Remember also that there are overall evaluation time limits.
One strategy might use existing stable publicly available SC data sets
from e.g.,
http://imlspenticton.uzh.ch:3838/conquer/
https://hemberg-lab.github.io/scRNA.seq.datasets/
These could be downloaded using BiocFileCache as a
I think it's a Mac thing, and it's decided to install binary (tgz), and
the annotation packages are source (tar.gz).
Have you set options(pkgType = "both") ?
On 07/20/2018 08:40 AM, Levi Waldron wrote:
I think the problem I was actually having was that
BiocManager::install("githubuser/repo")
the DESCRIPTION file yesterday, but the change is not reflected in
the
manual of the package.
Ahrim
On 6/30/18, 11:32 AM, "Martin Morgan"
wrote:
(cc'ing bioc-devel, where questions like this should be posted so other
developers can benefit / contribute)
I see
commit 5fea2c1f2e0f3407cb6804db6
I'm not able to confirm this, but since BiocManager::install() uses
remotes::install_github() when it sees a pattern "foo/bar", I think
BiocManager::install("foo/bar", dependencies = TRUE) will behave as
desired.
For local installs, I think we end up at utils::install.packages(),
where the
recent build started.
Martin
Thank you again,
On Monday, May 21, 2018 18:58 CEST, Hervé Pagès
wrote:
On 05/21/2018 05:50 AM, Martin Morgan wrote:
> Remember that 32-bit Windows can only address vectors that are less than
> 2^32 - 1 elements long -- it looks like your example is
butions/issues/787 ).
Thanks,
Koki
*差出人:* Bioc-devel が 露崎 弘毅
の代理で送信
*送信日時:* 2018年6月28日 20:56
*宛先:* Martin Morgan; Bioc-devel@r-project.org
*件名:* Re: [Bioc-devel] About Adding SSH Keys to GitHub Account
Hi, Martin
(cc'ing bioc-devel, where questions like this should be posted so other
developers can benefit / contribute)
I see
commit 5fea2c1f2e0f3407cb6804db638b565e0a2ea5dd
Author: Ahrim Youn
Date: Fri Jun 22 16:34:02 2018 -0400
update version number
DESCRIPTION | 2 +-
On 06/29/2018 06:44 PM, Paul Shannon wrote:
My package RCyjs reads an html/js/css file when the constructor is called, then
sends that file to the user’s browser.
The actual path to that file is calculated at global scope in RCyjs-class.R:
cyjsBrowserFile <-
Hi Koki --
The 'moderation' step requires a human to actually look at your
repository. Usually it is quick, but sometimes it can take up to a day.
Your package has been moderated and a reviewer assigned to it; further
instructions (basically, wait for up to two weeks while the reviewer
looks
My general approach is to make the build report as clean as possible, so
that (a) it's easy to see true positives and (b) I'm not provoked by
notes / warnings that I think of as irritating more than useful each
time I look at the build report :) . So yes, I'd recompress the data.
Martin
On
yes it would be useful to post this to R-devel as a 'using
parallel::makeCluster() question, removing BiocParallel from the
equation, where some general insight might be had...
Martin
On 06/13/2018 05:00 PM, Dario Strbenac wrote:
Good day,
I couldn't get a working param object. It never
It's more likely that it never starts, probably because it tries to
create socket connections on ports that are not available, or perhaps
because the file path to the installed location of the BiocParallel
package is on a network share, or the 'master' node needs to be
specified with an IP
On 06/07/2018 04:56 AM, Joris Meys wrote:
Dear all,
the following issue drew my attention. The new package "conflicted"
manipulates the search path and by doing so, highlighted that Rcpp is using
the BiocGenerics version of evalq() in case BiocGenerics is loaded.
Otherwise it uses the base
There is no cache; like users you get the 'current' version of the
package from the relevant repository. If your package used
concatenateObjects, then it needs to be updated. If your package is
broken through a third package, it needs to be fixed (perhaps it has
been but did not propagate, see
Save these under a folder inst/, conventionally inst/extdata/.
Access them using
system.file(package="YourPackage", "extdata", "")
Martin
On 05/23/2018 06:44 PM, Jordan Bisanz wrote:
Hello,
I have a developed a package called qiime2R which serves to facilitate the
analysis of files from
On 05/22/2018 05:46 AM, Sokratis Kariotis wrote:
Hi all,
After lots of tries we decided to follow your second suggestion. How can we
stop the support for 32-bit windows?
An obvious place to start is with a less comprehensive example data set;
> geo_sum_data
class: SummarizedExperiment
dim:
Remember that 32-bit Windows can only address vectors that are less than
2^32 - 1 elements long -- it looks like your example is trying to do
more than this, and the solution is to implement a more modest example.
Martin
On 05/18/2018 04:05 AM, Sergio Picart Armada wrote:
Dear Bioconductor
You can create a plain text file in the root directory of your package
.BBSoptions with the line
UnsupportedPlatform: win
Your package will not be available on Windows, losing about 1/2 your
potential audience. A better strategy is to figure out why you are
Suggests:'ing Rsubread, and find
On 05/18/2018 03:28 AM, Neumann, Steffen wrote:
Hi,
On Wed, 2018-05-09 at 18:11 -0400, Martin Morgan wrote:
...
- version() version of Bioconductor in use
- valid() are all Bioconductor packages from the same
Bioconductor
version?
I'd like to challenge the concept of the release
On 05/16/2018 10:23 AM, Nicolas Descostes wrote:
Dear Martin,
I am starting using BiocInstaller. Regarding the BiocManager::valid(),
would it be possible to retrieve a list with one element being a vector of
the packages to update? or to run BiocManager() as we do with biocLite()?
Running
One of your cell files is funky
> colSums(exprs(alldata) == 0)
GSM907854.CEL.gz GSM907866.CEL.gz GSM907857.CEL.gz GSM907863.CEL.gz
000 686388
GSM907856.CEL.gz GSM907862.CEL.gz GSM907855.CEL.gz GSM907861.CEL.gz
0
Installer (I removed BiocInstaller
from my library) for either the release or devel version of Bioconductor.
Please post issues / pull requests / etc to the github repository
https://github.com/Bioconductor/BiocManager
Martin
On 05/09/2018 06:11 PM, Martin Morgan wrote:
Developers --
A
Thank you, the reproducible example helps one think through things.
For what it's worth the warning can be generated via
> tools:::.check_Rd_xrefs(dir = "~/Downloads/Tester")
Looking at the code and reflecting on the issue, since limma is in the
Suggests: field, it is not guaranteed to be
On 05/11/2018 06:00 PM, Dario Strbenac wrote:
Good day,
limma was installed using biocLite, so it would be built before R CMD check was
run. I could summarise all of the relevant information and send to
R-package-devel mailing list to check if it is a bug.
the 'relevant information' needs
On 05/11/2018 01:37 PM, Kenneth Condon wrote:
Hi all,
I'm hoping to submit my package soon. But I am having issues with the
vignette.
R CMD check results0 errors | 1 warning | 0 noteschecking files in
‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
I'm not really sure about this, but Writing R Extensions says about
these forms of \link that they are seldom needed, except when linking to
"not-yet-installed packages". I think if you were to have installed
limma without first building it (e.g., R CMD INSTALL limma rather than R
CMD INSTALL
On 05/11/2018 01:00 AM, Dario Strbenac wrote:
Good day,
I have documented a parameter that is linked to lmFit's documentation.
\item{...}{Optional settings that are passed to \code{\link{lmFit}}.}
The package checking process displays a warning.
* checking Rd cross-references ... WARNING
Bioconductor, so there
can only be one BiocInstaller. BiocInstaller as it exists in
Bioconductor supports two different interfaces to package management
already ('legacy' biocLite, plus more recent BiocInstaller::biocLite())
and has 15 years of code; it is better to start with a clean implementat
ager seems the most sober of the lot. And
thematically appropriate - you might have an orchestra and conductor,
but you still need a manager to get everyone paid, fed and on the stage.
-Aaron
Martin Morgan wrote:
Developers --
A preliminary heads-up and request for comments.
Almost since project
or current and past
versions of Bioconductor. Going forward, it would go through a cycle of
deprecated and defunct.
Martin
-Ryan
On Wed, May 9, 2018 at 3:29 PM Martin Morgan
<martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>>
wrote:
Developers --
Developers --
A preliminary heads-up and request for comments.
Almost since project inception, we've used the commands
source("https://bioconductor.org/biocLite.R;)
biocLite(pkgs)
to install packages. This poses security risks (e.g., typos in the url)
and deviates from standard R package
The scholarships support up to $500 travel. The scholarship also covers
accommodation and registration.
A letter inviting you to the conference will be sent separately.
Martin
On 05/09/2018 01:13 AM, Pijush Das wrote:
Dear Martin Morgan,
Thank you Morgan for informing me to join your
On 05/08/2018 02:58 AM, Anand MT wrote:
Hi Developers,
I maintain Bioconductor package maftools, which has been failing to build on
WIndows platform since it the new release. Error seems to be originating while
running examples with the below error.
base::assign(".ptime", proc.time(), pos
On 04/30/2018 08:17 AM, Kasper Daniel Hansen wrote:
Still, it is convenient for some of us to have copy+paste code on the
landing page. How about having both https and ssh?
Supporting https:// would require account and password management. I
guess we have moved closer to that than
17, see
http://bioc2018.bioconductor.org/call-for-abstracts
http://bioc2018.bioconductor.org/scholarships
Martin Morgan
Bioconductor
This email message may contain legally privileged and/or...{{dropped:2}}
___
Bioc-devel@r-project.org mailing
b.com/Bioconductor/Contributions/issues/713
<https://github.com/Bioconductor/Contributions/issues/713>
The link is not opening. Is there any problem in github repository?
Please check it.
Thank you
regards
Pijush
On Thu, A
But that issue will be fixed, so Tim's advice is inappropriate.
On 04/30/2018 10:42 AM, Tim Triche, Jr. wrote:
Don't do that. Seriously, just don't.
https://github.com/Bioconductor/DelayedArray/issues/16
--t
On Mon, Apr 30, 2018 at 10:02 AM, Elizabeth Purdom <
epur...@stat.berkeley.edu>
For what it's worth, BiocParallel implemented as outlined in it's
vignette limits the number of cores via
if (nzchar(Sys.getenv("BBS_HOME")))
cores <- min(4L, cores)
i.e., checking an environment variable set on the build system. This is
highly fragile and I wouldn't necessarily
of changes in the original code.
So should we submit our package (sigFeature) as a new submission
or replace the contents of existing git repository with version
increment.
regards
Pijush
On Mon, Apr 16, 2018 at 5:01 PM, Martin Morgan <
in
On 24.04.2018 15:39, Martin Morgan wrote:
I don't see vignette warnings on the build report.
You should address the simple namespace issue by adding
importFrom("stats", "dnbinom", "kmeans", "optim", "ppois")
to your NAMESPACE fi
Results/3.7/bioc-LATEST/STAN/malbec2-checksrc.html
on my linux machine. The check runs smoothly, any idea why so?
Thank you again,
Rafael
On 11.04.2018 16:52, Martin Morgan wrote:
On 04/11/2018 10:47 AM, campos wrote:
Hi Martin,
when I run git status I get this:
On branch master
Your
It's not obvious or easy to test, and not meant cynically, but pull
requests welcome
https://github.com/Bioconductor/BBS/blob/master/3.8/report.js
and FWIW there is the single package version
https://bioconductor.org/checkResults/devel/bioc-LATEST/mzR
Martin
On 04/19/2018 08:53 AM,
On 04/18/2018 02:45 PM, Vincent Carey wrote:
On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan
<martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>>
wrote:
On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:
Dear Martin,
On Fri, 06-April
Also FWIW changing things like (there are a number of these changes)
sum(unlist(lapply(data, length)))/1e+06
to
sum(lengths(data)) / 1e6
actually has measurable effect on the speed of your code.
Martin
On 04/18/2018 10:47 AM, Carmen M. Livi wrote:
Dear Martin Morgan,
ok, I
I'm sorry not to respond to your first email. This is a problem in
BiocParallel that I am working on. In your particular case, where you
are relying on a third-party package that uses parallel::mclapply, I
think you should revert to using that.
Martin
On 04/18/2018 09:22 AM, Carmen M. Livi
If you are still having problems understanding warnings, it is probably
better to use the github issue -- it may take some time to get an
answer, because the reviewers have many responsibilities.
It looks like your 'webhook' is not correct, and that you are not
changing the version of your
I made a clean 'read only' clone of your git repository
git$ git clone https://git.bioconductor.org/packages/TissueEnrich
then tried to build it
git$ Rdev CMD build TissueEnrich
Bioconductor version 3.7 (BiocInstaller 1.29.6), ?biocLite for help
* checking for file 'TissueEnrich/DESCRIPTION'
Hi Klara --
You have code structured like
out <- tryCatch({
response = httr::GET(url)
...
}, error = function(cond) {
...
... htr::http_status(response)$message
})
so if GET() fails, response is undefined; I guess this is what happened,
the "why" is a mystery
The solution is, in the NAMESPACE, to import only those functions used
importFrom(SummarizedExperiment, "start", "end")
importFrom(stats, "mean")
or to import everything but
importFrom(stats, except = c(start, end))
or to explicitly resolve symbols in the code and not mention them in
On 04/14/2018 07:21 AM, Vincent Carey wrote:
But Annotated is defined in S4Vectors and RNeXML; the latter is not a
Bioconductor package.
The likelihood of collisions among class names defined in different
packages seems pretty high
as S4 adoption grows. So requiring a systematic approach to
STAN-knitr.R
1c4f140 upgrade version 2.7.3
if you don't, then I guess `git pull` or more pedantically `git fetch
origin; git merge origin/master master`.
Martin
Thanks a lot,
Rafa
On 11.04.2018 16:43, Martin Morgan wrote:
On 04/11/2018 09:58 AM, campos wrote:
Hi Martin,
thank you
end; you should git pull and not worry about pushing any further
commits for the moment.
Best,
Rafa
PS: If you ever stop by Cologne please let me know. I owe you a beer or
two!
tasty!
Martin
On 10.04.2018 23:44, Martin Morgan wrote:
Hi --
I'm not sure what you mean; the 'devel
I *think* this is back up; you could do a version bump or resubmit the
web hook (go to your repository --> settings --> webhooks -> edit ->
'Redeliver' the event with 'X-GitHub-event: push').
Thanks for the heads-up
Martin
On 04/10/2018 06:09 PM, Paul Shannon wrote:
Maybe this is already
Hi Aimin -- the problem is that your vignette has two VignetteEngine
commands in it
PathwaySplice/vignettes master$ grep VignetteEngine *
tutorial.Rmd: %\VignetteEngine{knitr::rmarkdown}
tutorial.Rmd: %\VignetteEngine{knitr::knitr}
Also, please avoid writing to files in the user system,
changed??
Thank you very much,
Rafael
On 10.04.2018 11:33, Martin Morgan wrote:
On 04/10/2018 05:27 AM, campos wrote:
Hi Martin,
Thank you very much, I am a bit concerned about the option of:
Last Changed Date: 2018-04-05 09:37:37 -0400 (Thu, 05 Apr 2018)
I did a change yesterday
This page was generated on 2018-04-09 09:50:05 -0400 (Mon, 09 Apr 2018).
Snapshot Date: 2018-04-08 16:45:28 -0400 (Sun, 08 Apr 2018)
If you pushed after the snapshot date then your changes are not yet visible.
Martin
Best,
Rafa
On 09.04.2018 16:44, Martin Morgan wrote:
I'll try
On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:
Dear Martin,
On Fri, 06-April-2018, at 18:59:00, Martin Morgan
<martin.mor...@roswellpark.org> wrote:
On 04/06/2018 10:44 AM, Lluís Revilla wrote:
I have recently faced a similar warning.
This is when a link to a help page of a
the last change date was friday. Any idea what is the problem?
I have tried to fix the problems with memory and all you told me.
Best,
Rafael
On 03.04.2018 17:06, Martin Morgan wrote:
> Please use 'reply all' so that the mailing list remains engaged.
>
> Check out the release schedul
On 04/06/2018 10:44 AM, Lluís Revilla wrote:
I have recently faced a similar warning.
This is when a link to a help page of another package is broken (there is
not such help page). Although those could be false positives:
mclapply help page does exists in parallel package.
as.MAList does
It seems like this has 'gone away', was that something you did, or...?
On 04/02/2018 04:34 PM, Vincent Carey wrote:
for two host-types I am seeing an error that I do not know how to address
Loading required package: ontologyIndex
sh: line 1: 76907 Abort trap: 6 'convert'
e no problems. I pushed
yesterday the changes, was I still on time for the new release? We want
to publish the changes and it would be really helpful if the package is
running on Bioconductor.
Thank you very much,
Rafael
On 02.04.2018 02:51, Martin Morgan wrote:
On 04/01/2018 08:06
On 04/01/2018 08:06 PM, Martin Morgan wrote:
On 04/01/2018 03:53 PM, campos wrote:
Dear Martin,
I am trying to fix this problem but I am really lost... Do you mean
C++ code? Becasue there is no C code in the whole package. I really
don't know what the problem might be.
Please keep
ld also help to
clean up the C code so that it compiles without warnings with the
-Wall -pedantic flags
Martin
Best,
Rafael
On 28.03.2018 01:08, Martin Morgan wrote:
When I try and install the version on the master branch of the
Bioconductor git repository I get
STAN master$ R
, Martin Morgan wrote:
When I try and install the version on the master branch of the
Bioconductor git repository I get
STAN master$ Rdev --vanilla CMD INSTALL .
* installing to library ‘/home/mtmorgan/R/x86_64-pc-linux-gnu-library
...
** testing if installed package can be loaded
Error: package
Hi Vivek...
On 03/29/2018 08:39 AM, Vivek Bhardwaj wrote:
Dear All
I have travis and appveyor CI running for my upcoming package in
development. I find that the appveyor CI fails for the function
`GenomicAlignments::summarizeOverlaps`, which is called by one of the
functions in my package. It
ase?
yes the changes committed today will be available in the next release.
Martin
Best,
Ding
2018-03-28 11:45 GMT-04:00 Martin Morgan <martin.mor...@roswellpark.org
<mailto:martin.mor...@roswellpark.org>>:
On 03/28/2018 11:19 AM, Hongxu Ding wrote:
Thank you very m
mps associated with the release.
Martin
Thank you very much!
Ding
2018-03-28 4:05 GMT-04:00 Martin Morgan <martin.mor...@roswellpark.org
<mailto:martin.mor...@roswellpark.org>>:
On 03/27/2018 11:14 AM, Hongxu Ding wrote:
Dear Nitesh,
I think I have similar proble
On 03/27/2018 11:14 AM, Hongxu Ding wrote:
Dear Nitesh,
I think I have similar problem...
I tried to push some updates to Bioconductor using *git push upstream
master *and having the following problem*:*
*To git.bioconductor.org:packages/iterClust.git ! [rejected]master
->
When I try and install the version on the master branch of the
Bioconductor git repository I get
STAN master$ Rdev --vanilla CMD INSTALL .
* installing to library ‘/home/mtmorgan/R/x86_64-pc-linux-gnu-library
...
** testing if installed package can be loaded
Error: package or namespace load
On 03/27/2018 12:11 PM, Mike Smith wrote:
I'm trying to do some auditing on how frequently questions are asked about
the packages I maintain (and also maybe whether I answer them). I can't
see anything in the forum API
(https://support.bioconductor.org/info/api/) about
tags but I thought
On 03/21/2018 10:14 AM, Henrik Bengtsson wrote:
A few quick comments:
* I don't think the limit was hardened in R 3.4.0; maybe you started to
experience it sound then because more dependent packages started to rely on
more DLLs?
* The limit is OS/platform specific so it's not that R core is
On 03/19/2018 01:45 PM, Marcel Ramos wrote:
Hi Kornel,
I downloaded your package from our git repo and ran check locally on
Windows 7.
It seems like there are some issues with the `data.table` (version
1.10.4-3) package.
Here is my result for the `i386` architecture:
R CMD check
On 03/10/2018 09:03 AM, Pariksheet Nanda wrote:
Hi Claris,
On Sat, Mar 10, 2018 at 2:49 AM, Claris Baby via Bioc-devel <
bioc-devel@r-project.org> wrote:
[1] "The following files are over 5MB in size:
'dataset/Caenorhabditis_elegans.WBcel235.dna.chromosome.I.fa'."
This as well as other
On 03/05/2018 11:53 AM, August Guang wrote:
I got approval from the SeqAn (www.seqan.de) team to repackage their
headers for easy use in a few other R packages I am writing. This package
has been called RSeqAn. (https://github.com/compbiocore/RSeqAn)
However, SeqAn doesn't have support for
On 03/03/2018 06:45 AM, Claris Baby via Bioc-devel wrote:
Dear all,I am trying to build a package for RNA-seq analysis combining
different existing packages in bioconductor and am facing problem while trying
to run
BiocCheck("/home/package_name", `no-check-vignettes`=TRUE)
The error
On 03/01/2018 09:32 AM, Martin, Tiphaine wrote:
hi,
I have a warning under windows (tokay2) for my devel version of my package
(coMET). I am not sure how to answer it:
* checking whether package 'coMET' can be installed ... WARNING
Found the following significant warnings:
Warning:
, DEFormats, and other
packages.
The Bioconductor core team really appreciates the help and first-rate
work that Andrzej has done, and wishes him the best as he transitions to
a new position.
Martin Morgan
Bioconductor
This email message may contain legally privileged and/or...{{dropped:2
if its documented anywhere; the code here
https://github.com/wch/r-source/blob/trunk/src/library/tools/R/build.R#L315-L324
seems to involve processing all vignettes with a single call to create a
new process.
Martin
Lluís
On 28 February 2018 at 15:03, Martin Morgan
<martin.
vignette are available (and conflict
with) packages loaded in the second.
Martin
On 02/28/2018 08:53 AM, Martin Morgan wrote:
On 02/28/2018 05:31 AM, Lluís Revilla wrote:
Dear bioconductor core,
The development version of my package hosted in Github cannot be
build. It
seems that another
On 02/28/2018 05:31 AM, Lluís Revilla wrote:
Dear bioconductor core,
The development version of my package hosted in Github cannot be build. It
seems that another package is loaded when it shouldn't and masks the
functions that are used in the vignette. (In case anyone wants to help here
is
On 02/23/2018 02:24 PM, Nicolas Descostes wrote:
Dear Bioconductor community,
When developing further a package, is the best practice to create a branch
and bump the version when a full new feature is merged or to stay on the
master without bumping when committing temporarily? More generally,
Hi Raymond -- Daniel provides a fix for this and ported it to release,
but it has failed to propagate for complicated git-related reasons. I
believe that installing from source
git clone https://git.bioconductor.org/packages/GenomicRanges
cd GenomicRanges
git checkout RELEASE_3_6
R CMD
Hi Divy --
Please don't be shy about providing specifics, like the package name or
issue!
The additional information is posted as a comment on your contribution
issue ('by email' is no longer inaccurate, it'll be updated).
https://github.com/Bioconductor/Contributions/issues/592
Thanks Thomas, countLines() in ShortRead 1.37.3 and later) will return
numeric() rather than integer() and hence support large files.
Martin
On 02/20/2018 10:08 PM, Thomas Girke wrote:
Dear Martin,
countLines in ShrotRead returns the line counts as integers which appears
to create problems
On 02/12/2018 07:01 AM, Claris Baby via Bioc-devel wrote:
Dear all,I am trying to build a package for RNA-seq analysis combining
different existing packages in bioconductor and am facing problem while trying
to run Check PackageThere is no error but a warning saying
checking Rd
in
Thanks,
Armen
On Thu, Feb 8, 2018 at 7:58 AM, Martin Morgan
<martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>>
wrote:
On 02/07/2018 05:01 PM, Armen Abnousi wrote:
Hi Valerie,
Thanks for your reply. I can make it work using snow I believe.
Date: Thu Feb 8 12:23:04 2018 +0200
Improve vignette and correct DESCRITPTION
has not yet built.
Did you build and check your package (with R-devel and current
Bioc-devel packages) before pushing your commits?
Martin Morgan
On 02/08/2018 01:31 PM, Oghabian, Ali wrote:
Hi again!
On 02/07/2018 05:01 PM, Armen Abnousi wrote:
Hi Valerie,
Thanks for your reply. I can make it work using snow I believe. But the
problem is that all functions in these packages that you have suggested
(including snow; as far as I have seen) return the answer to one node and
then if I want all
Bioc developers!
I've been exploring the Bioconductor nightly builds
http://bioconductor.org/checkResults/
a bit using this in-development package.
https://github.com/mtmorgan/BiocBuildReports
This
rpt <- report()
filter_recent(rpt) %>% print(n = n())
summarizes the packages
On 02/04/2018 10:04 AM, Sean Davis wrote:
Hi, Hillary.
Be sure that the email that you have listed in the maintainer field of the
package matches (exactly) the one that you used to subscribe to the mailing
list. That has gotten me in the past.
another problem is that the mailing list sends
On 02/01/2018 11:09 AM, Shraddha Pai wrote:
Hello BioC group,
I've recently moved my package repo from svn to github. Just noticed that
the changes in the github repo aren't visible in either the release or
devel version of BioC. e.g. I updated the Vignette and the new date on it
should be 8
On 01/31/2018 06:39 PM, Ludwig Geistlinger wrote:
Hi,
I am currently considering the following snippet:
data.ids <- paste0("d", 1:5)
f <- function(x) paste("dataset", x, sep=" = ")
res <- BiocParallel::bplapply(data.ids, function(d) f(d))
Using a recent R-devel on both a Linux machine
On 01/29/2018 02:41 PM, Armen Abnousi wrote:
Hi,
I'm trying to submit my first package. but I'm confused about the location
of the vignettes in my submitted package. It seems like BiocCheck is
expecting the vignettes to go in /vignettes directory but R
3.2+ expects them to go in /inst/doc
On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
GenomicFeatures_1.31.3 imports RMySQL.
I'm having great trouble installing RMySQL from source on a recent MacOS
(10.13.3) with homebrew.
The package's homepage says "The 'RMySQL' package contains an old
implementation based on legacy code from
On 01/23/2018 10:15 AM, Martin Morgan wrote:
On 01/22/2018 07:19 PM, Yuande Tan wrote:
Dear Martin,
I have install git and also built github and created public and
private keys and built config for automatically loading keys into the
ssh-agent and store passphrases in my keychain. my .ssh
Public Health
________
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Martin Morgan
<martin.mor...@roswellpark.org>
Sent: Friday, January 19, 2018 1:54 PM
To: Gabe Becker; Vincent Carey
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-
On 01/19/2018 12:23 PM, Vincent Carey wrote:
good question
some of the discussion on
http://sqlite.1065341.n5.nabble.com/Parallel-access-to-read-only-in-memory-database-td91814.html
seems relevant.
converting the relatively small annotation package content to pure R
read-only tables on the
Bioc developers!
A number of packages in the 'master' branch of their git repository
build and check successfully, but do not propagate to the 'devel'
repository (red light at the extreme right, e.g., ABSSeq; mouse over for
details)
Windows has a different
name.
On both my Linux and Windows boxes it's BamFile-class.
Jim
Best,
Leo
On Tue, Jan 16, 2018 at 4:58 PM, Martin Morgan
<martin.mor...@roswellpark.org> wrote:
On 01/16/2018 10:37 AM, Leonardo Collado Torres wrote:
Hi,
I have been seen warning
On 01/16/2018 04:44 PM, Rupji, Manali wrote:
Hello,
I have recently developed a shiny R package to perform clustering analysis. It
is currently in publication and under review. I wish to also create a
bio-conductor package for the same. Does bio-conductor allow a shiny tool to be
created as
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