds

Hi, We have made a temporary change to the schedule of the builds. Experiment Data packages will now build just once a week, on Saturdays during the day (Seattle time). Software packages will build every day of the week EXCEPT Friday night/Saturday morning. At the moment we're stuck with

[Bioc-devel] new Windows toolchain for R-3.3.0

Hello all, R is planning to use a new Windows toolchain (known as Rtools33) for the soon-to-be-released R-3.3.0. This toolchain will use gcc/g++ 4.9.3 (an upgrade from 4.6.3). We expect CRAN packages for Windows using this toolchain in a few days. We are currently building the devel branch of

Re: [Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available

I think it's a problem with igraph (a CRAN package) under the new toolchain. I was just in the process of filing a github issue with that package maintainer. Watch for it at https://github.com/igraph/igraph/issues/ . Dan - Original Message - > From: "Luca De Sano"

Re: [Bioc-devel] new Windows toolchain for R-3.3.0

need a VM. Dan - Original Message - > From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Thursday, March 31, 20

Re: [Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available

I can also run the example on i386. Seems to just affect x64; let me know if your experience is different when you try this on a 64-bit machine. I'll add this data point to the issue. Dan - Original Message - > From: "Ramon Diaz-Uriarte" <rdia...@gmail.com> &

Re: [Bioc-devel] build problem in package GSAR

- Original Message - > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Rahmatallah, Yasir" <yrahmatal...@uams.edu> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Friday, April 1, 2016 5:32:06 PM > Subject:

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

Sorry, my bad! It really should be ok now. Thanks for your patience. Dan - Original Message - > From: "Karim Mezhoud" <kmezh...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" > <bioc-devel@r-project.org&g

Re: [Bioc-devel] Can not commit to bioconductor

Should be ok now. Sorry about that. Dan - Original Message - > From: "Jianhong Ou" > To: "bioc-devel" > Sent: Friday, April 1, 2016 2:30:12 PM > Subject: [Bioc-devel] Can not commit to bioconductor > Hi, > > When I try to commit new

Re: [Bioc-devel] build problem in package GSAR

The issue has already been fixed and that should be reflected in Sunday's build report. Recent emails to R-devel have discussed the problem, which is related to a new toolchain for building windows packages, intended to be used with the soon-to-be-released R-3.3.0. Dan - Original Message

Re: [Bioc-devel] ggbio error

Yes, the ggbio issue is fixed and this will be reflected in tomorrow's build report. Dan - Original Message - > From: "Michael Lawrence" > To: "Ludwig Geistlinger" > Cc: "bioc-devel" > Sent:

Re: [Bioc-devel] namespace question

BTW, looks like the change has been made to R-devel: CHANGES IN R-devel NEW FEATURES * The ‘import()’ namespace directive now accepts an argument ‘except’ which names symbols to exclude from the imports. The ‘except’ expression should evaluate to a character vector (after substituting

Re: [Bioc-devel] SVN credentials

The error with pd.genomewidesnp.6 is related to a move to a new windows toolchain (which has been discussed on this list) and the fallout affecting a package (affxparser) which pd.genomewidesnp.6 depends on. THe biovizBase issue will be resolved in the next build report (on Sunday afternoon

Re: [Bioc-devel] dropping perceval and petty from supported platforms

Yes, you can remove it from devel. Dan - Original Message - > From: "Ramon Diaz-Uriarte" > To: "bioc-devel" > Cc: "ramon diaz" > Sent: Monday, April 4, 2016 2:30:34 AM > Subject: [Bioc-devel] dropping perceval and

[Bioc-devel] Bioconductor 3.3 release schedule has been updated to reflect R release delay

Bioconductors-- In case you missed it, R announced a delay in its release schedule: https://stat.ethz.ch/pipermail/r-announce/2016/000599.html Their full (updated) release schedule is at http://developer.r-project.org/ Accordingly, Bioconductor has updated its release schedule:

Re: [Bioc-devel] readVcf appears to cause Windows i386 check error

There are two installations of R on moscato2; one for the nightly builds and one for the single package builder. I can reproduce this problem on the latter but not the former. I will look into it further, pulling in others as necessary. Thanks for the report, Dan - Original Message -

Re: [Bioc-devel] readVcf appears to cause Windows i386 check error

There is a fresh build of your package now and it looks like this problem has cleared up. It seems there was a broken version of Biostrings installed, I'm investigating how it happened. Dan - Original Message - > From: "Riester, Markus" > To: "bioc-devel"

Re: [Bioc-devel] package build failing in Windows with "Failed to locate the 'texi2pdf' output file"

Actually your problem is different and does not affect windows. Which branch have you committed your changes to? Can you do the following? git checkout release-3.2 git checkout -b issue/vignette-problem # fix the problem git commit -a git push # then copy and paste the command that git

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] 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] 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] 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] 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

[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] 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] 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] \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

[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.

[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

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.

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] 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] 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] 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

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] 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 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 > >

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