09:52, Hervé Pagès wrote:
>
> Hi developers,
>
> pairwiseAlignement() and stringDist() have recently moved from
> Biostrings to the new pwalign package. This is causing a number of
> failures today on the 3.19 report. Since yesterday I've been actively
> repair
On 4/25/24 07:04, Kurt Hornik wrote:
...
> Sure, I'll look into adding something. (Too late for 4.4.0, of course.)
>
> Best
> -k
Great. Thanks!
H.
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML ver
ch
>
> *From:*Hervé Pagès
> *Sent:* Thursday, April 25, 2024 9:52 AM
> *To:* ulr...@bodenhofer.com
> *Cc:* bioc-devel@r-project.org; 'Martin Grigorov'
>
> *Subject:* Re: [Bioc-devel] Biostrings: substitution matrices disappeared?
>
> I'm done. Please resync you GitHub r
I'm done. Please resync you GitHub repo.
Best,
H.
On 4/25/24 00:14, Ulrich Bodenhofer wrote:
>
> Great, thanks, Hervé, so I’ll simply wait for the update. If there is
> anything I should do, just let me know.
>
> Thanks and best regards,
>
> Ulrich
>
> *From:*Herv
w to fix that on my side or, in case that this is an error in the
> current devel version of the ‘Biostrings’ package, to have a look into this.
>
> Thanks a lot in advance, best regards,
> Ulrich
>
> _______
> mailto:Bioc-devel@r-project
On 4/24/24 23:07, Kurt Hornik wrote:
>>>>>> Hervé Pagès writes:
>> Hi Kurt,
>> Is it intended that numeric_version() returns an error by default on
>> non-character input in R 4.4.0?
> Dear Herve, yes, that's the intention.
>
>> It seem
er(Sys.getenv("_R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_"))
>>> != "false")
>>> stop(msg, domain = NA)
>>> else
>>> warning(msg, domain = NA, immediate. = TRUE)
>>>
>>> If you use bugzilla before and have a handle, maybe file a bug report with
>>> this as patch athttps://bugs.r-project.org/
>>>
>>> Dirk
>>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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questions.
Best,
H.
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with
git.bioconductor.org when you get a chance.
H.
On 4/24/24 09:18, Hervé Pagès wrote:
>
> Hi Kristian,
>
> I believe that this is because the new report didn't get published yet
> so the links in the email you received still points to yesterday's
> report. We're investigating.
>
> Best,
>
9 -0400 (Tue, 23 Apr 2024).
>
> Should I just wait or where I can find the mentioned ERROR?
>
> Best regards
>
> Kristian
>
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r recommendations for this case?
>
> Best,
> Alexey
>
> [[alternative HTML version deleted]]
>
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[[alte
iting to ask if the package name ADAPT is available for use. I don't
>> see any package with this name on bioconductor but there is a package
>> called "adapt" archived many years ago on CRAN, so I am not sure. Any
>> suggestion is appreciated!
>>
>> Best,
>> Mukai
>>
>> --
>> Mukai Wang
>>
of the test this
> >> way?
> >> The test does pass like this, so this may be worrying about nothing.
>
> > Indeed, this could be educational; I think just adding
>
> > removeGeneric('as.data.frame')
asets methods base
other attached packages:
[1] BiocGenerics_0.49.1
loaded via a namespace (and not attached):
[1] compiler_4.4.0
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__
R-
builds or both those and the tests in test/? I'm
> wondering should I duplicate the tests in both folders that I want to
> run in both?
>
> Cheers,
> Alan.
> --------
> *From:* Hervé Pagès
> *Sent:* Tuesday 6
ect in your function which can't be called
> unconditionally. The workaround doesn't create such an object.
>
> Recognizing that your function never tries to call fun requires global
> inspection of toto(), and most of the checks are based on local
> inspection.
>
> Duncan Murdoch
>
> __
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t;
> If you have further questions or concerns please reach out on
> thebioc-de...@r-project.org<mailto:bioc-devel@r-project.org>
>
> We appreciate your quick attention to this matter
>
> Cheers,
> On behalf of the Bioconductor Core Team
>
> [[alternative HTML versi
lt;- function(mode)
{
if (mode == 1)
fun <- function(a, b) a*b
else
fun <- function(u, v, w) (u + v) / w
fun
}
Is that NOTE really intended? Hard to see why this code would be
considered "wrong".
I know it's just a NOTE but still...
Thanks,
H.
tat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98$
>>
>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!M-1zU
solution, the `menu[select]` seems to allocate more memory than
> `menu_env = list2env(menu); mget(select, envir = menu, ifnotfound =
> list(NULL)`. Or the sapply solution. Is this a benchmarking artifact?
>
> https://stackoverflow.com/q/77828678/4868692
>
> __
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y and confidentiality will be protected, and is not
> responsible for any unauthorized intervention to the e-mail content,
> viruses and/or any damage it may cause to your computer system.
>
> ___
> Bioc-devel@r-project.org m
>
> Sorry again for bothering you,
> Best regards,
> Jacopo
>
> [[alternative HTML version deleted]]
>
> _______
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FWIW I've documented the process of making a TxDb object for
T2T-CHM13v2.0 there:
https://github.com/Bioconductor/GenomicFeatures/issues/65
Please comment there for any follow-up.
Note that we're considering wrapping this is an TxDb package that we'll
make available to the community. It's a
now be a hard requirement for the package that contains the
STAR-related stuff.
This kind of separation might help with maintenance and quality control.
It might also help making things less confusing for the end user.
Best,
H.
> Kind Regards,
>
> Alex
>
--
Hervé Pa
Paraná - UFPR
> Rua Alcides Vieira Arcoverde, 1225
> Curitiba - PR 81520-260 - Brazil
>
> E-mail:mauro.cas...@ufpr.br
> Phone: +55-41-33614906
> https://orcid.org/-0003-4942-8131
>
> [[alternative HTML version deleted]]
>
> ___
, because the devel version of the package
>>> IS
>>> showing blue propagation status, and IS showing the
>>> documentation/package source etc.
>>>
>>>
>> https://bioconductor.org/packages/3.19/workflows/
or.org/checkResults/3.18/bioc-LATEST/DEWSeq/nebbiolo2-checksrc.html
>
> Could you please look into it ?
>
> Thank you in advance,
> Sudeep.
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org m
I see. We'll update soon. Thanks Martin.
On 11/4/23 06:52, Martin Maechler wrote:
>>>>>> Hervé Pagès
>>>>>> on Fri, 3 Nov 2023 15:10:40 -0700 writes:
> > Hi list,
>
> > Here is an example:
>
> > hpages@XPS15:~$ R
gnature
‘object="CoreSet"’: arguments (‘verbose’) after ‘...’ in the generic
must appear in the method, in the same place at the end of the argument list
Error: package or namespace load failed for ‘CoreGx’:
unable to load R code in package ‘CoreGx’
Best,
H.
On 11/3/23 15:10, Herv
prettyunits_1.2.0 tools_4.4.0 crayon_1.5.2
[9] desc_1.4.2 callr_3.7.3 pkgbuild_1.4.2 ps_1.7.5
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) after they've loaded
SNPhood, which would also break results(). I'll leave this to the
authors/maintainers of SNPhood and/or DESeq2 to open an issue on the
BiocGenerics repo to request this if they are interested.
On 10/31/23 13:49, Hervé Pagès wrote:
>
> Hmm.. so I was curious and did a
me day be in a similar place. For now, I am content with submitting
> packages for 3.19. :)
>
>> On Oct 31, 2023, at 4:49 PM, Hervé Pagès
>> wrote:
>>
>> Hmm.. so I was curious and did a little bit more investigation about
>> this.
>>
>> The other pa
.
On 10/31/23 09:44, Hervé Pagès wrote:
>
> On 10/31/23 07:22, Wolfgang Huber wrote:
>
>> Dear Christian
>>
>> If your vignette attaches another package that exports a “results” function,
>> after it attached SNPhood which defines its own results function, then t
is taken that causes the error?
>>
>> Any pointers?
>>
>>
>> Best
>>
>> Christian
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@
R-devel!}
> modified the behavior of `dim<-` somewhat
> such it does *not* unnecessarily drop dimnames,
> e.g., in your `dim(x) <- dim(x)` case above,
> one could really argue that it's a "true loss" if x loses
> dimnames "unnecessarily" ...
>
> OTOH, I k
Package is all green today on the 3.18 report:
https://bioconductor.org/checkResults/3.18/bioc-LATEST/groHMM/
Cheers,
H.
On 10/25/23 16:11, Hervé Pagès wrote:
>
> Addressed in S4Vectors 0.40.1. Today's builds have started already so
> the fix won't be reflected on tomorrow's report
_____
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> Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
> roger.biv...@nhh.no
> ___
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Addressed in S4Vectors 0.40.1. Today's builds have started already so
the fix won't be reflected on tomorrow's report (Thursday), only on Friday.
Sorry again for the inconvenience.
Best,
H.
On 10/25/23 15:34, Hervé Pagès wrote:
>
> Hi Tulip,
>
> I think this is caused by a
t; Thank you so much, atena builds and checks cleanly now on kunpeng2 too!!
>
> https://bioconductor.org/checkResults/3.18/bioc-LATEST/atena
>
> cheers,
>
> robert.
>
> On 10/23/23 20:46, Hervé Pagès wrote:
>>
>> On 10/23/23 11:45, Martin Grigorov wrote:
>&
L2 | 10 | 10 | 1 / 1
> - secondary alignment... L3 | 7801 | 4085 | 1.91 / 9
> o record is unmapped L4 | 0 | 0 | NA / NA
>
>
> Looks good ?
Looks good. Thanks Martin!
H.
>
> Regards,
> Martin
>
>
>
RY: processing the following file failed:
> ‘scaleSim_vignette.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.
le downloaded via
> ExperimentHub. This does not happen in any of the other platforms.
> Should we do anything about this?
>
> Thanks!
>
> robert.
>
--
Hervé Pagès
Bioconductor Core Team
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o your package doesn't work.
>
> Cheers,
> Ogan
>
> [[alternative HTML version deleted]]
>
> ___
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--
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0 Madison Ave, 6th Floor
> New York, NY 10029
> tel: 1- 212-824-9253
> Email:tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu>
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing
Reina C.
>
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>
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[[alternative HTML
it offline.
H.
>
>
> On Thu, 12 Oct 2023 at 20:37, Robert Castelo
> wrote:
>
> Hi,
>
> one of the kind of tools that Hervé is referring to is the package
> BiocPkgTools:
>
> https://bioconductor.org/packages/BiocPkgTools
>
> section "7 Depe
rce=email_medium=medarbejderemail_campaign=medarbejderemail_content=cancerdk>
www.cancer.dk <https://www.cancer.dk/international/> | Our privacy
policy <https://www.cancer.dk/om-os/privatlivspolitik/>
*From: *Hervé Pagès
*Date: *Wednesday, 11 October 2023 at 19.30
*To: *Matteo Tibe
ish Cancer Society
>
> [cid:image001.png@01D9FB90.6FE2D7A0]<https://www.cancer.dk/?utm_source=email_medium=medarbejderemail_campaign=medarbejderemail_content=cancerdk>
>
>
>
> www.cancer.dk<https://www.cancer.dk/international/> | Our privacy
> policy<https://w
ix" or
> "TsparseMatrix" or "dMatrix", "symmetricMatrix".
>
> In the case of as(, "dgTMatrix") , if you
> replace "dgTMatrix" by "TsparseMatrix"
> the result will be the same but also work in the future when the
> deprecation
__
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own%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=nb01Mwqu7SY%2FDc7Bbc1PAKyTKtGoe%2FjV7oovbvfNaNg%3D=0<https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!KyRp-e3er_j2IaXihvGE890iBaVn3BQgG6xwKWyaQaInWDt2geeRyBxA
On 9/25/23 07:05, Martin Maechler wrote:
>>>>>> Hervé Pagès
>>>>>> on Sat, 23 Sep 2023 16:52:21 -0700 writes:
> > Hi Martin,
> > On 9/23/23 06:43, Martin Maechler wrote:
> >>>>>>> Hervé Pagès
>
Hi Martin,
On 9/23/23 06:43, Martin Maechler wrote:
>>>>>> Hervé Pagès
>>>>>> on Fri, 22 Sep 2023 16:55:05 -0700 writes:
> > The problem is that you have things that are
> > **semantically** different but look exactly the sa
On 9/22/23 16:55, Hervé Pagès wrote:
> The problem is that you have things that are **semantically**
> different but look exactly the same:
>
> They look the same:
>
> > x
> [1] NA
> > y
> [1] NA
> > z
> [1] NA
>
> > is.na(x)
> [1] TRUE
>
> expecting identical() to treat different types as the same (e.g.
> identical(NA, NA_real_) is FALSE, as it should be). If you are using
> a different test, that's user error.
>
> Duncan Murdoch
>
> On 22/09/2023 2:41 p.m., Hervé Pagès wrote:
>> We could also question the
d Im() are not all NA:
>
>showC <- function(z) noquote(sprintf("(R = %g, I = %g)", Re(z), Im(z)))
>z <- complex(, c(11, NA, NA), c(NA, 99, NA))
>z
>showC(z)
>
> gives
>
>> z
>[1] NA NA NA
>> showC(z)
>[1] (R = 11, I = NA) (R = NA, I = 99) (R = NA, I
On 9/11/23 22:39, Prof Brian Ripley wrote:
> On 09/09/2023 01:56, Hervé Pagès wrote:
>> Hi Martin,
>>
>> Sounds good. Are there any plans to support the xz compression for
>> package source tarballs?
>
> What makes you think it is not supported?
I guess becaus
/?C=M;O=D
>
>
> Best,
> Martin
>
> __
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_
ot disrupt anything.
H.
On 6/15/23 13:51, Hervé Pagès wrote:
>
> I'd argue that at the root of the problem is that your qr.X() generic
> dispatches on all its arguments, including the 'ncol' argument which I
> think the dispatch mechanism needs to evaluate **before** dispatch can
> ac
he body of any method that might
>>>> evaluate
>>>> 'ncol'.
>>>>
>>>
>>> Perhaps I am misunderstanding something, but I think Mikael's
>>> expectations
>>> about the scoping rules of R are wrong. The enclosing environment
>>> of ncol
>>> is where it was _defined_
as documented in ?DataFrame.
H.
robert.
On 5/17/23 20:45, Hervé Pagès wrote:
Not sure why the colData default is DataFrame(). Seems like this has
been the default since the birth of the SummarizedExperiment class
back in 2010 (FWIW the class was born in the GenomicRanges package).
Anyways
On 5/19/23 14:37, Martin Maechler wrote:
Could you file a bug at R's bugzilla?
{I know we have too many open bugs there, notably related to S4,
but still you'd do a service to the R community.}
Done: https://bugs.r-project.org/show_bug.cgi?id=18538
Cheers,
H.
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quot;)
Method Definition:
function (x, ..., z = 22)
{
.local <- function (x, y = -5, ..., z = 22)
y
.local(x, ..., z = z)
}
Signatures:
x
target "raw"
defined "raw"
> foo(raw(1))
[1] -5
Best,
H.
On 5/19/23 14:37, Martin Maechler wrote:
UREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/Los_Angeles
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.0 codetools_0.2-19
--
Her
C_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/Los_Angeles
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.0 codetools_0.2-19
his is caught in the right place.
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Camperdown NSW 2050
Australia
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at some point.
Best,
-Deepayan
On Mon, Jan 30, 2023 at 12:02 PM Hervé Pagès wrote:
On 28/01/2023 19:42, Deepayan Sarkar wrote:
...
I'm open to suppressing the warning for \describe items (the warning
is more important for \arguments). Let me know.
Hi Deepayan, suppressing the warning
Hi developers,
A couple of days ago I moved the rowSums, colSums, rowMeans, colMeans generics
from *BiocGenerics* to *MatrixGenerics*, and this seems to break a lot of
packages on today's build report for devel, sorry for that. I didn't have
time to look closely at the damage caused by this
gt; Any ideas on how to fix this?
>
> Thank you so much for all your help!!
>
> Pooja
>
> On Tue, Mar 21, 2023, 4:50 PM Hervé Pagès
> wrote:
>
> On 21/03/2023 12:48, Pooja Gangras wrote:
>
>> Hi Herve,
>>
>> Thank you for the quick respo
hile I too wondered why the OP mentions unavailability "for months",
> now re-reading the OP's email, may be they meant "for months"
> granularity which is (now temporarily un)available! :D
>
> Cheers,
> Sarvesh
>
> On Mon, 20 Mar 2023 at 16:50, Hervé Pagès
> w
d and contact the maintainer for msa but hoping that it
> will fix itself before release because it was just fine until yesterday.
Unfortunately it won't fix itself.
H.
>
> Thanks,
> Pooja
>
> On Tue, Mar 21, 2023, 2:43 PM Hervé Pagès
> wrote:
>
> Hi Pooja,
>
/bioc-devel
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/stats/bioc/pathview/
https://bioconductor.org/packages/stats/bioc/BiocGenerics/
can you check on this? thanks.
Weijun Luo
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On 28/01/2023 19:42, Deepayan Sarkar wrote:
...
I'm open to suppressing the warning for \describe items (the warning
is more important for \arguments). Let me know.
Hi Deepayan, suppressing the warning for \describe would kind of make
sense. Thanks for the offer.
Best,
H.
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On 05/01/2023 18:52, Vincent Carey wrote:
>
>
> On Thu, Jan 5, 2023 at 7:08 PM Vincent Carey
> wrote:
>
>
>
> On Thu, Jan 5, 2023 at 1:44 PM Hervé Pagès
> wrote:
>
> Hi Martin,
>
> Linux runs on many architectures, ARM64 is just on
ailman/listinfo/bioc-devel
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ge in error, please notify the sender immediately by e-mail and
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Hi Ran,
First of all, please note that direct calls to external commands via
system() or system2() are not ideal so should only be used when there is no
other alternative. For example, if a CRAN or Bioconductor package already
provides the functionality that you are after, you should use that
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.
Thanks,
H.
On 09/12/2022 14:47, Hervé Pagès wrote:
Hi,
IFAA now passes BUILD and CHECK on all platforms on the BioC 3.17
build report:
https://bioconductor.org/checkResults/3.17/bioc-LATEST/IFAA/
The package is now available in BioC 3.17 via BiocManager::install():
https
. But that's because of an issue with an upstream
package on this platform that will hopefully be resolved soon. (Note
that BioC 3.17 users can still install the package from source on Windows.)
Cheers,
H.
On 07/12/2022 21:54, Hervé Pagès wrote:
Hi,
On 06/12/2022 22:10, Hervé Pagès wrote:
...
Anyways
FWIW the compilation error for SIMLR looks like a real error to me, not
a warning-induced one:
tsne.cpp:883:11: error: too few arguments to function ‘void dgemm_(...
It seems to be caused by a change in R-devel. We see it on all platforms
on the daily builds for BioC 3.17 and I also get it
Hi,
On 06/12/2022 22:10, Hervé Pagès wrote:
...
Anyways, the version of the Bioconductor package would need to be
bumped to 1.1.1. However you won't be able to push this bump to
git.bioconductor.org because we don't allow this kind of version bump.
So we'll take care of it. We'll let you know
ou know when it's done.
Best,
H.
Thanks,
Zhigang
https://sites.google.com/view/zlab
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available before*.*
Thanks and best,
Sarvesh
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f Biostatistics and Bioinformatics
> Duke University School of Medicine
> 2424 Erwin Road, Suite 1102 Hock Plaza Box 2721
> Durham, NC 27710, USA
>
>
>
> On Wed, Oct 19, 2022 at 10:29 PM Hervé Pagès
> wrote:
>
> Hi Jason,
>
> On 19/10/2022 19:10, Jaso
Box 2721
Durham, NC 27710, USA
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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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