wonder what the best practice is to resolve this issue.
>
> Thank you,
>
> Huang
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/
I replied the wrong email sorry. Please ignore.
On 5/23/24 11:40, Hervé Pagès wrote:
>
> Ok I downloaded the SecureLink Connection Manager (file
> connection-manager.run) on my Linux laptop (got a big warning from
> Chrome that this kind of file is dangerous, I found this p
your help.
H.
On 5/22/24 16:29, Hervé Pagès wrote:
>
> On 5/22/24 02:16, Vincent Carey wrote:
>
>> ...
>>
>> > Q4: Do you think a separate ExperimentData package satisfying
>> the specifications laid out in Background 2 is warranted? This
>>
d tarball size may not exceed 5MB. See
> https://contributions.bioconductor.org/general.html, sec 3.2.5.
oops! Yes of course. Thanks for the catch!
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
___
't include documentation on how the data was procured.
The availability of the original data is not strictly necessary but the
data still needs to be documented i.e. what's its nature, where it's
coming from, how it was imported/transformed, etc...
Best,
H.
>
> Thanks,
>
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
> repairing pa
Ulrich
>
> *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
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:
ce how 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-pr
know if you have any questions.
Best,
H.
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
itHub repo 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 inve
was generated on 2024-04-23 11:37:19 -0400 (Tue, 23 Apr 2024).
>
> Should I just wait or where I can find the mentioned ERROR?
>
> Best regards
>
> Kristian
>
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
l the
> checks? Or are there any other recommendations for this case?
>
> Best,
> Alexey
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hp
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
>
eekly 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:*
ows-LATEST/TCGAWorkflow>
>
> 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
>
>
8cc7d8%7C0%7C0%7C638424155200977608%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=0x4xNPvAHnkGyUcEz4PVIOM8eCVTEWNpNUOkskspUEQ%3D&reserved=0><https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOa
egrity 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.
gt; KEGG pathways, for example. What should I do?
>
> Sorry again for bothering you,
> Best regards,
> Jacopo
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bi
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 wo
would 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
>
--
Her
ersity of 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]]
>
> _____
gt;
>>>
>>> I suspect this is related, because the devel version of the package
>>> IS
>>> showing blue propagation status, and IS showing the
>>> documentation/package source etc.
>>>
>>>
>
bioconductor.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-proj
ESeq2 with library(DESeq2) 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:
>
>
some 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 pac
e.
H.
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, t
t; wrong result function is taken that causes the error?
>>
>> Any pointers?
>>
>>
>> Best
>>
>> Christian
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
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
10115 Berlin
>
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
> Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
> roger.biv...@nhh.no
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Co
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
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:
>&
1.08 / 10
> - primary alignment..... 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!
_vignette.Rmd’
>
> SUMMARY: processing the following file failed:
> ‘scaleSim_vignette.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
> ___
> Bioc-devel@r-project.org m
AM file 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
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
__
provided to your package doesn't work.
>
> Cheers,
> Ogan
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-deve
dicine
> 1470 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-proje
>
> Reina C.
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[altern
le to load 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 &q
ail&utm_medium=medarbejderemail&utm_campaign=medarbejderemail&utm_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.
> – a part of the Danish Cancer Society
>
> [cid:image001.png@01D9FB90.6FE2D7A0]<https://www.cancer.dk/?utm_source=email&utm_medium=medarbejderemail&utm_campaign=medarbejderemail&utm_content=cancerdk>
>
>
>
> www.cancer.dk<https://www.cancer.dk/international
___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
ta=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nb01Mwqu7SY%2FDc7Bbc1PAKyTKtGoe%2FjV7oovbv
aFrame deviates from
data.frame 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 G
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.
--
H
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:
11] LC_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
itted if this is caught in the right place.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Biocond
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 warnin
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 change
ST/msa/merida1-buildsrc.html
>
> 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,
>>
>>
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
&
ad 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 P
mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
/stats/bioc/pathview/
https://bioconductor.org/packages/stats/bioc/BiocGenerics/
can you check on this? thanks.
Weijun Luo
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch
-2Ddevel&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=BRxpnUxOEpNwBnvNz7_tvWT-eQ3eQOVrI6k5vXKWROddWJMxFsDhKTp5JOelaIM_&s=zjoOkX2-XpaR-_jfe7tHgtDLKlyMDnfppaDy0EInzP4&e=
[[alternative HTML version deleted]]
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
__
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.
--
Hervé
to revert.
H.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.g
ve HTML version deleted]]
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
___
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
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
message in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-
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 inst
________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
git.bioconductor.org.
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:
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:
...
An
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 o
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&
we'll take care of it. We'll let you know when it's done.
Best,
H.
Thanks,
Zhigang
https://sites.google.com/view/zlab
_______
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
in advance
Stijn
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
ause these system
requirements were available before*.*
Thanks and best,
Sarvesh
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
partment of 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 1
1102 Hock Plaza Box 2721
Durham, NC 27710, USA
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.g
and best,
Sarvesh
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
ould produce a clean R CMD check.
Hope 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 pa
Óscar
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-de
by this email.
www.icar.org.in
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
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,
+
_
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 as
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
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
usterProfiler 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)
>
help make the package 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.
ks in advance
Junpeng
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Windows builds. So
any Windows-related issue only gets detected once a contributed package
is added to the daily builds.
H.
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch
>
> http://bioconductor.org/packages/stats/bioc/ReadqPCR/
>
> 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
>
>
g the errors on 3.15 next.
Sounds good.
Cheers,
H.
Best,
Brian
On 5 Apr 2022, at 06:30, Hervé Pagès wrote:
Hi Brian,
Let's start by taking care of orthogene's failure in BioC 3.14 (this is
orthogene 1.0.0):
https://bioconductor.org/checkResults/3.14/bioc-LATEST/orthogene/
T
agation of the new version
(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 A
hensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263
This email message may contain legally privileged and/or...{{dropped:4}}
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailma
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r
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
!
Best wishes,
Sergi
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
tients in each
organisation.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Biocondu
ressee(s) and may contain 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 prohibite
1 - 100 of 1002 matches
Mail list logo
