arvesh
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this helps,
H.
Cheers, Óscar
On 12/10/2022, 20:07, "Hervé Pagès" wrote:
Hi Óscar,
On 12/10/2022 01:09, Lapuente Santana, Oscar via Bioc-devel wrote:
> Dear Bioconductor developers/maintainers,
>
> My package ‘easier’ checks with WARNING in bo
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Hi Ramon,
FWIW here's what I get when I run code chunk fdfmutex2 from the
OncoSimulR.Rmd vignette on kjohnson (Mac arm64):
> set.seed(1)
> s2fd <- oncoSimulIndiv(afe4,
+ muEF = mtfd,
+ model = "McFL",
+ onlyCancer = FALSE,
+
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On 28/09/2022 16:03, Hervé Pagès wrote:
Hi Burak,
Based on your description of what the package does, this is really a
software package in nature, so is in the wrong repository. We need to
fix this.
In 4 steps:
1. Please remove the ExperimentData term from the biocViews field as
well
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On 21/09/2022 07:57, Hervé Pagès wrote:
Just a workaround and not a real solution but maybe try to switch the
order of the clusterProfiler and SPONGE reports?
Oops, I meant "imports", not "reports".
But, again, reducing the huge number of dependencies of both miRsponge
Profiler and SPONGE reports?
Best,
H.
>
> Regards,
> Junpeng
>
> Hervé Pagès 于2022年9月21日周三 10:42写道：
>
> Looks like there's a nasty clash between dbplyr (CRAN) and the devel
> version of clusterProfiler:
>
> > library(clusterProfiler)
> > l
kage less
vulnerable to these sorts of clash. Many of those "loaded via a
namespace" packages are actually a consequence of SPONGE itself
importing many many things (it imports the full tidyverse!), so there's
probably some room for improvement on that side too.
Best,
H.
On 20
the Windows builds. So
any Windows-related issue only gets detected once a contributed package
is added to the daily builds.
H.
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>
> Not sure if this is related to the previous issue, i.e. problems
> accessing the
> latest CloudFront log files on S3 but I've used this thread anyway.
>
> Cheers,
>
> Jim
>
> On Thu, 1
n
(normally 1.20.1).
Cheers,
H.
> Best,
>
> Matteo
>
> *From: *Hervé Pagès
> *Date: *Tuesday, 22 March 2022 at 21.23
> *To: *Matteo Tiberti , bioc-devel@r-project.org
>
> *Subject: *Re: [Bioc-devel] macOS auto build fails with "graphics API
> version mismatch
. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263
This email message may contain legally privileged and/or...{{dropped:4}}
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Today's results for rrvgo:
https://bioconductor.org/checkResults/3.15/bioc-LATEST/rrvgo/
The vignette error is gone. There are still some errors but they are
different (org.Pf.plasmo.db was deprecated in BioC 3.14 and got removed
from BioC 3.15).
H.
On 11/01/2022 09:28, Hervé Pagès
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s in each
organisation.
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confidential and/or
> privileged information and may be legally protected from disclosure.
> If you are not the intended recipient, you are hereby notified
> that any use, dissemination, copying, or storage of this message or
> its attachments is strictly prohibited.
>
>> On 13. D
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
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
have any questions about this.
Best,
H.
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he help is not explicit what should
happen when the length "of the first ... argument" is zero, but the
above behavior effectively does something like:
answer <- list()
first <- "A"
names(answer) <- first[seq_along(answer)]
answer
named list()
Is there a need for the
]]
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https
ount 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 <mailto:hpages.on.git...@gmail.com>> wrote:
Hi Wanding,
A process cannot allocate more than 3Gb of memor
stinfo/bioc-devel
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Gabor
[...]
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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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021 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.
I can reproduce on
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)) :
error in eval
!
-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
.
Cheers,
H.
Best regards,
Felix
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ter. Thank you.
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://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 feeds
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
mediately by e-mail and
delete this email message from your computer. Thank you.
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/
If not, would it be possible to send those results to the package RSS
feed?
We'll add this.
Best,
H.
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and Statistical Computing
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
micha...@gene.com
Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
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=
{pname = 0x1, value = 0x0, internal = 0x0}, listsxp = {carval = 0x1,
cdrval = 0x0, tagval = 0x0}, envsxp = {frame = 0x1, enclos = 0x0,
hashtab = 0x0}, closxp = {formals = 0x1, body = 0x0, env = 0x0}, promsxp
= {value = 0x1, expr = 0x0, env = 0x0}}}
(gdb)
_
"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
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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
__ __
I will defer to Herve
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 Renaming S4
,
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 Renaming S4 Slots
Hi
NH1nVdRr9SsFOtMYhC%2BaXpdZiC7Nm%2BaUt37NvDWBfCg%3D=0>
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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
been 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 = "-")))
}
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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.
I meant
g mailing list
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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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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/bioc-LATEST/HPiP/
<http://bioc
/listinfo/bioc-devel
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On 10/09/2021 12:53, brodie gaslam wrote:
On Friday, September 10, 2021, 03:13:54 PM EDT, Hervé Pagès
wrote:
Good catch, thanks!
Replacing
if(ISNAN(vi) || (tmp = (int) vi) < 0 || tmp > 255) {
tmp = 0;
warn |= WARN_RAW;
}
pa[i] = (Rbyt
On 10/09/2021 09:12, Duncan Murdoch wrote:
On 10/09/2021 11:29 a.m., Hervé Pagès wrote:
Hi,
The first warning below is unexpected and confusing:
> as.raw(c(3e9, 5.1))
[1] 00 05
Warning messages:
1: NAs introduced by coercion to integer range
2: out-of-range val
Thanks Martin!
Best,
H.
On 10/09/2021 02:24, Martin Maechler wrote:
Hervé Pagès
on Thu, 9 Sep 2021 17:54:06 -0700 writes:
> Hi,
> I just stumbled across these 2 lines in RealFromComplex (lines 208 & 209
> in src/main/coerce.c):
> double
code can be fixed in a similar manner:
> as.raw(c("3e9", 5.1))
[1] 00 05
Warning messages:
1: NAs introduced by coercion to integer range
2: out-of-range values treated as 0 in coercion to raw
Cheers,
H.
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_
to ignore them). In any case they should
probably be removed.
Cheers,
H.
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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 mm10 genome
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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...@gmail.
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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 de Almeida ;
bioc-devel@r
Proteínas e Peptídeos
(LQFPP/CBB/UENF - RJ/Brazil)/
/Personal website: /https://almeidasilvaf.github.io
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*De:* Hervé Pagès
*Enviado:* segunda-feira, 23 de agosto de 2021 16:57
*Para:* Fabricio de Almeida ;
bioc-devel@r
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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:
> Thanks so m
> 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:
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e
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
the timeout issue. Thanks again!
Best,
Nuno
On 11 Jun 2021, at 06:29, Hervé Pagès
nks!
Best regards,
Nuno Agostinho
PhD student
Nuno Morais Lab
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hpages.o
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-devel
e I depend on?
Thanks,
R.
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iology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org<mailto:hpa...@fredhutch.org>
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
rience solving this issue?
Best regards,
Waldir
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h Institute
Imperial College London
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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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viz'
--- failed re-building cyanoFilter.Rmd
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}}
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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:
:
amrs[2]
# suddenly works again:
GRangesList(amrs)[[1]][2]
Best regards,
Oleksii
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ad 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 this.
Best,
H.
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
*To:* Murphy, Alan E ; bioc
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.co
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 March 2021 22:53
*To:*
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/packa
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