it assumption was "As soon as the user sees the Unrecoverable
exception, they will not try to do a plot". But this is obviously not a good
way to do it, as I can see :-) . My bad.
Thanks a lot again.
Best,
R.
> Cheers,
>
> H.
>
>
> On 04/10/2022 03:45, Ramon Diaz-Uria
n the other platforms there will be no consequences for remaining in the bioc
> ecosystem.
>
> On Tue, Oct 4, 2022 at 5:22 AM Ramon Diaz-Uriarte wrote:
>
> Dear All,
>
> It is unclear to me if the deadline of 28-October-2022 for "packages passing
> ‘‘R
> CMD build’’ and
w arm64 binaries so
> you should no longer need Xcode.
>
>
> Jennifer Wokaty
> they/them
> Bioconductor Core Team
> CUNY SPH
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://
lable.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
the case for at least a few days (weeks?). I can see no
obvious pattern, nor what could maintainers do to fix this.
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
dasilvaf.github.io/home/
>
>
> [[alternative HTML version deleted]]
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
> H.
>
> On 11/05/2021 16:38, Ramon Diaz-Uriarte wrote:
>> To partially answer myself, on looking more carefully, the INSTALL problem
>> seems to happen in the call to curl.exe (i.e., not in the R package
>> installation itself per se). It seems this failed
>> C:\
On Tue, 11-May-2021, at 20:15:24, Ramon Diaz-Uriarte wrote:
> Dear All,
>
> I package I maintain (OncoSimulR), which has not experienced any changes in
> the last week, has failed Install and Check (but not Build or Build bin) on
> Windows
> (https://bioconductor.org/ch
or a
problem caused by a package I depend on?
Thanks,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
https
sections" error or the linker never finishing. E.g.,
https://sourceforge.net/p/mingw-w64/discussion/723797/thread/c6b70624/
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-4
; has been a todo list item for me, for a while, and I should really try to
> resolve it.
>
> But for a quick fix, look at affxparser.
>
> Best,
> Kasper
>
> On Fri, May 24, 2019 at 10:16 AM Ramon Diaz-Uriarte
> wrote:
>
>>
>> Dear All,
>>
>
-obj -O3
## Ignored
PKG_CXX11FLAGS = -Wa,-mbig-obj -O3
## Ignored
PKG_CXX11FLAGS += -Wa,-mbig-obj -O3
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmai
sed 'R CMD check' on all platforms and propagated so this is why you
> see it on the package landing page.
>
> I addressed the issue with the script so hopefully the report will get
> updated today around 10 am EST. We should see OncoSimulR 2.13.1 on this
> new report.
>
> Best,
&
ut it.
Thanks,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http
rtin.mor...@roswellpark.org>>
>> wrote:
>>
>>
>>
>> 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...@roswellp
ps://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> rec
Dear Martin,
On Mon, 09-April-2018, at 17:35:47, Martin Maechler
<maech...@stat.math.ethz.ch> wrote:
>>>>>> Ramon Diaz-Uriarte <rdia...@gmail.com>
>>>>>> on Mon, 9 Apr 2018 16:51:38 +0200 writes:
>
> > Dear Martin,
&g
ystem (it might have been broken prior to my commit...).
OK, thanks.
Best,
R.
>
> Martin
>
>>
>> HTH
>>
>> On 6 April 2018 at 16:35, Vincent Carey <st...@channing.harvard.edu> wrote:
>>
>>> ive seen this too apropos bigrquery on windows
>
; treated as a topic
>> >
>> >
>> >
>> > that I cannot reproduce under Linux and that I think are false
>> > positives. Is there a way to avoid this warning? As far as I can tell,
>> > those links really exist.
>> >
>> > Best,
&
are false
positives. Is there a way to avoid this warning? As far as I can tell,
those links really exist.
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
______
> From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Ramon
> Diaz-Uriarte <rdia...@gmail.com>
> Sent: Wednesday, April 4, 2018 11:20:27 AM
> To: bioc-devel@
> Cc: ramon.d...@iib.uam.es
> Subject: [Bioc-devel] BioC 3.7: build failing on Ma
?
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto.org/rdiaz
Dear Martin,
On Fri, 13-October-2017, at 12:27:31, Martin Morgan
<martin.mor...@roswellpark.org> wrote:
> On 10/12/2017 07:08 AM, Ramon Diaz-Uriarte wrote:
>> Dear All,
>>
>> I have noticed that on the latest build report, a package I maintain,
>> OncoS
s), or the employee
>>>or agent responsible for the delivery of this message to the intended
>>>recipient(s), you are hereby notified that any disclosure, copying,
>>>distribution, or use of this email message is prohibited. If you have
>>>received this message in
tin for looking into this and letting me know.
Best,
R.
>
> Cheers,
> H.
>
>
> On 04/08/2017 06:34 AM, Ramon Diaz-Uriarte wrote:
>>
>> Dear Martin,
>>
>>
>> On Fri, 07-04-2017, at 12:55:55, Martin Morgan
>> <martin.mor...@roswellpa
Dear Martin,
On Fri, 07-04-2017, at 12:55:55, Martin Morgan <martin.mor...@roswellpark.org>
wrote:
> On 04/07/2017 03:55 AM, Ramon Diaz-Uriarte wrote:
>>
>> Dear Martin and Valerie,
>>
>>
>> I am not sure how to proceed here since the 14th is approaching
I actually expect it to go away
> when things are sorted out with the new El Capitan binaries.
> Unfortunately it's not something we fully control so let's wait
> and see...
>
> Cheers,
> H.
>
>
> On 04/07/2017 12:55 AM, Ramon Diaz-Uriarte wrote:
>>
>> Dear Marti
03-04-2017, at 18:34:26, Martin Morgan <martin.mor...@roswellpark.org>
wrote:
> On 03/31/2017 04:19 AM, Ramon Diaz-Uriarte wrote:
>>
>> Dear All,
>>
>> A package I maintain, ADaCGH2, is failing to build in veracruz2 with a
>> segfault that seems to happen whe
Dear Martin,
Thanks a lot for looking into this. I'll wait then.
Best,
R.
On Mon, 03-04-2017, at 18:34, Martin Morgan <martin.mor...@roswellpark.org>
wrote:
> On 03/31/2017 04:19 AM, Ramon Diaz-Uriarte wrote:
>>
>> Dear All,
>>
>> A package I maint
xl), dots))
It seems that what triggers the problem is an innocuous plot.default
followed by dev.hold? (none of which I call explicitly in my code)
At least another package, arrayQualityMetrics seems to experience a
somewhat similar problem:
http://bioconductor.org/checkResults/devel/bioc-LATEST
Uriarte wrote:
>> Dear All,
>>
>> Sorry to return to this issue, but on Morelia (Mac OS X, stable), we are
>> still seeing packages break during build with this message
>>
>> "GeomTextRepel was built with an incompatible version of ggproto.
>> Pleas
alted"
that affects many (all?) packages that depend on ggrepel or other packages
that depend on ggplot2/ggproto.
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2
ge issue tracker:
>
> https://github.com/GuangchuangYu/ggtree/issues/91
Thanks for the link.
Best,
R.
>
> Best,
> Diego
>
> On Mon, Nov 14, 2016 at 7:50 PM, Ramon Diaz-Uriarte <rdia...@gmail.com> wrote:
>> Dear All,
>>
>> At least some packages (part
, at least for the package I maintain, OncoSimulR, there are no
issues with R-devel in my local machines or with Travis
(https://travis-ci.org/rdiaz02/OncoSimul), or Appveyor
(https://ci.appveyor.com/project/rdiaz02/OncoSimul).
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad d
on the build machines should be gone in
> today's report.
>
> Cheers,
> H.
>
> On 10/17/2016 01:34 AM, Ramon Diaz-Uriarte wrote:
>> Dear All,
>>
>> Several packages (at least ADaCGH2, snapCGH, tilingArray, cellHTS2) are now
>> (last 24 to 48 hours?) failing
ned because I think the creation of the
BioC 3.4 release branch is today and release is tomorrow.
Best and apologies for the noise if this issue is known,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28
Yes, that was the strange thing (for me at least): some packages showed
"all" and some showed "some" and a cursory look did not reveal any pattern.
R.
On Fri, 23-09-2016, at 08:26, Hervé Pagès <hpa...@fredhutch.org> wrote:
> On 09/22/2016 11:09 PM, Ramon Di
Martin, thanks a lot and thanks too for the details and the workaround for
packageDescription.
best,
R.
On Tue, 30-08-2016, at 00:17, Martin Morgan <martin.mor...@roswellpark.org>
wrote:
> On 08/29/2016 05:40 PM, Ramon Diaz-Uriarte wrote:
>>
>> Dear All,
>>
&g
s not been updated
in the last two builds.
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto
On Fri, 19-08-2016, at 15:41, Sean Davis <seand...@gmail.com> wrote:
>> On Aug 19, 2016, at 9:10 AM, Ramon Diaz-Uriarte <rdia...@gmail.com> wrote:
>>
>>
>>
>>
>> On Wed, 17-08-2016, at 15:08, Sean Davis <seand...@gmail.com> wrote:
>&
prefer to have access to also the
>> intermediate plain Markdown / TeX rather than the final HTML / PDF product,
>> e.g. because they work better with screen readers.
>>
>> The only way I see you can have a PDF and a HTML version at the same time
>> is to create to
ere I've left the PDF (produced
using pdf_document or similar)? (Aside from not inserting the link and not
having to produce the PDF, which can be automated via hooks or similar).
Best,
R.
> Sean
>
>
>>
>> Martin
>>
>>
>>>
>>> Henrik
&
Rmd (not Rnw, even if I really, really, prefer LaTeX :-).
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.ua
Hi Dan,
Thanks for fixing it.
R.
On Tue, 26-07-2016, at 21:27, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
> Hi Ramon,
>
> Thanks for letting us know about this. We've identified and fixed the problem.
>
> Dan
>
>
> - Original Message -
>&
er supported by BioC
either).
How can this be fixed, so that the information is updated?
Thanks,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Emai
I'm not sure what happened to the windows machine, maybe someone from the
> core team has more insight into this.
>
Best,
R.
P.S. Sorry for misspelling your name in the previous email :-)
> Cheers,
> Andrzej
>
> On Mon, Jul 4, 2016 at 2:10 PM, Ramon Diaz-Uriarte <rdia...@
age was generated on 2016-07-03 15:29:33 -0700 (Sun, 03 Jul 2016).*
> From what I see the builds are up to date and reflect recent changes to the
> svn.
>
> Maybe some browser caching issue on your side?
>
> Cheers,
> Andrzej
>
> On Mon, Jul 4, 2016 at 12:50 PM, Ram
/bioc/html/OncoSimulR.html).
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto
On Fri, 29-04-2016, at 23:49, Martin Morgan <martin.mor...@roswellpark.org>
wrote:
> On 04/29/2016 05:23 PM, Ramon Diaz-Uriarte wrote:
>> Dear All,
>>
>> In case it matters, and since we are past the 22, I just noticed that a
>> package I maintain (ADaCGH2) is
to Depends.
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto.org/rdiaz
vel; you'll have to wait for
> testthat to be updated.
Sorry, I think I was not clear: after adding a "print" it will work under
both 0.11 and 1.0.0. So I made the change and updated.
Best,
R.
>
>
> On Thu, Apr 14, 2016 at 9:22 AM, Ramon Diaz-Uriarte <rdia...@gmail.com>
devel) need to be
> compatible with the changes in the new testthat.
>
> Dan
>
>
> - Original Message -
>> From: "Ramon Diaz-Uriarte" <rdia...@gmail.com>
>> To: "bioc-devel" <bioc-devel@r-project.org>
>> Cc: "ramon diaz" &l
ese are show stopper bugs depends on whether testthat
will be upgraded to 1.0
I am inclined to upgrade, but want to make sure that is the right course of
action.
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobis
#next-devel-bioconductor-33), and I can
remove that file. Is that correct?
Thanks,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
issue is not showing there).
On Fri, 01-04-2016, at 12:31, Ramon Diaz-Uriarte <rdia...@gmail.com> wrote:
> Hi Dan,
>
> I cannot reproduce the issue on a machine that claims to be 64-bit. I run
> your two examples of igraph and graph just fine (using the 32 and 64 bit R
> execu
version.string R version 3.3.0 beta (2016-03-30 r70404)
nickname Supposedly Educational
>
Best,
R.
On Fri, 01-04-2016, at 01:20, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
> I can also run the example on i386. Seems to just affect x64; let
rgetics of the Italian National
>> Research Council (IBBE-CNR)
>>
>> email: l.des...@campus.unimib.it
>> PEC: luca.des...@pec.it
>>
>> [[alternative HTML version deleted]]
>>
>> ___
OK, thanks. Will wait until it becomes Thursday over there :-)
On Thu, 31-03-2016, at 08:22, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
> There will be an answer tomorrow (Thursday Seattle time).
> Dan
>
>
> - Original Message -
>> From: "Ramon
.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto.org/rdiaz
t the 'solution' is to wait until the next build report and it
> will be gone.
>
> I just manually built your package on moscato2 and it was fine.
>
> Dan
>
>
> - Original Message -
>> From: "Ramon Diaz-Uriarte" <rdia...@gmail.com>
>> To: &
m not sure how to proceed.
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto
Hi Dan,
On Tue, 20-10-2015, at 23:56, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
> Hi Ramon,
>
> - Original Message -
>> From: "Ramon Diaz-Uriarte" <rdia...@gmail.com>
>> To: "bioc-devel" <bioc-devel@r-project.org>
>>
g R-devel?
> Btw. there are no instructions anymore at
> https://www.bioconductor.org/developers/how-to/useDevel/
>
> Best,
> Kasper
>
> [[alternative HTML version deleted]]
>
> _______
> Bioc-devel@r-project.org mailing l
erstanding (from https://support.bioconductor.org/p/69140/)
that the coverage calculation was done a few times a week so I was
expecting it to be in place a few days after the release.
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma
Thank you.
Best,
R.
On Fri, 26-06-2015, at 20:03, Dan Tenenbaum dtene...@fredhutch.org wrote:
- Original Message -
From: Ramon Diaz-Uriarte rdia...@gmail.com
To: bioc-devel bioc-devel@r-project.org
Cc: ramon diaz ramon.d...@iib.uam.es
Sent: Friday, June 26, 2015 6:22:51 AM
. R package version 1.3.2. it should say BioConductor package version
1.99.0. (that is what I have in the CITATION file)
It is like if the CITATION is stuck from several versions ago (in
devel). But the rest of the info in that page does not show anything
strange.
Best,
R.
--
Ramon Diaz
related.
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto.org/rdiaz
Thanks Dan.
Best,
R.
On Thu, 18-06-2015, at 20:10, Dan Tenenbaum dtene...@fredhutch.org wrote:
- Original Message -
From: Ramon Diaz-Uriarte rdia...@gmail.com
To: bioc-devel@r-project.org
Cc: ramon diaz ramon.d...@iib.uam.es
Sent: Thursday, June 18, 2015 11:00:51 AM
Subject
,
Andrzej
On Sat, Sep 27, 2014 at 8:51 AM, Ramon Diaz-Uriarte
rdia...@gmail.com
wrote:
Dear All,
I am now using BiocStyle for most of the latex I produce (even
non-bioc
related, such as teaching class notes) but I find that the text of
the
caption is often not distinct enough from
user customization and is up to us to do it if we want, so disregard
if irrelevant).
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia
.
If there are no objections I would be happy to incorporate this into
BiocStyle.
Best,
Andrzej
On Sat, Sep 27, 2014 at 8:51 AM, Ramon Diaz-Uriarte rdia...@gmail.com
wrote:
Dear All,
I am now using BiocStyle for most of the latex I produce (even non-bioc
related, such as teaching class
to the upcoming 2.13, but this can be set by the
environment variable R_BIOC_VERSION, e.g. in file Renviron.site.
Martin Morgan,
Bioconductor
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
be
moved to R-devel (I asked here because an identical question was dealt
with in this list).
Best,
R.
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia
of the two vignettes (which I think is due to the long.Rnw not
having been processed).
Best,
R.
Kasper
On Tue, Sep 17, 2013 at 9:26 AM, Ramon Diaz-Uriarte rdia...@gmail.comwrote:
Dear Kasper,
kasperdanielhan...@gmail.com writes:
As you describe this, this seems to be a change
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