[Bioc-devel] Struggles with correct import of bumphunter::annotateNearest - IRanges::distance

scales_0.2.3stats4_3.0.2 [55] stringr_0.6.2 tcltk_3.0.2 tools_3.0.2 VariantAnnotation_1.8.5 whisker_0.3-2 XML_3.95-0.2 [61] xtable_1.7-1XVector_0.2.0 zlibbioc_1.8.0 Leonardo Collado Torres, PhD student Department of Biostatistics

Re: [Bioc-devel] Struggles with correct import of bumphunter::annotateNearest - IRanges::distance

resolved? Did you import nearest from IRanges? Can you run nearestgene under debug and step through it, seeing how nearest is resolved? Do you only get an error from CMD check and not in real life? On Nov 20, 2013, at 12:16 PM, Leonardo Collado Torres wrote: Dear BioC-devel list, I have what

Re: [Bioc-devel] Struggles with correct import of bumphunter::annotateNearest - IRanges::distance

the GenomicRanges strand and elementMetadata functions, as well as the IRanges distanceToNearest, IRanges and subjectHits functions. Best, Leo On Wed, Nov 20, 2013 at 2:46 PM, Leonardo Collado Torres lcoll...@jhsph.edu wrote: Hi Harris, Answering your question from your first email, I do not think

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

Hello, Currently I'm unable to load ggbio 1.13.6 (BioC-devel) due to some namespace issues. The basic error is: Error : object ‘cols’ is not exported by 'namespace:AnnotationDbi' Error: package or namespace load failed for ‘ggbio’ I'm reporting this because a user reported a similar issue with

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 tengfei@sbgenomics.com To: Leonardo Collado Torres lcoll...@jhsph.edu Cc: bioc-devel@r-project.org Sent: Thursday, May 22

[Bioc-devel] Confusing namespace issue with IRanges 1.99.17

BiocParallel::MulticoreParam() in terms of keeping the memory under control. Thank you for your help! Leo Leonardo Collado Torres, PhD student Department of Biostatistics Johns Hopkins University Bloomberg School of Public Health Website: http://www.biostat.jhsph.edu/~lcollado/ Blog: http

Re: [Bioc-devel] Cannot interact with a BigWig file on the web with rtracklayer (Windows specific)

wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: bioc-devel@r-project.org Cc: Dan dtene...@fhcrc.org Sent: Tuesday, September 30, 2014 8:00:53 AM Subject: Cannot interact with a BigWig file on the web with rtracklayer (Windows specific) Hello, I ran

Re: [Bioc-devel] Cannot interact with a BigWig file on the web with rtracklayer (Windows specific)

library and are not supported on windows. This is documented at ?import.bw ?`BigWigFile-class` This problem isn't specific to an 'over the network' example. Trying to import() a local BigWig on Windows will also fail. Valerie On 09/30/2014 08:00 AM, Leonardo Collado Torres wrote: Hello

[Bioc-devel] AnnotationDbi::loadDb() now requires dbType and dbPackage?

Hi, I think that the docs for ?loadDb (AnnotationDbi) need to be updated as described below. According to ?loadDb in AnnotationDbi 1.27.19 dbType dbType - not required dbPackage dbPackage - not required However, R CMD check for derfinder 0.99.5 and R CMD build for GenomicFeatures 1.17.21

Re: [Bioc-devel] AnnotationDbi::loadDb() now requires dbType and dbPackage?

On Fri, Oct 10, 2014 at 11:24 AM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi, I think that the docs for ?loadDb (AnnotationDbi) need to be updated as described below. According to ?loadDb in AnnotationDbi 1.27.19 dbType dbType - not required dbPackage dbPackage

Re: [Bioc-devel] AnnotationDbi::loadDb() now requires dbType and dbPackage?

Ahh ok! Thanks =) On Fri, Oct 10, 2014 at 11:28 AM, Martin Morgan mtmor...@fhcrc.org wrote: On 10/10/2014 08:24 AM, Leonardo Collado Torres wrote: Hi, I think that the docs for ?loadDb (AnnotationDbi) need to be updated as described below. According to ?loadDb in AnnotationDbi 1.27.19

Re: [Bioc-devel] Git-svn bridge for BioC 3.0

Awesome! Thanks for the info Dan! On Tue, Oct 14, 2014 at 10:37 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: bioc-devel@r-project.org Sent: Tuesday, October 14, 2014 7:05:21 AM Subject: [Bioc-devel] Git-svn

Re: [Bioc-devel] runnable examples for internal function ?

On Thu, Oct 16, 2014 at 7:42 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: Hervé Pagès hpa...@fhcrc.org To: Tiphaine Martin tiphaine.mar...@kcl.ac.uk, Michael Lawrence lawrence.mich...@gene.com, Dan Tenenbaum dtene...@fhcrc.org Cc:

[Bioc-devel] Why be default 'D' is not dropped from coverage?

Hi, A collaborator of mine is working on a new software and we while we were doing a sanity check to compare the base-level coverage from BAM files and bigWig files generated from his software we realized that by default bases corresponding to a 'D' on the CIGAR string get counted when reading

Re: [Bioc-devel] Why be default 'D' is not dropped from coverage?

Cheers, Leo On Mon, Oct 20, 2014 at 5:45 PM, Hervé Pagès hpa...@fhcrc.org wrote: Hi Leo, On 10/18/2014 10:50 AM, Leonardo Collado Torres wrote: Hi, A collaborator of mine is working on a new software and we while we were doing a sanity check to compare the base-level coverage from BAM

[Bioc-devel] A more flexible GenomeInfoDb::mapSeqlevels(): used supported info but don't break with new organisms/toy examples

simply assume some other default values and guarantee continuity with how I was doing things previously. Naturally, R CMD check now shows a NOTE because I'm using the ::: syntax for un-exported functions from `GenomeInfoDb`. Cheers, Leo Leonardo Collado Torres, PhD Candidate Department

Re: [Bioc-devel] [devteam-bioc] Whom to contact for adding an organism to GenomeInfoDb?

...@bioconductor.org but maybe there's a specific channel for this. Thanks, Leo Leonardo Collado Torres, PhD Candidate Department of Biostatistics Johns Hopkins University Bloomberg School of Public Health Website: http://www.biostat.jhsph.edu/~lcollado/ Blog: http://lcolladotor.github.io

Re: [Bioc-devel] [devteam-bioc] A more flexible GenomeInfoDb::mapSeqlevels(): used supported info but don't break with new organisms/toy examples

On Wed, Oct 22, 2014 at 6:59 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi Sonali, The recent changes in GenomeInfoDb (1.3.3) look great! On Wed, Oct 22, 2014 at 1:53 PM, Sonali Arora sar...@fhcrc.org wrote: Hi Leo, To summarize, These are the concerns raised in your previous

Re: [Bioc-devel] [devteam-bioc] A more flexible GenomeInfoDb::mapSeqlevels(): used supported info but don't break with new organisms/toy examples

FALSE TRUE FALSE LGI T packageVersion('GenomeInfoDb') [1] ‘1.3.3’ Cheers, Leo On Wed, Oct 22, 2014 at 7:03 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: On Wed, Oct 22, 2014 at 6:59 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi Sonali, The recent changes

[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1

Hi, I can't seem to install devel packages via biocLite() and I wonder if something is broken or if I'm missing something. For example, take GenomeInfoDb which is at 1.3.6 and is passing all checks. The usual code using a fresh R 3.1.2-patched install isn't working as it downloads the latest

Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1

...@gmail.com wrote: You should not be using R-3.1.2 patched with the current devel version of Bioconductor; use R-devel. Best, Kasper On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi, I can't seem to install devel packages via biocLite() and I wonder

Re: [Bioc-devel] More than 1 citation in landing page

...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: bioc-devel@r-project.org Cc: Jeff Leek jtl...@gmail.com Sent: Friday, October 31, 2014 4:05:11 AM Subject: [Bioc-devel] More than 1 citation in landing page Hi, I'm wondering if it's

[Bioc-devel] Confused by readGAlignments(scanBamParam( which ))

Hi, It took me a while, but I was confused by getting different results when using 'which' in reading BAM files. In my use case, I have a GRanges with 15 ranges (different exons from the transcripts of a gene) and I get much higher coverage values than simply using the range of the 15 ranges. I

Re: [Bioc-devel] BamTallyParam argument 'which'

Related to my post on a separate thread (https://stat.ethz.ch/pipermail/bioc-devel/2015-February/006978.html), I think that if 'which' is not being reduced by default, a simple example showing the effects of this could be included in the functions that have such an argument. Also note that

Re: [Bioc-devel] R 3.3 for snow leopard

Thanks Dan and Nicolas! I'll likely upgrade my Mac OS soon(ish), but use R-3.2.0-patched until then. On Mon, Apr 20, 2015 at 3:32 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Dan Tenenbaum dtene...@fredhutch.org To: Leonardo Collado Torres lcoll

[Bioc-devel] R 3.3 for snow leopard

Hi, This is not BioC related, but should hopefully be quick. According to http://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-R-under-OS-X there may be a separate installer package, R-3.3.0-snowleopard.pkg. I'm not seeing any at http://r.research.att.com/. Has anyone heard if

Re: [Bioc-devel] recalling methods

Somewhat related to this topic, some folks made this package: https://github.com/hilaryparker/explainr It could be related to Wolfgang's idea of learning which methods are more important, its just that people would have to write the explanation. Then a new user can learn about it. On Mon, Apr 6,

Re: [Bioc-devel] BrowserViz: curious but needs a small tweak to run example

Forgot to add bioc-devel On Fri, Apr 3, 2015 at 4:55 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi, From the April newsletter I got curious about BrowserViz but I couldn't run the simple example as-is. From http://bioconductor.org/checkResults/devel/bioc-LATEST/BrowserViz/ I can

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

Hi, Dan previously said: Try starting over again. Remove your local repository and do a fresh clone: git clone https://github.com/leekgroup/derfinderHelper.git cd derfinderHelper bash /path/to/update_remotes.sh git checkout devel git svn rebase git merge master --no-edit git svn dcommit

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

Hi, This sounds great! Not having to setup all those bridges everytime a new BioC version is released should be a great feature, plus keeping the commit history tidy. And we can still use Travis or other things like Slack notifications on our own bridges. I guess that it'd be good to remind

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

On Tue, Jun 16, 2015 at 8:55 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi, This sounds great! Not having to setup all those bridges everytime a new BioC version is released should be a great feature, plus keeping the commit history tidy. And we can still use Travis or other things

Re: [Bioc-devel] Use and Usability metrics / shields

://github.com/leekgroup/derfinderData On Fri, Jun 12, 2015 at 12:32 AM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Thursday, June 11, 2015 9:26:13 PM

Re: [Bioc-devel] Use and Usability metrics / shields

Ahh, I missed the 2 versions on the platforms shield. I am using both build shields. I'll make some edits then. On Fri, Jun 12, 2015 at 2:49 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

On Tue, Jun 16, 2015 at 10:02 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Ryan C. Thompson r...@thompsonclan.org Cc: Dan Tenenbaum dtene...@fredhutch.org, bioc-devel bioc-devel@r-project.org Sent: Tuesday

Re: [Bioc-devel] Use and Usability metrics / shields

on CRAN, snare drum, ... am I to eager if I already now start wishing for a hi-hat as well? /Henrik On Tue, May 19, 2015 at 12:47 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Dan Tenenbaum dtene

[Bioc-devel] Cairo error on Mac OS X Snow Leopard (10.6.8) / x86_64

Hi, My package regionReport just reported errors on both release and devel when running R CMD check on Mac OS X Snow Leopard (10.6.8) / x86_64. The error is: Error: .onLoad failed in loadNamespace() for 'Cairo', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load

[Bioc-devel] Redirect workers output to STDERR, how to do so with current BiocParallel::SnowParam()?

Hi, This might be a BioC support website question, but maybe it's a bug. In previous versions of BiocParallel, you could specify where to direct the output from the workers by using the 'outfile' argument. For example, SnowParam(outfile = Sys.getenv('SGE_STDERR_PATH')). I'm not finding how to do

[Bioc-devel] rtracklayer::import( as = 'NumericList' ) doesn't work with more than 1 range

either. Cheers, Leo Leonardo Collado Torres, PhD Candidate Department of Biostatistics Johns Hopkins University Bloomberg School of Public Health Website: http://www.biostat.jhsph.edu/~lcollado/ Blog: http://lcolladotor.github.io/ ___ Bioc-devel@r

Re: [Bioc-devel] Use and Usability metrics / shields

Regarding the 'posts' tag, I can see that it includes a closed questions component. For example, http://www.bioconductor.org/packages/release/bioc/html/derfinder.html is 3/1/9/0 right now meaning that 0 questions are closed. From https://support.bioconductor.org/info/faq/, only moderators can

Re: [Bioc-devel] Redirect workers output to STDERR, how to do so with current BiocParallel::SnowParam()?

, Leonardo Collado Torres wrote: Hi Valerie, My other recent thread about SnowParam (https://stat.ethz.ch/pipermail/bioc-devel/2015-July/007788.html) allowed me to see a small difference. In R 3.1.x, using 'outfile' as in https://github.com/lcolladotor/SnowParam-memory/blob

Re: [Bioc-devel] Memory issues with BiocParallel::SnowParam()

. SnowParam(log = TRUE) Valerie On 07/10/2015 01:12 PM, Leonardo Collado Torres wrote: Hi, I ran my example code with SerialParam() which had a negligible 4% memory increase between R 3.2.x and 3.1.x This 4% could very well fluctuate a little bit and might be non significantly different

Re: [Bioc-devel] [bithelp] Memory issues with BiocParallel::SnowParam()

information related to this bug report available in github. Having that space to record thoughts, store log/memory files and provide code really works well. =) Valerie On 07/14/2015 01:33 PM, Leonardo Collado Torres wrote: Hi Valerie, I have re-run my two examples twice using log = TRUE

Re: [Bioc-devel] Redirect workers output to STDERR, how to do so with current BiocParallel::SnowParam()?

On 05/21/2015 07:58 AM, Leonardo Collado Torres wrote: Hi, This might be a BioC support website question, but maybe it's a bug. In previous versions of BiocParallel, you could specify where to direct the output from the workers by using the 'outfile' argument. For example, SnowParam

[Bioc-devel] Vignette questions: location of html BiocStyle vignette, fake + real vignettes not necessary?

Hi, I'm planning on switching some vignettes to BiocStyle (html version). Is there any particular reason why the html vignette for BiocStyle is outside of the /vignettes directory? I see it at /inst/rmarkdown/templates/html_document/skeleton/skeleton.Rmd with /vignettes/HtmlStyle.Rmd linking to

[Bioc-devel] Coverage test badge not updating

Hi, In my packages I enabled testing (via testthat) a few weeks ago. I did so as can be seen in https://github.com/leekgroup/derfinderHelper/commit/26d9d5543d9082f85bbb2d0ae9f02c5c309b9a48 for the changes to tests/test-all.R You can see that the tests are actually being run at

[Bioc-devel] citation() error for BiocParallel and S4Vectors

Hi, The daily build report showed a similar error in several of my packages when building on Linux and Windows. I was able to reproduce this error under R-devel on Windows and it pops up when using the citation() function. In particular with BiocParallel and S4Vectors. This error doesn't pop up

Re: [Bioc-devel] Vignette questions: location of html BiocStyle vignette, fake + real vignettes not necessary?

Awesome, thanks for the replies and clarifications! On Thu, Oct 29, 2015 at 7:18 PM, Andrzej Oleś wrote: > Hi Leonardo, > > thank you for considering using BiocStyle for your vignettes! Please read > below. > > On Thu, Oct 29, 2015 at 10:17 PM, Dan Tenenbaum

[Bioc-devel] BiocStyle::doc_date() not found when testing on Travis via metacran/r-builder

Hi, I was going to ask this as an issue at the Bioconductor/BiocStyle repo, but the issue tracker is disabled. I ran into a bug which I'm not sure where it comes from. It happens during R CMD build using BiocStyle to generate an html vignette. For example, here is one such error: Quitting from

Re: [Bioc-devel] BiocStyle::doc_date() not found when testing on Travis via metacran/r-builder

I should add that in my local machine I have pandoc 1.13.1 installed. Also, I just noted that metacran/r-builder uses pandoc 1.12.4.2 at https://github.com/metacran/r-builder/blob/master/pkg-build.sh#L17 So this could be a pandoc issue. On Mon, Nov 2, 2015 at 11:07 PM, Leonardo Collado Torres

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

Hi, I recommend using git cherry-pick as Jim described in other threads. You might also want to check out Mike's instructions. You'll find all the links at https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008141.html Cheers, Leo On Mon, Oct 19, 2015 at 5:35 AM, Elena Grassi

Re: [Bioc-devel] Github Bioconductor-mirror not updating for repo's that still had bridges?

wrote: > The git-svn bridge is deprecated and we recommend migrating to the git > mirrors. > At some point the git-svn bridge will no longer be supported. > I will take a look at this. > Dan > > > - Original Message ----- >> From: "Leonardo Collado Torres" <

[Bioc-devel] Github Bioconductor-mirror not updating for repo's that still had bridges?

but that commit is not at https://github.com/Bioconductor-mirror/derfinder/commits/master yet. It's on svn though. Cheers, Leo Leonardo Collado Torres, PhD Candidate Department of Biostatistics Johns Hopkins University Bloomberg School of Public Health Website: http://lcolladotor.github.io

[Bioc-devel] Git-svn: getting it to work while keeping your git history

the svn history to git). It's not super clean, but it works. Or is there another option that I'm missing? Is there any reason why I should not follow Mike's steps? I'm guessing that any alternatives to git-svn will take a while to develop. Thanks, Leo Leonardo Collado Torres, PhD Candidate Department

Re: [Bioc-devel] Git-svn: getting it to work while keeping your git history

git log master > git cherry-pick 52a6636565..408659187 > > git svn dcommit > ``` > > In this way your devel branch remains completely linear (so no conflicts > from git-svn) and you can retain your > full git history in your master branch. > > I hope this makes sense, let

Re: [Bioc-devel] Github Bioconductor-mirror not updating for repo's that still had bridges?

t state soon. > > Jim > > On Thu, Oct 15, 2015 at 12:06 PM, Leonardo Collado Torres <lcoll...@jhu.edu> > wrote: >> >> I know that the git-svn bridge is deprecated as of the new release >> yesterday. I'm migrating to using the git mirror, but they are not >&g

Re: [Bioc-devel] Memory issues with BiocParallel::SnowParam()

be a basis for defining better instrumentation tools for both diagnosis and planning. On Fri, Jul 10, 2015 at 12:23 AM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi, I have a script that at some point generates a list of DataFrame objects which are rather large matrices. I then feed

[Bioc-devel] Tracing a build error on moscato2: could it be that pandoc is not updated?

Hi, I'm trying to reproduce a build error on Windows for derfinder (v1.5.10) shown at http://bioconductor.org/checkResults/devel/bioc-LATEST/derfinder/moscato2-buildsrc.html I'm copying the end of the log here: Warning: running command '"C:/progra˜2/Pandoc/pandoc" +RTS -K512m -RTS

Re: [Bioc-devel] seqlevelsStyle on alternate chromosomes

I've also found https://github.com/dpryan79/ChromosomeMappings useful On Thu, Dec 17, 2015 at 6:40 PM, Hervé Pagès wrote: > Hi Michael, > > On 12/17/2015 02:45 PM, Michael Lawrence wrote: >> >> Seems like seqlevelsStyle<- between e.g. UCSC and NCBI does not work >> outside

Re: [Bioc-devel] git svn trouble on release branch

Hi Kyle, What I've done in your situation is to simply svn checkout the release branch. Then copy the latest files from my local release code into it, then use svn to push it to the Bioc-release trunk. Here's an example using my `derfinder` package: ```bash ## Work somewhere where the

Re: [Bioc-devel] Coverage test badge not updating

y are now > re-enabled. > > Please let us know if you notice any other problems > > Jim > > On Tue, Nov 17, 2015 at 12:16 PM, Leonardo Collado Torres <lcoll...@jhu.edu> > wrote: >> >> Hi, >> >> In my packages I enabled testing (via testt

Re: [Bioc-devel] Issue importing bigwig files with rtracklayer from Amazon Cloud Drive

or zlibbioc 1.19.0 2016-05-05 Bioconductor On Tue, May 31, 2016 at 2:02 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > Thanks for pointing out that buglet. Fixed. > > On Tue, May 31, 2016 at 10:55 AM, Leonardo Collado Torres > <lcoll...@jhu.e

Re: [Bioc-devel] Issue importing bigwig files with rtracklayer from Amazon Cloud Drive

veloper tools. The > error response header claims a JSON content type, but no JSON is actually > sent, so there is no further description of the error. I think this is a bug > in Amazon. > > Seems like for now you'll need to download the file first. > > Michael > > On Thu, M

Re: [Bioc-devel] Issue importing bigwig files with rtracklayer from Amazon Cloud Drive

Awesome, thanks! On Tue, May 31, 2016 at 4:11 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > Sure, done. > > On Tue, May 31, 2016 at 11:18 AM, Leonardo Collado Torres > <lcoll...@jhu.edu> wrote: >> Hi Michael, >> >> Thanks! >> >&

Re: [Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

email? (off list is fine) > > On Fri, Jun 17, 2016 at 1:44 PM, Leonardo Collado Torres <lcoll...@jhu.edu > > wrote: > >> Hi, >> >> I'm trying to figure out what is going wrong with an error that pops >> up on Windows only. It's currently the only error fo

Re: [Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

Thanks Martin! Using mode='wb' solved the issue. On Sat, Jun 18, 2016 at 10:41 AM, Martin Morgan <martin.mor...@roswellpark.org> wrote: > On 06/18/2016 12:58 AM, Leonardo Collado Torres wrote: >> >> Hi, >> >> I get the same error while hosting the data somewhere e

Re: [Bioc-devel] Some granges() accessors broken in devel

I was going to say that for the tutorial users it might be easier to use devtools::install_github('Bioconductor-mirror/GenomicRanges') rather than svn. However, from https://github.com/Bioconductor-mirror/GenomicRanges/blob/master/DESCRIPTION#L13 you can see that it's outdated. On Mon, Jun 20,

[Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

Hi, I'm trying to figure out what is going wrong with an error that pops up on Windows only. It's currently the only error for a package that I recently submitted to Bioc. The function is fairly simple: it downloads a Rdata file from the web and loads it. If I try to download and load the file

Re: [Bioc-devel] Out of sync repo between svn and the Bioc git mirror

Thanks! On Wed, Feb 3, 2016 at 3:09 PM, Dan Tenenbaum wrote: > Should be in sync now. > Dan > > > - Original Message - >> From: "lcollado" >> To: "bioc-devel" >> Sent: Wednesday, February 3, 2016 12:06:22 PM >>

[Bioc-devel] Out of sync repo between svn and the Bioc git mirror

Hi, I noticed that https://github.com/Bioconductor-mirror/derfinder/commits/master is out of sync with svn. The latest commit there starts with "v1.5.19". But if I do: svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinder svn log | head I see that there is one more commit

Re: [Bioc-devel] BiocInstaller not supporting R 3.4.0 -- yes, it's early, but shouldn't it default to using Bioc-devel instead of Bioc-release in this scenario?

Check Jim Hester's thoughts on this issue https://github.com/travis-ci/travis-ci/issues/5809#issuecomment-199858950 One way of solving it is by having BiocInstaller allow using Bioc-devel with R 3.4.0. On Tue, Mar 22, 2016 at 10:43 AM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote

Re: [Bioc-devel] BiocInstaller not supporting R 3.4.0 -- yes, it's early, but shouldn't it default to using Bioc-devel instead of Bioc-release in this scenario?

versions of Bioconductor will use the R-3-3-branch, because that will be the > 'user' version of R available for both the 3.3 and 3.4 releases of > Bioconductor. > > Thanks for the request, Leo. > > Martin > > > On 03/22/2016 11:24 AM, Leonardo Collado Torres wrote: >&

Re: [Bioc-devel] NAMESPACE issue in bumphunter

>> Index: NAMESPACE >> === >> --- NAMESPACE (revision 115247) >> +++ NAMESPACE (working copy) >> @@ -19,6 +19,7 @@ >> importFrom(GenomicRanges, GRanges, makeGRangesFromDataFrame) >> import

[Bioc-devel] NAMESPACE issue in bumphunter

-19,6 +19,7 @@ importFrom(GenomicRanges, GRanges, makeGRangesFromDataFrame) importMethodsFrom(GenomicRanges, sort) importFrom(locfit, locfit) +importFrom(locfit, lp) importFrom(utils, data, packageDescription) importFrom(parallel, mclapply, stopCluster) importFrom(GenomicFeatures, exonsBy, cdsBy, transcriptsBy

Re: [Bioc-devel] ggbio error

Hi, ggbio's error also cause some of my packages to fail the latest build. But I'm confident it'll get fixed before the release. Best, Leo On Sat, Apr 2, 2016 at 4:48 AM, Ludwig Geistlinger wrote: > Hi, > > I am wondering whether this is only something

Re: [Bioc-devel] FDR estimation for Biological ChIP-Seq replicate in the context of GRanges.

I see that you posted this at https://support.bioconductor.org/p/80782/ which is more appropriate for your question than this mailing list. On Wed, Apr 13, 2016 at 10:28 AM, Jurat Shayidin wrote: > Hi, BioC devel: > > I have been working on my packages and it is about to

Re: [Bioc-devel] Custom build of packages

You could also run tests on Travis CI. That's what I do for my packages. See https://travis-ci.org/lcolladotor/derfinder and https://github.com/lcolladotor/derfinder/blob/master/.travis.yml for an example. If you want to use Travis, check the main docs https://docs.travis-ci.com/user/languages/r

Re: [Bioc-devel] new download stats

Awesome, thanks Hervé! Cheers, Leo On Thu, May 12, 2016 at 1:55 PM, Hervé Pagès wrote: > Hi, > > We've refactored the download stats a little: > > https://bioconductor.org/packages/stats/ > > 2 new visible features are (1) yearly stats since 2009 to present > and (2)

Re: [Bioc-devel] Version numbers incremented?

Hi, Does your package use knitr for creating the vignettes? If so, it must be because of https://github.com/lcolladotor/derfinder/commit/c70ede92fb14e83a0fe0032353f7f897ff55b5d5 (the equivalent commit for your package). Best, Leonardo On Tue, May 17, 2016 at 4:18 AM, Ulrich Bodenhofer

Re: [Bioc-devel] 3.3 branch created

Hi Dan, Everything looks great! Thanks for all the hard work!! My one question is regarding when we can resume using https://github.com/Bioconductor-mirror/. Right now https://github.com/Bioconductor-mirror/derfinder and

Re: [Bioc-devel] R CMD check error related to data docs in a new package

Awesome, thanks Martin! You make it look easy! On Thu, May 5, 2016 at 6:08 AM, Martin Morgan <martin.mor...@roswellpark.org> wrote: > > > On 05/05/2016 02:05 AM, Leonardo Collado Torres wrote: >> >> Hi, >> >> I need some help with a new package I'm coding

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

Hi, I had the same error at derfinder's devel build report yesterday morning (v1.7.0), and it went away on the build from yesterday afternoon (v1.7.1). Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", : It seems you should call rmarkdown::render() instead of

[Bioc-devel] R CMD check error related to data docs in a new package

Hi, I need some help with a new package I'm coding (which we plan to submit to BioC). I keep getting a warning in R CMD check that I haven't been able to figure out what is wrong. I'm guessing that it's something fairly straightforward, I'm just not seeing it right now. The warning is: checking

[Bioc-devel] Issue importing bigwig files with rtracklayer from Amazon Cloud Drive

Hi Michael, I have a use case that is similar to https://support.bioconductor.org/p/81267/#82142 and looks to me like it might need some changes in rtracklayer to work. That's why I'm posting it here this time. Basically, I'm trying to use rtracklayer to import a bigwig file over the web which

Re: [Bioc-devel] Issue importing bigwig files with rtracklayer from Amazon Cloud Drive

gt; rtracklayer finds it during its build process. > > Michael > > On Thu, May 5, 2016 at 2:01 PM, Leonardo Collado Torres <lcoll...@jhu.edu> > wrote: >> >> Hi Michael, >> >> I have a use case that is similar to >> https://support.bioconductor.org/p/

[Bioc-devel] Zenodo DOIs for packages released (every 6 months, tied to the Bioc release)

away from the papers (if a package has been described in a paper) to the Zenodo DOIs. That is, would someone cite the paper and the package DOI? Or just one of the two? Anyhow, it got me curious and would like to know what others think about it. Best, Leo Leonardo Collado Torres, PhD Candidate

Re: [Bioc-devel] Zenodo DOIs for packages released (every 6 months, tied to the Bioc release)

Err, had a few typos. Sorry! On Fri, Apr 15, 2016 at 3:59 PM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > Hi, > > I looked at https://guides.github.com/activities/citable-code/ after > reading http://biorxiv.org/content/early/2016/04/15/048744 (Laurent > Ga

Re: [Bioc-devel] Minor issue with rtracklayer

3.98-1.4 2016-03-01 CRAN (R 3.3.0) XVector0.13.6 2016-07-08 Bioconductor zlibbioc 1.19.0 2016-05-05 Bioconductor > Importing getCurlInfo from RCurl in the namespace should fix this. Thanks, Leo On Wed, Jul 13, 2016 at 4:05 PM, Leonardo Collado Torres <lcoll...@jh

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

Thanks Dan for finding the /tmp/udcCache error and fixing it! I assume that recount will build properly next time. The error related to SRP009615-results.Rmd is likely related to https://github.com/leekgroup/recount/blob/master/vignettes/Makefile. I'm using that Makefile trick to include the

Re: [Bioc-devel] Minor issue with rtracklayer

<lawrence.mich...@gene.com> wrote: > Thanks, made the change. > > On Wed, Jul 13, 2016 at 12:28 PM, Leonardo Collado Torres > <lcoll...@jhu.edu> wrote: >> Hi, >> >> I have a simple issue with rtracklayer::import.bw() which I believe >> can b

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

Hi, Currently the build for `recount` is failing in the Linux build machine http://www.bioconductor.org/checkResults/3.4/bioc-LATEST/recount/zin1-buildsrc.html. It's been failing with the same error message for a while. The build message ends with: Setting

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

Thanks Dan! On Wed, Jun 29, 2016 at 3:54 PM, Dan Tenenbaum wrote: > Indeed, you are right, Leo. I was able to identify the thing that had changed > and to restore it to its previous behavior. It should now behave as before, > only updating the rss feed when the build

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

Hi, recount has built well on the last 2 builds (Aug 14 and 11th) on Linux and I see that now https://bioconductor.org/packages/devel/bioc/html/recount.html is up. My guess is that the directory that Dan removed fixed things in time for the Aug 11th build. Thanks again! Best, Leo On Fri, Aug

[Bioc-devel] GenomicFeatures::makeTxDbFromGFF leads to a S4Vectors error

Hi, I think that a recent change in S4Vectors broke GenomicFeatures::makeTxDbFromGFF(). I ran this code about a week ago without problems, but it's failing now. Best, Leo ## Unevaluated code library('GenomicFeatures') library('devtools') txdb <-

[Bioc-devel] Citation info not displayed correctly

Hi, I'm wondering why the citation info for recount is not shown properly at http://bioconductor.org/packages/devel/bioc/html/recount.html. For example, http://bioconductor.org/packages/devel/bioc/html/derfinder.html is working well. You can also see at

Re: [Bioc-devel] Citation info not displayed correctly

Thanks for looking into this Martin! Best, Leo On Thu, Aug 25, 2016 at 12:14 AM, Martin Morgan <martin.mor...@roswellpark.org> wrote: > On 08/24/2016 09:45 PM, Leonardo Collado Torres wrote: >> >> Hi, >> >> I'm wondering why the citation info for recount

Re: [Bioc-devel] Citation info still not displayed correctly for some packages

Hi Ramon, I also noticed this earlier https://stat.ethz.ch/pipermail/bioc-devel/2016-August/009640.html and Martin said that they are working on fixing it. Best, Leo On Mon, Aug 29, 2016 at 5:40 PM, Ramon Diaz-Uriarte wrote: > > Dear All, > > At least for some packages >

Re: [Bioc-devel] Merging two CharacterList objects doesn't work in Bioc-devel

Thanks Hervé for fixing this! Best, Leo On Sat, Sep 10, 2016 at 5:47 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Leonardo, > > Not really intended. Should be addressed in S4Vectors 0.11.14. > > Cheers, > H. > > > On 09/08/2016 12:14 PM, Leonar

[Bioc-devel] Merging two CharacterList objects doesn't work in Bioc-devel

Hi, With Bioc-release I can run without problems the following code: library('GenomicRanges') l <- CharacterList(list(NA, NA, '1', '2')) r <- CharacterList(as.list(letters[1:4])) tmp <- merge(l, r, all = TRUE) However, it gives an error with Bioc-devel: Error in V_recycle(value, x, x_what =

Re: [Bioc-devel] Availability shield URLs

Awesome, thanks Dan! On Tue, Nov 8, 2016 at 9:40 AM, Martin Morgan <martin.mor...@roswellpark.org > wrote: > On 11/02/2016 11:54 AM, Leonardo Collado Torres wrote: > >> Hi, >> >> I'm just curious why >> http://www.bioconductor.org/shields/availability/rel

Re: [Bioc-devel] github-mirror of ensembldb out of sync with BioC svn

Hi, The same is true for recount and regionReport. derfinder and my other packages are in sync though. Best, Leo On Wed, Oct 19, 2016 at 3:34 AM, Rainer Johannes wrote: > I just wanted to report that the github-mirror for ensembldb is out of > sync with the BioC

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