On 12/12/2021 03:49, Philipp A. wrote:
I think the easiest fix was to just switch to HTML vignettes, then destiny
is no longer dependent on Bioconductor’s LaTeX environment staying stable.
Let’s see in the next build if it worked.
Just in case someone is watching this thread and wondering what
Hi Brian,
Note that Rsamtools does not relies on any CLI tools. It contains C/C++
code that is _compiled_ and _linked_ against Rhtslib rather than relying
on the standalone `samtools` and `tabix` commands.
Installing MAGMA at package installation time in the package
installation folder of MA
now if you have any questions about this.
Best,
H.
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Bio
erminal.
It would be awesome if 'R CMD check' could do the above for us i.e.
report the amount of memory used by the examples. Any volunteer to
request this feature on the R-devel mailing list?
Hope this helps,
H.
Very best,
Wanding
On Nov 29, 2021, at 12:15 PM, Hervé Pagès <ma
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/bioc-longtests-LATEST/biodbHmdb/
*
http://bioconductor.org/checkResults/release/bioc-longtests-LATEST/biodbChebi/
*
http://bioconductor.org/checkResults/release/bioc-longtests-LATEST/biodbKegg/
*
http://bioconductor.org/checkResults/release/bioc-longtests-LATEST/biodbUniprot/
*
http:/
Kind regards,
Evgenii Chekalin, PhD,
Research associate,
Michigan State University, College of Human Medicine
Department of Pediatrics and Human Development
Secchia Center, room 732
15 Michigan St. NE
Grand Rapids, MI 49503
+1(616) 617-1746
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st,
Mike
On Thu, 4 Nov 2021 at 20:42, Hervé Pagès <mailto:hpages.on.git...@gmail.com>> wrote:
Hi Nico,
This looks like the usual flakiness of the Ensembl Mart service. I see
these errors on the build report every day for various packages. The
exact set of packages varies
compiler_4.1.1
On 03/11/2021 15:15, Nicolas Delhomme wrote:
Hej!
The easyRNASeq package fails with the following error on nebbiolo2:
easyRNASeq RUnit Tests - 20 test functions, 1 error, 0 failures
ERROR in test_getAnnotation_BiomaRt: Error in h(simpleError(msg, call)) :
err
!
-Ursprüngliche Nachricht-
Von: Hervé Pagès
Gesendet: Dienstag, 26. Oktober 2021 21:53
An: Felix Ernst ; bioc-devel@r-project.org
Betreff: Re: [Bioc-devel] Windows specific error during CHECK
Hi Felix,
On 26/10/2021 12:10, Felix Ernst wrote:
Hi Bioc-Team,
I have got a problem with an error on Windows
x27;ll try to get back to
this tomorrow.
Cheers,
H.
Best regards,
Felix
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from your computer. Thank you.
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CFMessagePortCreateRemote" errors in that there is a problem with the
installation of Java:
https://stackoverflow.com/questions/15289059/install-java-on-mac-osx-10-8-2-error-calling-cfmessageportcreateremote
PS: I removed the "which java" call.
Thanks,
Augustin Luna
On Mon, Oc
https://bioconductor.org/developers/rss-feeds/ shortly.
Cheers,
H.
On 21/10/2021 09:36, Hervé Pagès wrote:
On 20/10/2021 22:40, Pierrick Roger wrote:
It seems the results of the long tests are not sent to the package RSS
feed. Am I missing something? Is there another feed?
We only have RSS feed
Hi Shraddha,
I don't think you want to start the business of building and
distributing Mac binary packages from other people to your users. Even
if you were doing this, BiocManager::install() would not know about
these binaries, and I'm not sure that there would be a simple way to
make your u
ge in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
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not, would it be possible to send those results to the package RSS
feed?
We'll add this.
Best,
H.
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Office +1 (650) 225-7760
micha...@gene.com
Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
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= 0x55a2d550, gengc_next_node = 0x55a2f438,
gengc_prev_node = 0x55a7e308, u = {primsxp = {offset = 1}, symsxp =
{pname = 0x1, value = 0x0, internal = 0x0}, listsxp = {carval = 0x1,
cdrval = 0x0, tagval = 0x0}, envsxp = {frame = 0x1, enclos = 0x0,
hashtab = 0x0}, closxp = {formals =
",
nFeatures_call=substitute(nFeatures_call))
}
H.
On 15/10/2021 14:41, Hervé Pagès wrote:
Hi Dario,
It would be good if you could provide a little bit more context about
ResubstituteParams objects and how they are typically used in practice.
As you found out, delayedAssign() won&#
yedAssign("r@nFeatures", nrow(measurements))
measurements <- matrix(1:100, ncol = 10)
r@nFeatures # Still the value from empty constructor.
[1] 10 20 30 40 50 60 70 80 90 100
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Austr
5, 2021 1:31 PM
*To:* Chris Eeles mailto:christopher.ee...@outlook.com>>
*Cc:* Hervé Pagès mailto:hpages.on.git...@gmail.com>>; bioc-devel@r-project.org
<mailto:bioc-devel@r-project.org>
*Subject:* Re: [Bioc-devel] Best Practices for Renaming S4 Slots
__ __
available on the Bioconductor website at all? It would have been useful to find
out sooner.
Best,
Chris
-Original Message-
From: Bioc-devel On Behalf Of Chris Eeles
Sent: October 15, 2021 1:10 PM
To: Hervé Pagès ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Best Practices for R
d.
Thanks,
H.
I plan to put in the work so that those using accessors shouldn't notice a
difference.
Best,
Chris
-Original Message-----
From: Hervé Pagès
Sent: October 15, 2021 12:39 PM
To: Chris Eeles ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Best Practices for Renami
3A%2F%2Fwww.uhn.ca%2F&data=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084204675&sdata=NH1nVdRr9SsFOtMYhC%2BaXpdZiC7Nm%2BaUt37NvDWBfCg%3D&reserved=0>
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University Health
Network<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.uhn.ca%2F&data=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87
I guess it's a situation where the unit tests were missing to cover an
important situation ("important" as in "it's important that the returned
object be always sorted"). ;-)
Cheers,
H.
On 13/10/2021 17:46, Pariksheet Nanda wrote:
Hi Hervé,
On 10/13/21 12:43
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, Herve! It makes sense to me now. I imported R2jags in
my package, which depends on rjags.
Regards,
Zhi Yang
On Tue, Oct 12, 2021 at 1:14 PM Hervé Pagès <mailto:hpages.on.git...@gmail.com>> wrote:
Hmm.. so a new version of rjags (4-11) got published on CRAN on Sept 24:
https
modified" error
but shouldn't you be doing '!any(idx)' instead of 'length(idx) == 0L' here?
Best,
H.
return(gr)
sort(c(
gr[! idx],
`strand<-`(gr[idx], value = "+"),
`strand<-`(gr[idx], value = "-"
On 12/10/2021 14:24, Hervé Pagès wrote:
Probably the build/ folder that doesn't belong to a package source tree.
You removed it today (commit 546e727eb21be2f1da8cd063f431a227345847da)
but that was after the builds started so this will only be reflected on
Wednesday's build report.
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.y.exe (for any x >=0, y>=0)
fromhttp://www.sourceforge.net/projects/mcmc-jags/files
Execution halted
ERROR: lazy loading failed for package 'HiLDA'
* removing 'D:/biocbuild/bbs-3.14-bioc/meat/HiLDA.buildbin-libdir/HiLDA'
Regards,
Zhi Yang
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Best,
H.
On Mon, Oct 4, 2021 at 4:21 PM Hervé Pagès <mailto:hpages.on.git...@gmail.com>> wrote:
Hi,
Are you using the same settings as the build machines as explained in
the rectangular box on the following page?
http://bioconductor.org/checkResults/devel/bi
t
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t but it
should turn green on Wednesday. Let us know if it doesn't.
Best,
H.
On 30/08/2021 09:56, Hervé Pagès wrote:
Hi,
It's still on my list to reforge BSgenome.Mmusculus.UCSC.mm10.masked. I
reforged BSgenome.Mmusculus.UCSC.mm10 back in June after the UCSC folks
updated the
you.
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other question: does this mean that there should be two packages,
one for code and another one for the database?
Yes. One is what we call the software package and the other one the
accompanying data package.
Cheers,
H.
On Wed, Aug 25, 2021 at 6:58 AM Hervé Pagès <mailto:hpages.on.git...@g
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io de Química e Função de Proteínas e Peptídeos
(LQFPP/CBB/UENF - RJ/Brazil)/
/Personal website: /https://almeidasilvaf.github.io
--------
*De:* Hervé Pagès
*Enviado:* segunda-feira, 23 de agosto de 2021 18:53
*Para:* Fabricio d
ica e Função de Proteínas e Peptídeos
(LQFPP/CBB/UENF - RJ/Brazil)/
/Personal website: /https://almeidasilvaf.github.io
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*Enviado:* segunda-feira, 23 de agosto de 2021 16:57
*Para:* Fabricio de Almeida
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On Wed, Aug 18, 2021 at 4:36 AM Hervé Pagès <mailto:hpages.on.git...@gmail.com>> wrote:
There's been no activity on Rsubread since Aug 8. You might want to
open
an issue on GitHub. It might help.
H.
On 17/08/2021 16:26, Ruijia Wang wrote:
> T
__
> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>
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Hi Shraddha,
Note that we only see this error for the release version of netDx:
https://bioconductor.org/packages/3.13/netDx
The devel version does not have it:
https://bioconductor.org/packages/3.14/netDx
With the release version, I get:
> library(netDx)
Attaching package: ‘netDx
advance!
Best,
Ruijia
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non-interactive R sessions. Now, it correctly prints the output in the vignette
without opening the browser! Still, I find it weird that this issue is only a
problem since Bioconductor 3.13 and for Windows only...
Anyway, just updated the new version in Bioconductor, let's see if it solves
t
help would be greatly
appreciated. Thanks!
Best regards,
Nuno Agostinho
PhD student
Nuno Morais Lab
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SL is not the most reliable build host for BioC
packages.
Best wishes,
Mark
*From:* Kern, Lori
*Sent:* Wednesday, 21 April 2021 9:31 PM
*To:* Hervé Pagès ; Mark Pinese
; bioc-devel@r-project.org
*Subject:* Re: [Bioc-
ncies or a
problem caused by a package I depend on?
Thanks,
R.
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Phone: (206) 667-5791
Fax:(206) 667-1319
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Hi Shraddha,
Hundreds of Bioconductor packages are affected since yesterday. Please
ignore.
Today we've upgraded R to R 4.1 alpha on machv2, and made a tweak to the
setup, so hopefully these errors will be gone on tomorrow's report.
Best,
H.
On 4/30/21 2:46 PM, Shraddha Pai wrote:
Hello B
e. If I understood
correctly, this is only a problem on headless servers, so PCs running macOS
would probably install the package fine.
Does anyone have experience solving this issue?
Best regards,
Waldir
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elp would be greatly appreciated.
Thanks,
Kelly Street
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E: mpin...@ccia.org.au | W: www.ccia.org.au
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s lab
UK Dementia Research Institute
Imperial College London
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t from GitHub on all the build machines. Hopefully
the error will go away on tomorrow's build report.
Please note that if your vignette requires markdown or rmarkdown then
the recommendation of the knitr authors to have these packages in your
Suggests field still applies.
Cheers,
H.
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there is no package called 'Rgraphviz'
--- failed re-building cyanoFilter.Rmd
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10
Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
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PM, Hervé Pagès wrote:
Hi Oleksii,
It looks like we have a long-standing bug in the rbind() method for
DataFrame objects that is somehow surfacing now. Here is a simple example:
library(IRanges)
DF1 <- DataFrame(A=I(list(11:12, 21:23)))
DF2 <- DataFrame(A=IntegerList(31:34, 41:
s(amrs)
amrs
# error:
amrs[2]
# suddenly works again:
GRangesList(amrs)[[1]][2]
Best regards,
Oleksii
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/20 11:33 PM, Stian Lågstad wrote:
Thank you very much for the help so far!
On Fri, Apr 24, 2020 at 8:08 AM Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
OK, thanks testing that. This suggests that the problem is on our
side... sigh! I will need to dig deeper into th
I would try to use a persistent ExperimentHub cache. This
should improve speed on all the platforms. Let's discuss this on GitHub.
Thanks,
H.
Kind regards,
Alan.
----
*From:* Hervé Pagès
*Sent:* 26 March 2021 16:13
*T
Tuesday, I understand there *should* have been one last
night:
https://bioconductor.org/checkResults/3.13/workflows-LATEST/
<https://bioconductor.org/checkResults/3.13/workflows-LATEST/>
Cheers,
Jim
On Wed, 24 Mar 2021 at 19:25, Hervé Pagès <mailto:hpages.on.git...@gmail.com>> w
5.11 0.06 5.33
generate.celltype.data 4.64 0.17 5.03
drop.uninformative.genes 4.34 0.25 6.11
Kind regards,
Alan.
--------
*From:* Hervé Pagès
*Sent:* 25 Mar
Let's keep this conversation on the bioc-devel mailing list where it
started.
On 3/25/21 5:31 PM, Xinan Yang wrote:
Herve,
on March 25, 2021 3:58 PM Hervé Pagès wrote:
With Bioconductor packages you push
changes to your package git repo at
> https://git.bioconductor.org/
<- get_ExperimentHub()
eh[["EH5373"]]
Does anyone know what could be causing this issue? Again to note this fail only
occurs on the Windows build and not the mac/linux.
Kind regards,
Alan.
Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial C
AJ Kinstlick
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ar 2021 at 19:25, Hervé Pagès <mailto:hpages.on.git...@gmail.com>> wrote:
The devel builds are up and running again, with nebbiolo1 instead of
rex3:
https://bioconductor.org/checkResults/3.13/bioc-LATEST/
<https://bioconductor.org/checkResults/3.13/bioc-LATEST/>
Th
The devel builds are up and running again, with nebbiolo1 instead of rex3:
https://bioconductor.org/checkResults/3.13/bioc-LATEST/
The fate of rex3 is still unclear.
Cheers,
H.
On 3/19/21 1:56 PM, Hervé Pagès wrote:
Hi maintainers,
If you've not noticed already, the build report fo
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file
+}
+
+## Exported.
+load_tt_alzh <- function()
+{
+eh <- get_ExperimentHub()
+eh[["EH5373"]]
+}
Sorry again if I have misinterpreted your approach.
Kind regards,
Alan.
*From:* Hervé Pagès
*Sent:* 23 March 2021 19:08
*To:* Murphy, Alan E ; Martin Morgan
; K
ntHub()
.set_eh(eh)
}
eh
}
toto()
}
This seems to work in that the script runs (I can tell based on the
output with devtools::check()) but I still get an error that eh doesn't
exist in my test functions.
Kind regards,
Alan.
# the entire R session
The package contains calls to the datasets in internal functions,
examples, tests and the vignette so eh it would need to be available to
all. Sorry I don't have much experience using experiment datasets.
Kind regards,
Alan.
-
oc-devel
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his should reduce 'R CMD check' by a few more minutes.
H.
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sion deleted]]
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16, 2021 at 11:40 PM Hervé Pagès <mailto:hpages.on.git...@gmail.com>> wrote:
Hi Thomas, Kevin,
openbabel3 is now on malbec1 (Ubuntu 18.04). Kevin's
ubuntu_18.04_openbabel3_debs.tar.gz worked like a charm. Thanks for
making it so easy.
Note that this additi
periencing connectivity issues that have prevented the daily builds
from running normally. The problem is being investigated and we'll
provide updates here as the situation evolves.
Thanks for your patience and sorry for the inconvenience.
H.
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r.org/checkResults/3.12/bioc-LATEST/ChemmineOB/malbec1-install.html
Cheers,
H.
On 3/16/21 10:24 AM, Hervé Pagès wrote:
@Kevin: Thanks for providing openbabel3 for Ubuntu 18.04. Will take a
look ASAP.
@Thomas: Yes, the Ubuntu 18.04 builds are only used for the BioC 3.12
builds (release). BioC 3.1
ll with all the deb files in here:
http://cluster.hpcc.ucr.edu/~khoran/ubuntu_18.04_openbabel3_debs.tar.gz
<http://cluster.hpcc.ucr.edu/~khoran/ubuntu_18.04_openbabel3_debs.tar.gz>
Kevin
On 3/15/21 10:10 AM, Hervé Pagès wrote:
> Hi Thomas, Kevin,
>
>
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wishes,
Lara
Lara Selles
lara.selle...@imperial.ac.uk
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SOJI
mailto:oluwafemi.olus...@uhasselt.be>>:
Hello Herve,
Thank you for the insight, but after rewriting the man pages by
hand. I still get the same error after the latest commit. I am
really at a loss here because this builds perfectly on my system.
Reg
st 'MarginEvents'
generic 'summaries' and siglist 'PhytoFilter'
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they are usually statically linked, but installing
Linux binary packages is an entirely new game.
H.
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7;s
not clear to me what to recommend.
Thanks,
H.
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mailto:goldstein.leon...@gene.com>> wrote:
Thanks for the explanation Hervé.
Best wishes
Leonard
On Tue, Aug 18, 2020 at 10:06 AM Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
On 8/18/20 01:40, Kasper Daniel Hansen wrote:
> In light of this,
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