FYI, it appears that packages with periods in their names doesn't work, e.g.
http://bioconductor.org/rss/build/packages/aroma.light.rss
http://bioconductor.org/rss/build/packages/cn.farms.rss
vs
http://bioconductor.org/rss/build/packages/illuminaio.rss
Thanks,
Henrik
On Wed, Aug 7, 2013 at
Hi,
the new Bioconductor 2.13 release, aka BioC 2.13, is out. Previous
release was 2.12 and before that 2.11 and so on. Have you considered
to follow the x.y(.z) version scheme of BioC packages
[http://bioconductor.org/developers/package-guidelines/#versions] for
this too, i.e. letting the
On Wed, Oct 16, 2013 at 12:20 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
- Original Message -
From: Henrik Bengtsson h...@biostat.ucsf.edu
To: bioC-devel bioc-de...@stat.math.ethz.ch
Sent: Wednesday, October 16, 2013 11:11:57 AM
Subject: [Bioc-devel] SUGGESTION: BioC version (e.g
Hi,
in BiocParallel, is there a suggested (or planned) best standards for
making *locally* assigned variables (e.g. functions) available to the
applied function when it runs in a separate R process (which will be
the most common use case)? I understand that avoid local variables
should be
in troubleshooting
and the mailing lists from why doesn't my parallel code not work
messages. Such protection may be better suited for the 'parallel'
package though. Unfortunately, it's beyond my skills/time to pull
such a thing together.
/Henrik
Michael
On Sun, Nov 3, 2013 at 12:39 PM, Henrik
On Mon, Nov 4, 2013 at 12:46 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
- Original Message -
From: Tim Triche, Jr. tim.tri...@gmail.com
To: bioc-devel@r-project.org
Sent: Monday, November 4, 2013 12:25:19 PM
Subject: [Bioc-devel] disappearing .tex file when running R CMD Sweave on
Some quick ideas:
1. Before making the full call, call res - system2(perlbin, -v) to
assert no errors about running Perl itself. If an error, catch it and
given an information message (Failed to run 'perl -v' or something).
That will be user friendly as well for future users who run into
for the report. Martin
On 04/18/2014 06:37 PM, Henrik Bengtsson wrote:
When I re-index Rsamtools::extdata/ex1.bam I get a different and
larger index file:
bam - system.file(extdata, ex1.bam, package=Rsamtools)
bai - system.file(extdata, ex1.bam.bai, package=Rsamtools)
# Reindex
bam2 - basename(bam
On Mon, May 12, 2014 at 1:32 AM, Moritz Gerstung m...@sanger.ac.uk wrote:
Hi all
Following Kasper's idea from a couple of months ago: Would it be possible to
have the git-svn bridge synchronise a branch other than master?
If so, one could use the git subtree command,
git subtree split -P
On Thu, Jul 24, 2014 at 5:34 PM, Hervé Pagès hpa...@fhcrc.org wrote:
Hi Henrik,
On 07/24/2014 06:03 AM, Henrik Bengtsson wrote:
On Thu, Jul 24, 2014 at 3:16 AM, Hervé Pagès hpa...@fhcrc.org wrote:
Hi Andrzej,
On 07/22/2014 02:28 PM, Andrzej Oleś wrote:
Hi Hervé,
thank you
A few questions about the Bioconductor Git-SVN bridge:
Q1. Is it safe to add, delete, add, delete, add, ... a bridge over and
over for the same package and GitHub repository? Not that I want to
do it, but I wonder if I had to, will I break something?
Q2. Can you change the SVN / Git wins
On Sun, Sep 21, 2014 at 1:35 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On September 21, 2014 1:07:29 PM PDT, Henrik Bengtsson
h...@biostat.ucsf.edu wrote:
A few questions about the Bioconductor Git-SVN bridge:
Q1. Is it safe to add, delete, add, delete, add, ... a bridge over and
over
-r 4:HEAD to truncate history to rev4 in svn)
- git push to github
- setup git-svn bridge
- work with git as normal
Sean
On Mon, Sep 22, 2014 at 6:58 PM, Henrik Bengtsson h...@biostat.ucsf.edu
wrote:
On Sun, Sep 21, 2014 at 1:35 PM, Dan Tenenbaum dtene...@fhcrc.org wrote
Maybe you could use
\RequirePackage{Bioconductor}
and then set the TEXINPUTS environment variable via Sys.setenv().
Internally tools::texi2dvi() is used that that listens to TEXINPUTS.
Just FYI: I use this trick in
https://github.com/HenrikBengtsson/R.rsp/blob/master/R/compileLaTeX.R
to
On Mon, Oct 6, 2014 at 5:33 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 10/06/2014 04:52 PM, Henrik Bengtsson wrote:
Maybe you could use
\RequirePackage{Bioconductor}
and then set the TEXINPUTS environment variable via Sys.setenv().
Internally tools::texi2dvi() is used that that listens
On Mon, Oct 6, 2014 at 6:48 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote:
On Mon, Oct 6, 2014 at 5:33 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 10/06/2014 04:52 PM, Henrik Bengtsson wrote:
Maybe you could use
\RequirePackage{Bioconductor}
and then set the TEXINPUTS environment
On Mon, Oct 6, 2014 at 7:03 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote:
On Mon, Oct 6, 2014 at 6:48 PM, Henrik Bengtsson h...@biostat.ucsf.edu
wrote:
On Mon, Oct 6, 2014 at 5:33 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 10/06/2014 04:52 PM, Henrik Bengtsson wrote:
Maybe you could
On Wed, Oct 8, 2014 at 12:20 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 10/08/2014 11:41 AM, Henrik Bengtsson wrote:
You may want to make those function local to latex(). I haven't
verified it works (won't have time), but I bet a beer that it will
work.
I'll take you up on the bet
It's been a while since I worked with experimental packages. Where
can I find documentation on how to (Subversion) update our
AffymetrixDataTestFiles package with additional data files? All I
know is that the SVN repository only contains a stub of the package
and
On Wed, Oct 29, 2014 at 1:07 PM, Vincent Carey
st...@channing.harvard.edu wrote:
On Wed, Oct 29, 2014 at 2:15 PM, Hervé Pagès hpa...@fredhutch.org wrote:
Hi,
On 10/28/2014 08:51 PM, Vincent Carey wrote:
On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès hpa...@fredhutch.org
[Re-posting since messages send to ...@r-project.org bounced for a
period of ~12-14h on Monday Nov 17]
Hi, I've experiences the exact same thing on both a Windows and a
Linux installation. It actually took me a while to realize I didn't
get Bioc devel updates, because I run those in the
Thanks for the quick fix. No need to be sorry. /Henrik
On Fri, Jan 30, 2015 at 9:36 AM, Michael Lawrence
lawrence.mich...@gene.com wrote:
Just checked in the fix to R-devel. No more error, and the warning is also
fixed.
Sorry,
Michael
On Fri, Jan 30, 2015 at 9:29 AM, Henrik Bengtsson h
On Tue, Mar 10, 2015 at 12:30 PM, Martin Morgan mtmor...@fredhutch.org wrote:
On 03/10/2015 11:08 AM, Kasper Daniel Hansen wrote:
Ok, I had to manually remove the BiocInstaller package, restart R and then
run biocLite and I am now on BiocInstaller 1.17.5 ~ Bioconductor 3.0
any idea how
Not that long ago DESCRIPTION field 'Additional_repositories' was
introduced which the purpose of providing references to non-mainstream
package repositories, e.g. R-Forge. Interestingly, by mainstream
they mean CRAN and Bioconductor. The 'Additional_repositories' field
is also enforced for CRAN
On Wed, Mar 4, 2015 at 2:29 PM, Michael Lawrence
lawrence.mich...@gene.com wrote:
Welcome.
For those who don't know, Jim is also the author of the neat lintr
package, which checks your R code as you type, across multiple editors.
https://github.com/jimhester/lintr
Not to mention
It seems unnecessary that BiocGenerics have the same package under
Imports as under Depends. The former can be dropped.
packageDescription(BiocGenerics)
Package: BiocGenerics
Title: S4 generic functions for Bioconductor
Description: S4 generic functions needed by many Bioconductor packages.
For affxparser, we've got the following in DESCRIPTION:
URL: https://github.com/HenrikBengtsson/affxparser
BugReports: https://github.com/HenrikBengtsson/affxparser/issues
But t's only the URL field that is listed on the package page(s):
directly versus
expressing them in an indirect manner (e.g. by relying on side
effects). I think the latter is wrong. Hope that makes sense.
Thanks for clarifying. I simply thought it was a mistake/cut'n'paste typo.
H..
Cheers,
H.
On 04/25/2015 01:12 PM, Henrik Bengtsson wrote:
It seems
Beautiful. Thxs Henrik
On Mon, Apr 27, 2015 at 6:47 PM, Dan Tenenbaum dtene...@fredhutch.org
wrote:
- Original Message -
From: Henrik Bengtsson henrik.bengts...@ucsf.edu
To: bioC-devel bioc-de...@stat.math.ethz.ch
Sent: Sunday, April 26, 2015 7:14:20 PM
Subject: [Bioc-devel
Sweet; you went live with the badges/shields, e.g.
http://bioconductor.org/packages/release/bioc/html/affxparser.html
A positive side effect is that now there's a link from the package
page to to the package's check results, which I always wanted :)
Thanks for adding this
/Henrik
On Sun,
On Apr 16, 2015 9:44 PM, Dan Tenenbaum dtene...@fredhutch.org wrote:
- Original Message -
From: Henrik Bengtsson henrik.bengts...@ucsf.edu
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioc-devel bioc-devel@r-project.org
Sent: Thursday, April 16, 2015 6:57:45 PM
Subject: Re
On Thu, Apr 16, 2015 at 1:23 PM, Dan Tenenbaum dtene...@fredhutch.org wrote:
The BioC 3.1 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
It's a new Bioc package, correct? Then it just got into the Bioc release
branch yday. That Bioc branch requires R 3.2.0 (the new recommended R
version everyone should run) regardless what your package declares. Your
package does not install on R 3.2.0 using the Bioc installers, even if
your
It's a new Bioc package, correct? Then it just got into the Bioc release
branch yday. That Bioc branch requires R 3.2.0 (the new recommended R
version everyone should run) regardless what your package declares. Your
package does not install on R 3.2.0 using the Bioc installers, even if
your
So, lots of things are happening in a few months: Jim Hester starts
working at Bioconductor, we get Bioc shields/badges, Jim'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
On Wed, Jun 24, 2015 at 5:42 PM, Dan Tenenbaum dtene...@fredhutch.org wrote:
Hello Bioconductors,
We're pleased to announce a new shield to join the ones we rolled out in May.
The new shield measures test coverage of a package, as determined by Jim
Hester's covr package.
Coverage is a
Just got the email asking me to sign up. The thing is that I've
already signed up, but using a different email address that the one
listed as the maintainer of my package(s). Is there a way to have
multiple associated email addresses on
https://support.bioconductor.org/? I cannot find such an
case motivating that change.
I will bring it up with the rest of the devteam today.
Jim
On Fri, Jul 24, 2015 at 11:12 AM, Henrik Bengtsson
henrik.bengts...@ucsf.edu wrote:
Currently, the codetoolsBioC package is available via:
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks
Currently, the codetoolsBioC package is available via:
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codetoolsBioC
Can codetoolsBioC be mirrored on GitHub like the other BioC packages,
or is that only possible for built and distributed BioC package?
Thanks,
Henrik
For your Linux problem:
You might have build R differently from what you had in the past, e.g.
static vs dynamic.
Try to explicitly re-install those failed dependences and see if you any
further. If so, you might wanna remove all your installed packages and
start over with a fresh package
If you have R-devel you can get those NOTEs using:
R CMD check --as-cran *.tar.gz
(It's been reported by --as-cran since Oct 2015 or so).
/Henrik
On Fri, Mar 11, 2016 at 2:45 PM, Hartley, Stephen (NIH/NHGRI) [F]
wrote:
> Thanks. I'll try that. I'm surprised, as my
;
> Dan
>
>
> - Original Message -
> > From: "Henrik Bengtsson" <henrik.bengts...@gmail.com>
> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> > Cc: "Maarten van Iterson" <mviter...@gmail.com>, "bioc-devel&qu
I *cannot* reproduce this:
% R --vanilla
## The IDAT file
> pathname <- system.file(package="minfiData", "extdata", "5723646053",
> "5723646053_R05C02_Grn.idat")
> file.info(pathname)$size
[1] 8091452
> unname(tools::md5sum(pathname))
[1] "dfc33fdaf3e91d872be896643a0c837f"
>
R CMD build, which is what triggers vignette building, only supports one
output file (HTML or PDF) per vignette. It will basically ignore duplicate
output formats. This is by design / legacy reasons. Technically it wouldn't
be hard to add support for multiple output formats, but that would
A few times I'd wish there was a way to support:
pkg::fun()
while _not_ "exposing" fun() on the search() path when attaching pkg.
Although it would be part of the public / exported API, the only way
to call the function would be via pkg::fun(). This would cover Sean's
use case. It would also
On Thu, Aug 18, 2016 at 4:45 PM, Wolfgang Huber <whu...@embl.de> wrote:
>
>
>> On 17 Aug 2016, at 13:02, Henrik Bengtsson <henrik.bengts...@gmail.com>
>> wrote:
>>
>> R CMD build, which is what triggers vignette building, only supports one
I've noticed this for a while and thought it was a temporary glitch,
or maybe I missed some announcement about it, but it appears that NEWS
files are no longed listed on the Bioc package pages, e.g.
https://bioconductor.org/packages/devel/bioc/html/Biobase.html. A
mistake?
/Henrik
Hi folks, I'm a person who prefers to use Git as my main source for my
Bioc packages. These Git repositories are then synced online to
GitHub for each collaboration yada yada. This also means that these
days I also tend to think of the Bioconductor SVN repository mostly as
a communication
e package root (or possibly via a
global Bioc one that everyone can commit to), e.g.
```r
hb = Henrik Bengtsson <henr...@braju.com>
j...@foo.com = John Doe <j...@someone.org>
```
and then Bioc can use this mapping when exporting to Git?
Finally, will people like me who already done the
Hi. FYI / Is anyone else experiencing:
Error in c(x, values) :
could not find symbol "recursive" in environment of the generic function
errors for some Bioconductor packages when running under R 3.3.3 while
they don't occur with R 3.3.2? This seems realted to the following R
3.3.3 NEWS entry:
ty across minor R releases is a myth :-/
>
> H.
>
>
> On 03/09/2017 05:38 PM, Henrik Bengtsson wrote:
>>
>> Hi. FYI / Is anyone else experiencing:
>>
>> Error in c(x, values) :
>> could not find symbol "recursive" in environment of the ge
t that is a pretty start difference.
>>
>> Best,
>> Kasper
>>
>>
>>
>> On Fri, Oct 6, 2017 at 3:12 AM, Wolfgang Huber <wolfgang.hu...@embl.de
>> <mailto:wolfgang.hu...@embl.de>> wrote:
>>
>> On Mac OSX 10.12.16:
>> $ ul
more easilly maintain multiple libraries
>> which contain, for example, different bioc versions in them.
>>
>> NB: switchr is subject to the caveat Martin pointed out and will fail to
>> retrieve a buildable version of the package if said buildable version is not
>> the
Is there an easily accessible archive for Bioconductor packages
similar to what is provided on CRAN where you can find all released
versions of a package, e.g.
https://cran.r-project.org/src/contrib/Archive/PSCBS/?
Say I want to access the source code for affy 1.18.0. Here are the
two approaches
Note that NEWS.md (Markdown) is only partially supported, e.g. news()
does _not_ pick it up, cf.
https://github.com/HenrikBengtsson/Wishlist-for-R/issues/40
/Henrik
On Sat, Sep 9, 2017 at 4:43 PM, Martin Morgan
wrote:
> On 09/09/2017 06:11 PM, Levi Waldron wrote:
About the DLL limit:
Just wanna make sure you're aware of "new" environment variable
R_MAX_NUM_DLLS available in R (>= 3.4.0). It allows you to push the
current default limit of 100 open DLLs a bit higher. It can be set in
.Renviron or before, e.g.
$ R_MAX_NUM_DLLS=500 R
This, of course,
R.cache (>= 0.6.0) does the following to acquire a persistent cache
(root) folder. This behavior was introduced after getting prompted by
CRAN not to write to disk by default (because they found "funny"
folders on their check servers) and a following email conversation
with CRAN (2011-12-29), and
Hi. Is there a way, without using R, to query bioconductor.org (or
any other reliable/maintained resources) for what the current release
version of Bioconductor is? Something like:
$ curl https://bioconductor.org/api/version
3.6
or possibly something fancy like:
$ curl
release_version: "3.6"
>
> Hope this is what you are looking for.
>
> Nitesh
>
>> On Nov 16, 2017, at 8:09 PM, Henrik Bengtsson <henrik.bengts...@gmail.com>
>> wrote:
>>
>> Hi. Is there a way, without using R, to query bioconducto
Are there any plans for an online interface to https://git.bioconductor.org/?
I've recently looked into solutions for an open-source in-house
"GitHub/GitLab"-ish, and I've found https://gitea.io/ to be really
nice. It is very easy to install. It has support for various common
user authentication
I lean to agree with Yaoyong, because I find it helpful to specify (or read):
Depends: R (>= 3.0.0)
which sends a message that "the code is relying on features in R that
was not available prior to R 3.0.0". Also, if that's the only
dependency you have, then if it passed R CMD check on R 3.0.0
On Thu, May 10, 2018, 00:29 Martin Morgan
wrote:
> 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
I'm using
Depends: R (>= 2.12.0)
to communicate that I've tested/verified that the package works as far
back as R 2.12.0.
Also, since R (>= 3.5.1) and R (>= 3.5.0) has been mentioned here, in
'Writing R Extensions' there is:
"It is inadvisable to use a dependence on R with patchlevel (the
Note that in R-devel, we have that
(https://cran.r-project.org/doc/manuals/r-devel/NEWS.html):
* news() gains support for ‘NEWS.md’ files.
That is, news(package = pkg) not only finds NEWS.md (as before) but
also parses it (into sections etc.) analogously to how it parses
NEWS.Rd and NEWS.
:
https://github.com/wch/r-source/blob/d20943d71407f9209cb6c7581ac0fce3b3517419/src/library/tools/R/news.R#L62-L66
/Henrik
On Tue, Sep 25, 2018 at 3:58 PM Henrik Bengtsson
wrote:
>
> Note that in R-devel, we have that
> (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html):
>
>
On Sat, Dec 22, 2018 at 10:56 AM Michael Lawrence
wrote:
>
> Anything that eventually lands in inst/doc is a vignette, I think, so
> there might be a hack around that.
Just so this is not misread - it's *not* possible to just hack your
vignette "product" files (PDF or HTML) into inst/doc and
On Mon, Jan 7, 2019 at 4:09 AM Martin Morgan wrote:
>
> I hope for 1. to have a 'local socket' (i.e., not using ports) implementation
> shortly.
>
> I committed a patch in 1.17.6 for the wrong-seeming behavior of 2. We now have
>
> > library(BiocParallel)
> > set.seed(1); p = bpparam(); rnorm(1)
Just an FYI, *if* all you're doing is rbind():ing those data frames,
then you're better of doing:
df <- do.call(rbind, dfs)
than
df <- Reduce(rbind, dfs)
because the former is faster and more memory efficient:
> dfs <- rep(list(iris), times=100)
> bench::mark(df <- Reduce(rbind,
(posting this here since I think it's not a support question per se)
Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1 setup:
> BiocManager::install(version = "3.10")
Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y
Bioconductor version 3.10 (BiocManager
ik
PS. I also tried setting ditto env var because it looked more like an
env var than R option name to me.
>
> On Thu, Oct 31, 2019 at 2:21 PM Henrik Bengtsson
> wrote:
>>
>> (posting this here since I think it's not a support question per se)
>>
>> Hi, I just st
I'm interested in finding out what customization Bioconductor servers
do to R CMD check, e.g. _R_CHECK_***_ settings. I think someone
pointed me to some location in the past, but I cannot locate it. I
think a natural place to document those would be on the 'Node Info'
pages together with the
Thank you - sounds great. /Henrik
On Tue, Dec 3, 2019 at 9:23 AM Pages, Herve wrote:
>
> Hi Henrik,
>
> On 12/3/19 09:13, Henrik Bengtsson wrote:
> > I'm interested in finding out what customization Bioconductor servers
> > do to R CMD check, e.g. _R_CHECK_***_ se
In case it's not known, paraphrasing from CRAN notification email,
CRAN [sic!] packages:
TROM, demi, diffMeanVar, maGUI, metaboGSE
risk being archived on December 7 because broken Bioconductor dependencies:
Heatplus, missMethyl, oligo, oligoClasses, topGO
prevent pdInfoBuilder from being
On Wed, Sep 25, 2019 at 2:28 PM Stuart Lee wrote:
>
> Chiming in to say +1 to this. I also use pkgdown for the same purpose as
> Laurent. With some kind of CI service you can automate the build of the
> website after a successful R CMD CHECK. Not sure how tricky this would be to
> integrate
This is great news. For those who wish to reproduce this locally when
running R CMD check, I suggest creating '~/.R/check.Renviron' with:
## Check for bugs like if (c(TRUE, FALSE)) ... Supported since R 3.4.0
_R_CHECK_LENGTH_1_CONDITION_=package:_R_CHECK_PACKAGE_NAME_,verbose
## Check for bugs
ng Bioconductor is really missing right now.
This would lower the friction for contributing to packages that you
don't work on on a regular basis, e.g. typos, bug fixes, etc.
Henrik
>
> Martin
>
> On 2/11/20, 5:16 PM, "Bioc-devel on behalf of Henrik Bengtsson"
>
> wro
d communicating
> > with users directly in the repository would be very nice, as well as the
> > ability to reference source code directly.
> >
> > On Thu, Oct 26, 2017 at 8:50 AM, Henrik Bengtsson <
> > henrik.bengts...@gmail.com> wrote:
> >
>
Maybe it's related to:
* The plot() S3 generic function is now in package base rather than
package graphics, as it is reasonable to have methods that do not use
the graphics package. The generic is currently re-exported from the
graphics namespace to allow packages importing it from there to
onductor git
> repository.
>
> Nitesh
>
> On Oct 1, 2020, at 11:57 AM, Henrik Bengtsson
> wrote:
>
> Doesn't a git rewrite break all existing clones, forks out there? I'm
> happy to be corrected, if this is not the case.
>
> /Henrik
>
> On Thu, Oct 1, 2020, 08:16
Doesn't a git rewrite break all existing clones, forks out there? I'm happy
to be corrected, if this is not the case.
/Henrik
On Thu, Oct 1, 2020, 08:16 Nitesh Turaga wrote:
> Hi,
>
> The BiocCheck will complain on the build system about the > 5MB package
> size.
>
> The rewrite of the history
action reports? We would like to submit the package for moderation soon
> but we're unsure if we can due to this problem. Thank you.
>
> Il 29/07/2020 19:25, Henrik Bengtsson ha scritto:
> > From a very quick look at this, I think you also need to explicitly
> > install the p
FWIW,
> sapply(X, length) - always numeric(1) (integer(1) or double(1) for vectors of
> more than 2^31 - 1 elements)
Actually, the length of length(x) may not be 1L, e.g.
> x <- Formula::Formula(~ x)
> length(x)
[1] 0 1
>From help("length", package = "base"):
"Warning: Package authors have
RStudio provides pre-built R package for Linux and since a some weeks
now, they can be used on GitHub Actions
(https://github.com/r-lib/actions). In addition, the run-time limit
on GitHub Actions is several hours compared to the 50 minutes you've'
got on Travis, so even if you install from
On Wed, Jun 3, 2020 at 10:40 PM Vincent Carey
wrote:
>
> On Wed, Jun 3, 2020 at 11:48 PM stefano wrote:
>
> > Hello Community,
> >
> > I am used to document function although hey are not exported
> >
> >
> I suppose you are talking about tidybulk? I am somewhat mystified by the
> behavior
> of
>From a very quick look at this, I think you also need to explicitly
install the package itself for it to be available in external R
session (contrary to when using forked processing as on Linux and
macOS). Something like this:
- name: Install dependencies
run: |
On Thu, Jun 17, 2021 at 2:32 AM wrote:
>
> Dear colleagues,
>
> It seems to me that, starting with the latest BioC devel branch (3.14), the
> build systems have become more pedantic about logical vectors of length > 1
> in conditions. Two of the packages I am maintaining, 'kebabs' and 'procoil'
>
Related: Does Bioconductor support 'Additional_repositories'? From RWE:
The ‘Additional_repositories’ field is a comma-separated list of
repository URLs where the packages named in the other fields may be
found. It is currently used by R CMD check to check that the packages
can be found, at least
FYI, I just sent an email to 'maintai...@bioconductor.org' regarding
this but it bounced with the below errors (I've truncated your
address):
From: Mail Delivery System
Date: Thu, Feb 25, 2021 at 12:39 PM
Subject: Undelivered Mail Returned to Sender
To: ...
This is the mail system at host
> I believe in the past we tried suggesting removing a R dependency altogether
> but that R CMD check complained not having an R dependency? Maybe someone
> remembers more about this.
There are no such requirements in 'R CMD check'. The only requirement
around 'Depends: R (>= x.y.z)', if
that is different from the check asking for a specific version for no
> particular reason (as far as I can ascertain).
>
> Best,
> Kasper
>
> On Thu, Apr 8, 2021 at 8:13 PM Henrik Bengtsson
> wrote:
>>
>> > I believe in the past we tried suggesting removing a R d
FWIW, I ran into a similar problem when I moved R.cache
(https://cran.r-project.org/package=R.cache) from using ~/.Rcache to
~/.cache/R/R.cache (etc). I decided on making it 100%-backward
compatible, i.e. if there's already a legacy ~/.Rcache cache folder,
it'll keep using that, otherwise the new
Can you go via a temporary file instead, i.e. output what you want to
grab to a temporary file and pull the info from that instead?
Side tracking ...
> I thought about using --vanilla but I use .Rprofile to set my library path,
> so ignoring that file completely defeats the point in my setup.
Correcting: the env var is R_LIBS_USER and nothing else.
/Henrik
On Wed, Apr 7, 2021 at 1:20 PM Henrik Bengtsson
wrote:
>
> Can you go via a temporary file instead, i.e. output what you want to
> grab to a temporary file and pull the info from that instead?
>
> Side tracking ...
Hi,
I seem to have "lost" write access to several Bioconductor git
repositories that I had git push access for before;
$ ssh -T g...@git.bioconductor.org | grep -E
"(affxparser|aroma.light|illuminaio|QDNAseq)$"
X11 forwarding request failed on channel 0
R packages/QDNAseq
R
> Dana Farber Cancer Institute
>
> > On Aug 19, 2021, at 8:08 AM, Henrik Bengtsson
> > wrote:
> >
> > Hi,
> >
> > I seem to have "lost" write access to several Bioconductor git
> > repositories that I had git push access for before;
> &g
In addition to checking with Valgrind, the ASan/UBsan and rchk
platforms on R-Hub (https://builder.r-hub.io/) can probably also be
useful;
> rhub::check(platform = "linux-x86_64-rocker-gcc-san")
> rhub::check(platform = "ubuntu-rchk")
/Henrik
On Tue, Oct 12, 2021 at 4:54 PM Martin Morgan
If you're willing to depend on R (>= 4.0.0), then tools::R_user_dir() can
replace the 'rappdirs' package.
/Henrik
On Mon, Oct 18, 2021, 09:05 Shraddha Pai wrote:
> Hi all,
> Despite moving rarely-used packages to Suggests and eliminating some (e.g.
> TCGAutils), the number of dependencies is
For CRAN packages it's easy. Packages on CRAN are eternal. They may be
archived, but they are never removed, so in a sense they're always
"currently on CRAN". Archived packages may still be installed, but only
with some efforts of the user. Some packages go in an out of "archived"
status depending
The easiest is to use withr::with_seed(), e.g.
> withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6))
[1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F" "#B15CD8" "#A2B9D5"
> withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6))
[1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F"
I'm throwing in another 1 cent.
I agree that utils::globalVariables() is risky; since it goes in the
root of the package code, it applies to *all* functions in the
package, which is a bit too broad of a stroke for my taste. The way I
deal with false globals from non-standard evaluation (NSE), is
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