Hi BioC-devel,
Since 2018 I've been interacting with rOpenSci's organizers. For those
that don't know, rOpenSci https://ropensci.org/ is a non-profit that
aims to
> make scientific data retrieval reproducible. Over the past seven years we
> have developed an ecosystem of open source tools, we ru
Hi BioC-devel,
I spent some time yesterday getting my Windows laptop ready to debug a
Windows OS-only issue in regionReport (bioc-release 3.10), but
ultimately I couldn't reproduce it. Since the error seems to be some
type of cache, I bumped the version number but it still failed today
and it then
xt:
* linux_reprex_derfinderPlot_output.txt: the example fails here too!
Which makes me even more confused. I mean, it's consistent with
regionReport and the ggbio reprex. However, I then don't understand
why this hasn't failed in the BioC builds.
Best,
Leo
Leonardo Collado Torres, Ph. D.
te a recent fix.
>
> Michael
>
> On Thu, Apr 9, 2020 at 7:11 AM Leonardo Collado Torres
> wrote:
>>
>> Hi BioC-devel,
>>
>> I was able to trace a regionReport error back to ggbio & biovizBase.
>> However, I'm completely clueless as to why (a)
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 a
e:
>>
>> OrganismDbi 1.7.2 (available via biocLite()) has already fixed this so you
>> shouldn't have to change anything.
>>
>> Dan
>>
>>
>> - Original Message -
>> > From: "Tengfei Yin"
>> > To: "Leonardo
is tiny package is then loaded on a
BiocParallel::blapply() call using BiocParallel::SnowParam() which
performs much better than BiocParallel::MulticoreParam() in terms of
keeping the memory under control.
Thank you for your help!
Leo
Leonardo Collado Torres, PhD student
Department of Biostatist
s need to be refactored which
> I'm planning to do this week.
>
> Cheers,
> H.
>
>
>>
>> Limiting imports is unlikely to reduce loading time. It may actually
>> increase it. There are good reasons for it though.
>>
>>
>>
>> On Tue, Jul 8, 2014 a
Hi Tengfei and BioC-devel,
ggbio 1.13.11 fails to load due to recent changes in IRanges'
namespace as shown further below. Basically, some of IRanges previous
code now lives in S4Vectors.
On a recent thread Hervé exposed his view on specific imports versus
importing the whole package (see
https:/
> Date: Wed, 23 Jul 2014 11:33:44 -0700
> From: Martin Morgan
> To: Matthew McCall , Michael Lawrence
>
> Cc: "bioc-devel@r-project.org"
> Subject: Re: [Bioc-devel] Distinction between release and devel
> package websites
> Message-ID: <53d8.1090...@fhcrc.org>
> Content-Type:
On Thu, Jul 24, 2014 at 12:17 AM, Martin Morgan wrote:
> On 07/23/2014 06:41 PM, Leonardo Collado Torres wrote:
>>
>> Finally, regarding the issue of pushing new features to devel versions
>> (and not release), I understand the reasons for doing so. In my case,
>> what
ctors * 0.2.42014-09-14 Bioconductor
sendmailR 1.2.12014-09-21 CRAN (R 3.1.1)
stringr 0.6.22012-12-06 CRAN (R 3.1.0)
XML 3.98.1.1 2013-06-20 CRAN (R 3.1.0)
XVector 0.5.82014-09-07 Bioconductor
zlibbioc
On Tue, Sep 30, 2014 at 11:06 AM, Dan Tenenbaum wrote:
>
>
> - Original Message -
>> From: "Leonardo Collado Torres"
>> To: bioc-devel@r-project.org
>> Cc: "Dan"
>> Sent: Tuesday, September 30, 2014 8:00:53 AM
>> Subject: Cannot int
acklayer make use of the Kent
> C 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 Wind
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
On Fri, Oct 10, 2014 at 11:24 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
>
> "
> dbType
> dbType - not required
&g
Ahh ok! Thanks =)
On Fri, Oct 10, 2014 at 11:28 AM, Martin Morgan 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.
>>
>>
>
Hi,
I know it might be too early for this, but well, given Dan's BioC 3.0
branch announcement
https://stat.ethz.ch/pipermail/bioc-devel/2014-October/006462.html
could you update the options in
https://gitsvn.bioconductor.org/newproject to show the new branch? I
just want to have everything set and
Awesome! Thanks for the info Dan!
On Tue, Oct 14, 2014 at 10:37 AM, Dan Tenenbaum wrote:
>
>
> - Original Message -
>> From: "Leonardo Collado Torres"
>> To: bioc-devel@r-project.org
>> Sent: Tuesday, October 14, 2014 7:05:21 AM
>> Subjec
On Thu, Oct 16, 2014 at 7:42 PM, Dan Tenenbaum wrote:
>
>
>
> - Original Message -
> > From: "Hervé Pagès"
> > To: "Tiphaine Martin" , "Michael Lawrence"
> > , "Dan Tenenbaum"
> >
> > Cc: bioc-devel@r-project.org
> > Sent: Thursday, October 16, 2014 11:43:32 AM
> > Subject: Re: [Bioc-de
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
cov
/genomecov.html
Cheers,
Leo
On Mon, Oct 20, 2014 at 5:45 PM, Hervé Pagès 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
for adding an organism, and then
return the original sequence names.
I have a slightly modified version in derfinder
https://github.com/lcolladotor/derfinder/blob/master/R/extendedMapSeqlevels.R
or
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinder/R/extendedMapSeqlevels.R
wher
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-project.org mailing
who to
>> contact with the required information.
>>
>> My guess is maintai...@bioconductor.org but maybe there's a specific
>> channel for this.
>>
>> Thanks,
>> Leo
>>
>> Leonardo Collado Torres, PhD Candidate
>> Department of Biosta
as expected
>
> fl <- system.file("extdata", "ex1.bam", package="Rsamtools",
>
> + mustWork=TRUE)
>
> library(GenomicAlignments)
> names(scanBamHeader(BamFile(fl))$targets)
>
> [1] "seq1" "seq2"
>
&
On Wed, Oct 22, 2014 at 6:59 PM, Leonardo Collado Torres
wrote:
> Hi Sonali,
>
> The recent changes in GenomeInfoDb (1.3.3) look great!
>
>
>
> On Wed, Oct 22, 2014 at 1:53 PM, Sonali Arora wrote:
>>
>> Hi Leo,
>>
>> To summarize, These are the con
ed it to work with 'JGI2' given
## that this was the output from seqlevelsStyle('T')
> mapSeqlevels('LGI', 'JGI2.F')
[1] "T"
## Although a user could find the correct name
> head(genomeStyles('Populus trichocarpa'), 1)
circu
Hi,
I'm wondering if it's possible to display more than 1 citation entry
on the landing page.
In my particular use case, the package I developed is based on a
proposed statistical framework which is already published. So for now,
we want the citation info to include the details for the software b
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 rele
t; 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
> wrote:
>>
>> Hi,
>>
>> I can't seem to install devel packages
1, 2014 at 1:57 PM, Dan Tenenbaum wrote:
>
>
> - Original Message -
>> From: "Leonardo Collado Torres"
>> To: bioc-devel@r-project.org
>> Cc: "Jeff Leek"
>> Sent: Friday, October 31, 2014 4:05:11 AM
>> Subject: [Bioc-devel] More t
I believe that this question is better suited for the support site:
https://support.bioconductor.org/
On Thu, Dec 4, 2014 at 2:13 PM, Ian Misner wrote:
> Hello,
>
> I’m working with cummeRbund in R 3.1.1 and I’m trying to get a different
> point size for my csVolcano plot. I’ve tried two approac
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 n
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 'reducin
Welcome Jim! I'm a fan of your knitrBootstrap
https://github.com/jimhester/knitrBootstrap and rex
https://github.com/kevinushey/rex packages! Plus gmailR
https://github.com/jimhester/gmailr
I look forward to your future work at BioC!
Cheers,
Leo
On Fri, Mar 6, 2015 at 3:11 PM, Jim Hester wrote:
Hi,
I noticed that BiocParallel::SnowParam() changed. It now uses the
futile.logger package, but it's only suggested by BiocParallel as seen here
https://github.com/Bioconductor/BiocParallel/blob/master/DESCRIPTION#L19
This leads to some errors as shown at
https://travis-ci.org/lcolladotor/derfind
Forgot to add bioc-devel
On Fri, Apr 3, 2015 at 4:55 PM, Leonardo Collado Torres
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/BrowserV
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
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
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 wrote:
>
>
> - Original Message -
>> From: "Dan Tenenbaum"
>> To: "Leonardo Collado Torres&
hr21
1.202603
It's not the mean of the non-zero positions 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/
_
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 clo
>
>> I'll let Michael answer the summary() question.
>>
>> Valerie
>>
>>
>>
>> On 05/19/2015 12:10 PM, Leonardo Collado Torres wrote:
>>
>>> Hi,
>>>
>>> While playing around with importing BigWig files I found that
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
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 shar
Awesome, thanks Dan!
On Wed, Jun 10, 2015 at 7:21 PM, Dan Tenenbaum wrote:
>
>
> - Original Message -
>> From: "Leonardo Collado Torres"
>> To: bioc-devel@r-project.org
>> Sent: Wednesday, June 10, 2015 4:19:42 PM
>> Subject: [Bioc-devel] C
27;s covr
>> package is released 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
>> wrote:
>> >
>> >
>> > - Ori
https://github.com/leekgroup/derfinderData
On Fri, Jun 12, 2015 at 12:32 AM, Dan Tenenbaum wrote:
>
>
> - Original Message -----
>> From: "Leonardo Collado Torres"
>> To: "Dan Tenenbaum"
>> Cc: bioc-devel@r-project.org
>> Sent: Thursday, Jun
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 wrote:
>
>
> - Original Message -
>> From: "Leonardo Collado Torres"
>&
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 users
On Tue, Jun 16, 2015 at 8:55 PM, Leonardo Collado Torres
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 o
On Tue, Jun 16, 2015 at 10:02 PM, Dan Tenenbaum wrote:
>
>
> - Original Message -
>> From: "Leonardo Collado Torres"
>> To: "Ryan C. Thompson"
>> Cc: "Dan Tenenbaum" , "bioc-devel"
>>
>> Sent: Tuesday
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 --add-au
Hi,
I have a script that at some point generates a list of DataFrame
objects which are rather large matrices. I then feed this list to
BiocParallel::bplapply() and process them.
Previously, I noticed that in our SGE managed cluster using
MulticoreParam() lead to 5 to 8 times higher memory usage a
allows
> replication of
> the condition you are seeing on EC2. This could help with diagnosis and
> might 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
> wrote:
>
#x27;outfile' from snow further with the ability to add messages that can be
> filtered by threshold.
>
> The package also has a new errors/logging vignette:
>
> http://www.bioconductor.org/packages/3.2/bioc/vignettes/BiocParallel/inst/doc/Errors_Logs_And_Debugging.pdf
>
> Valerie
&g
/lcolladotor/SnowParam-memory/blob/gh-pages/logs/snow-3.2.x.o6463213
> https://github.com/lcolladotor/SnowParam-memory/blob/gh-pages/logs/snow-3.2.x.o6463239
>
>
>
> On 07/14/2015 10:23 AM, Leonardo Collado Torres wrote:
>>
>> Hi Valerie,
>>
>> My other recent t
og output for SnowParam and MulticoreParam now includes
> gc(), system.time() and other stats from the workers.
>
> SnowParam(log = TRUE)
>
>
> Valerie
>
>
>
>
> On 07/10/2015 01:12 PM, Leonardo Collado Torres wrote:
>>
>> Hi,
>>
>> I ran my ex
ut this. Maybe
>> you've already gone down this road and there are relatively small
>> default memory allocations per slot so it's necessary to specify h_vmem.
>>
>>
>> I like how you've made information related to this bug report available
>
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.gith
devel" to merge back 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
ridge 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"
>> To: bioc-devel@r-proj
t 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, le
gt; On Thu, Oct 15, 2015 at 12:06 PM, Leonardo Collado Torres
> 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
>> updated for packages that had a bridge.
>>
&
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 wrote:
>> Then
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 it.
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
> wrote:
>>
>>
>>
>> - Original M
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 line
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
Hi,
Thanks for the ideas! It does work when using BiocStyle::doc_date(). I
also have to load BiocStyle immediately after the YAML header.
Otherwise I get an error that functions like Biocpkg() are not found.
Best,
Leo
___
Bioc-devel@r-project.org mailing
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 i
Hi,
I have the same problem with changes I recently made in the devel
branch of `derfinder`. The old vignettes were compiled the last time
on November 4th and the new ones on November 12th. Maybe in the next
1-2 days (with the Wednesday nightly build) the old ones will be
dropped.
Cheers,
Leo
O
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
http://bioconductor.
> Please let us know if you notice any other problems
>
> Jim
>
> On Tue, Nov 17, 2015 at 12:16 PM, Leonardo Collado Torres
> wrote:
>>
>> Hi,
>>
>> In my packages I enabled testing (via testthat) a few weeks ago. I did
>> so as can be seen in
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
derfinder-users
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 of the "standard" chrom
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 'derfinder
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
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
>> Subject: [Bioc-devel] Out of sync repo between svn and the Bioc git mirror
>
ifying that I want
them to be run on R 3.3.0 for now.
I'm guessing that other developers who use R-travis might run into
this issue in these 4 weeks before R 3.3.0 is released.
Best,
Leo
Leonardo Collado Torres, PhD Candidate
Department of Biostatistics
Johns Hopkins University
Bloomber
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
wrote:
> Hi,
>
> This
tor 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:
>>
>&
y)
@@ -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, transcri
=
>> --- NAMESPACE (revision 115247)
>> +++ NAMESPACE (working copy)
>> @@ -19,6 +19,7 @@
>> importFrom(GenomicRanges, GRanges, makeGRangesFromDataFrame)
>> importMethodsFrom(GenomicRanges, sort)
>> importFrom(locfit, locfit)
>> +importFrom(locfit, lp)
>>
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 temporary, but given that
> the new Bioc r
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 close up works except
> F
o them or simply move them 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 Col
Err, had a few typos. Sorry!
On Fri, Apr 15, 2016 at 3:59 PM, Leonardo Collado Torres
wrote:
> Hi,
>
> I looked at https://guides.github.com/activities/citable-code/ after
> reading http://biorxiv.org/content/early/2016/04/15/048744 (Laurent
> Gatto is the 2nd author).
>
&g
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
O
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
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinder/DESCRI
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
Awesome, thanks Martin!
You make it look easy!
On Thu, May 5, 2016 at 6:08 AM, Martin Morgan
wrote:
>
>
> On 05/05/2016 02:05 AM, Leonardo Collado Torres wrote:
>>
>> Hi,
>>
>> I need some help with a new package I'm coding (which we plan to
>> submit
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 is
visible to pkg-config, so that
> rtracklayer finds it during its build process.
>
> Michael
>
> On Thu, May 5, 2016 at 2:01 PM, Leonardo Collado Torres
> wrote:
>>
>> Hi Michael,
>>
>> I have a use case that is similar to
>> https://support.bi
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
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) downloadable stats in tabu
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
wrote:
>
refox's developer 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
&
0.13.0 2016-05-05 Bioconductor
zlibbioc 1.19.0 2016-05-05 Bioconductor
On Tue, May 31, 2016 at 2:02 PM, Michael Lawrence
wrote:
> Thanks for pointing out that buglet. Fixed.
>
> On Tue, May 31, 2016 at 10:55 AM, Leonardo Collado Torres
> wrote:
>> Hi Mich
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