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
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
>>
ball size may not exceed 5MB. See
> https://contributions.bioconductor.org/general.html, sec 3.2.5.
oops! Yes of course. Thanks for the catch!
--
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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,
> Vilhelm Suksi
> Turku Data Science Gr
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
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
questions.
Best,
H.
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with
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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
>>
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
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
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
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
>
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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
>
--
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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
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> ___
, 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
) 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@
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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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.
>
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o your package doesn't work.
>
> Cheers,
> Ogan
>
> [[alternative HTML version deleted]]
>
> ___
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> New York, NY 10029
> tel: 1- 212-824-9253
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>
>
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>
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Reina C.
>
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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
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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
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:
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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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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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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.
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Camperdown NSW 2050
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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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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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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
ion deleted]]
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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.
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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.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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> privileged information and may be legally protected from disclosure.
> If you are not the intended recipient, you are hereby notified
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>
>> 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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