urphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London
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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/>
The fate of
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
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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
; Kern, Lori ;
bioc-devel@r-project.org
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 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.
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hpag
ce 'R CMD check' by a few more minutes.
H.
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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 addition wi
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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/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 3.13
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,
>
> We stil
org mailing list
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llo 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.
Regards,
Daniel
Op do 11 mrt. 2021 om 03:11 schreef He
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they are usually statically linked, but installing
Linux binary packages is an entirely new game.
H.
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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 thi
sequence?
Certainly doable but note that by using BSgenome.Hsapiens.UCSC.hg38 you
stay away from this mess. I'm not sure that adding yet another BSgenome
package would make the situation less confusing.
On Fri, Aug 14, 2020 at 6:17 PM Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
n.
Cheers,
Felix
-Ursprüngliche Nachricht-
Von: Bioc-devel Im Auftrag von Hervé Pagès
Gesendet: Freitag, 14. August 2020 01:08
An: Leonard Goldstein ; bioc-devel@r-project.org
Cc: charlotte.sone...@fmi.ch
Betreff: Re: [Bioc-devel] BSgenome changes
Hi Leonard,
On 8/12/20 15:22, Leonard
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wnload)
and the many possible reverse dependencies downstream, i'd suggest that
either readVcf() issues an error or, maybe even better, overrides the
sequence level style in the VCF file maybe with a warning, when the
'genome' argument does not match the sequence style of the VCF file.
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On 7/7/20 02:50, Hervé Pagès wrote:
On 7/7/20 02:46, Bhagwat, Aditya wrote:
Thankyou Herve!
I guess that means that I can pull the fix in a day or two, is that
right?
Yes, as soon as BSgenome 1.57.4 propagates, which should take between
24h and 48h.
To be clear: BSgenome 1.57.4
On 7/7/20 02:46, Bhagwat, Aditya wrote:
Thankyou Herve!
I guess that means that I can pull the fix in a day or two, is that right?
Yes, as soon as BSgenome 1.57.4 propagates, which should take between
24h and 48h.
H.
Aditya
From: Hervé Pagès
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Hi Vince, Robert, Kasper,
I've done some work on this. Starting with GenomeInfoDb_1.25.7 the
seqlevelsStyle() setter has 2 major improvements:
1. It knows how to rename contigs and scaffolds, not just the chromosomes:
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
seqinfo(txdb)
# Seqinfo
ritating to the user.
Thanks,
Martin
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*Sent:* Monday, June 22, 2020 2:18 AM
*To:* Martin Morgan
*Cc:* Vincent Carey ; Hervé Pagès
; bioc-devel ; Shepherd,
Lori
*Subject:* Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly
from S4Vectors)
Excellent catch Martin.
I was able to confirm the iss
the build
machines so would make it easier to reproduce the errors they see on the
build report.
H.
Martin
On 6/8/20, 10:20 PM, "Hervé Pagès" wrote:
On 6/5/20 07:52, Martin Morgan wrote:
> no, the build system should only propagate packages that have passed
build an
On 6/8/20 19:20, Hervé Pagès wrote:
On 6/5/20 07:52, Martin Morgan wrote:
no, the build system should only propagate packages that have passed
build and check -- the goal is to make the life of the user easier and
more reliable, us developers have to sweat the details!
This makes a lot
> >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
https://urldefense.proofpoint.com
Excellent! Thanks Martin.
H.
On 5/28/20 00:39, Martin Maechler wrote:
Martin Maechler
on Wed, 27 May 2020 13:35:44 +0200 writes:
Hervé Pagès
on Tue, 26 May 2020 12:38:13 -0700 writes:
>> Hi Martin, On 5/26/20 06:24, Martin Maechler wrote: ...
>>>
> related with what the OP brought up (behavior of the 'collapse'
operation).
> Cheers,
> H.
>>
>> ~G
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On 5/24/20 00:26, Gabriel Becker wrote:
On Sat, May 23, 2020 at 9:59 PM Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
On 5/23/20 17:45, Gabriel Becker wrote:
> Maybe my intuition is just
> different but when I collapse multiple character vectors together,
On 5/23/20 17:45, Gabriel Becker wrote:
Maybe my intuition is just
different but when I collapse multiple character vectors together, I
expect all the characters from each of those vectors to be in the
resulting collapsed one.
Yes I'd expect that too. But the **collapse** operation in
On 5/22/20 18:12, brodie gaslam wrote:
FWIW what convinces me is consistency with other aggregating functions applied
to zero length inputs:
sum(numeric(0))
## [1] 0
Right.
And 1 is the identity element of multiplication:
> prod(numeric(0))
[1] 1
And the empty string is the identity
oofpoint.com/v2/url?u=http-3A__tibco.com=DwMFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Z1o-HO3_OqxOR9LaRguGvnG7X4vF_z1_q13I7zmjcfY=7ZT1IjmexPqsDBhrV3NspPTr8M8XiMweEwJWErgAlqw=>
On Fri, May 22, 2020 at 9:12 AM Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
.
On 5/22/20 03:00, Gabriel Becker wrote:
Hi Martin et al,
On Thu, May 21, 2020 at 9:42 AM Martin Maechler
mailto:maech...@stat.math.ethz.ch>> wrote:
>>>>> Hervé Pagès
>>>>> on Fri, 15 May 2020 13:44:28 -0700 writes:
> There is still
ror if
recycle0 were TRUE and collapse were declared in the same call. I don't
think the value of recycle0 should be silently ignored if it is actively
specified.
~G
On Fri, May 15, 2020 at 11:05 AM Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
Totally agree with that.
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Thanks for the fix.
H.
On 5/12/20 23:29, Tomas Kalibera wrote:
Thanks, fixed.
Tomas
On 5/13/20 5:14 AM, Dirk Eddelbuettel wrote:
On 12 May 2020 at 19:59, Hervé Pagès wrote:
| While reading about the new 'recycle0' argument of paste/paste0, I
| spotted a mysterious "cd" floating
‘NULL’) should lead to the zero-length ‘character(0)’.
cd
^^
This is in R 4.0.0 Patched and R devel.
Cheers,
H.
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you soon.
Juan
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E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
=
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E-mail: hpa...@fredhutch.org
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a new report before the end
of the week.
Thanks for your comprehension and sorry for the inconvenience.
Best,
H.
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oblems. I apologize for not realizing that.
It sounds like I should wait a little while to do that. However, I think this
does sound correct, and I will make that change.
Thank You,
Charles
-Original Message-----
From: Hervé Pagès
Sent: Tuesday, April 28, 2020 10:32 AM
To: Charles War
BN6aWrEGgHdGQ=>
So, if I understand everything, I think this is OK.
Thanks Again,
Charles
*From:*Shepherd, Lori
*Sent:* Tuesday, April 28, 2020 5:29 AM
*To:* Charles Warden ; Hervé Pagès
; 'bioc-devel@r-project.org'
*Subject:* Re: [Bioc-devel] Windows Development Build Error Message for
C
evel@r-project.org mailing list
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LOL
On 4/24/20 15:00, Jianhong Ou, Ph.D. wrote:
Hi Hervé,
Thank you! You saved me.
Best!
Your sincerely,
Jianhong Ou
On Apr 24, 2020, at 5:59 PM, Hervé Pagès wrote:
Hi Jianhong,
I just updated R from R 4.0 alpha to the final R 4.0.0 on machv2 and the good
news is that I no longer get
, 4:14 PM, "Hervé Pagès" wrote:
For some reasons the generation of the plots in the vignette is VERY
slow on machv2. 'R CMD build' actually completed... after 6h! This is
still under investigation.
Best,
H.
On 4/17/20 12:11, Jianhong Ou, P
a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0
The vignette looks okay as far as I can tell.
-Kylie
On Apr 24, 2020, at 1:40 AM, Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
Interesting indeed. Thanks for checking this.
Even though I'm not sure what conclusion to
d
the lower-alpha colors don’t appear at all.
However, in the merida1 vignette, the figures appear as I’d normally get
form quartz() or pdf() locally, which don’t produce warnings for me on
macOS 10.15.3.
-Kylie
On Apr 24, 2020, at 12:39 AM, Hervé Pagès <mailto:hpa...@fredhutch.org
SPKYxnfvicYz3rNyk04PTXhxU=itZMZz7G1z4hEn_h6m-WLnSXgIbD-41KOovzdseVHT4=>
On Apr 23, 2020, at 11:28 PM, Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
Ok so I'm changing my mind about this. I suspect that the error is
actually related to the warning. The error comes from
Y_wJYbW0WYiZvSXAJJKaaPhzWA=Q1W5ctHOQ2Hjw49pX7VAGBn7-u5l3mAqH1rt9tFNnZM=A7jGEFF5ehz2Hsxmlr_vGmPSX3Xy2SwZErgyi1mPIuw=
If anyone has seen something like this before then I'd appreciate some
help. Thank you!
--
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5ctHOQ2Hjw49pX7VAGBn7-u5l3mAqH1rt9tFNnZM=A7jGEFF5ehz2Hsxmlr_vGmPSX3Xy2SwZErgyi1mPIuw=
If anyone has seen something like this before then I'd appreciate some
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On 4/23/20 12:52, Hervé Pagès wrote:
On 4/23/20 12:45, Hervé Pagès wrote:
On 4/23/20 10:45, Kevin Horan wrote:
Bioc,
The build of ChemmineOB is failing on windows, which is also causing
3 other packages to fail (ChemmineR, eiR, and fmcsR). I was able to
build the package on my own
unzip on the Windows
builders.
Thanks,
H.
Kevin
On 4/23/20 12:52 PM, Hervé Pagès wrote:
On 4/23/20 12:45, Hervé Pagès wrote:
On 4/23/20 10:45, Kevin Horan wrote:
Bioc,
The build of ChemmineOB is failing on windows, which is also causing
3 other packages to fail (ChemmineR, eiR
=wmRn4CjxRi7ewvrtWLIyKM2Tockd3ZOaWfhhytkrbCM=RuXC_DouGnZ1Y3CsW5TtbzVY-lzbyy3KiFm28uqNOos=
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E-mail: hpa...@fredhutch.org
Phone
On 4/23/20 12:45, Hervé Pagès wrote:
On 4/23/20 10:45, Kevin Horan wrote:
Bioc,
The build of ChemmineOB is failing on windows, which is also causing 3
other packages to fail (ChemmineR, eiR, and fmcsR). I was able to
build the package on my own windows machine (Windows Server 2012 R2
=XPXcrRcaBbNEyoFMIPIoktRM6TXaJ1KWsll3KDmNPHA=
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E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax
of the R session. Even though there are ways to achieve this with
the temporary stuff you write in the user home, it's not automatic and
hard to get right.
Cheers,
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100
, so R-4.0.0 and R-4.1.0 should both
work with same Windows setup (which is afterall what the Rtools webpage says).
Thanks
Gordon
-Original Message-
From: Hervé Pagès
Sent: Tuesday, 21 April 2020 2:55 PM
To: Gordon K Smyth ; Martin Morgan
; bioc-devel@r-project.org
Cc: Yunshun Chen
t be using
the older toolchain. I had associated that toolchain in my mind with Rtool3.5,
but perhaps without any proper justification. Maybe Rtools4.0 supports both the
4.0.0 and 4.1.0 pipelines.
Thanks
Gordon
-Original Message-----
From: Hervé Pagès
Sent: Tuesday, 21 April 2020 12:01 PM
To: Gord
Hi Gordon,
The Bioconductor version to be released (BioC 3.11) uses R 4.0, not R
4.1. The latest Windows built of R 4.0 is available on CRAN here:
https://cran.r-project.org/bin/windows/base/rpatched.html
Note that the upcoming devel version of Bioconductor (BioC 3.12) will
still be based
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson
/developers/release-schedule/
Thanks,
H.
Thanks,
Peng
On 4/10/20, 7:13 PM, "Hervé Pagès" wrote:
On 4/10/20 16:54, Yang,Peng wrote:
> Hi Herve,
>
> Thank you so much for hearing back from you.
>
> Actually we are thinking to switch OpenMP int
on macOS) is
probably your best option for now. Thanks for taking care of this.
Best,
H.
Thanks,
Peng
On 4/10/20, 12:31 PM, "Hervé Pagès" wrote:
Hi Peng,
You cannot "push" binaries. DeMixT has a compilation error (+ some
imporant warnings) th
to install for Mac
under the developed version.
Does that mean I need to rebuild the package under the official Mac build of R
4.0.0 alpha and push it again?
Thanks,
Peng
On 4/9/20, 4:13 PM, "Bioc-devel on behalf of Hervé Pagès"
wrote:
Hello Bioconductor developers,
the binaries are not available.
Please let us know if you run into any problem with this.
Cheers,
H.
--
Hervé Pagès
Program in Computational Biology
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
of that specific test error.
OK, always good to know, thanks! The error seems to be related to the
code I added recently for handling on-disk dimnames. I only started to
look at this and will report here when I find something.
H.
On Mon, Apr 6, 2020 at 1:13 PM Hervé Pagès <mailto:
om/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=r6WLJ5dXWo2qb7mQwONaCxYeeWgKwycd3y89JoqY-oY=ABvG3sGKR5ln27FVCM8dlmZ82X93ZCTigbMxHeBEb6E=
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Resea
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Hervé Pagès
Program in Computatio
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research C
On 3/27/20 15:19, Hadley Wickham wrote:
On Fri, Mar 27, 2020 at 4:01 PM Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
On 3/27/20 12:00, Hadley Wickham wrote:
>
>
> On Fri, Mar 27, 2020 at 10:39 AM Hervé Pagès
mailto:hpa...@fredhutch.org&g
On 3/27/20 12:00, Hadley Wickham wrote:
On Fri, Mar 27, 2020 at 10:39 AM Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
Hi Tomas,
On 3/27/20 07:01, Tomas Kalibera wrote:
> they provide an over-approximation
They can also provide an "under-appro
that case:
setRefClass("A", fields=c(stuff="ANY"))
object.size(new("A", stuff=raw(0))) # 680 bytes
object.size(new("A", stuff=runif(1e8))) # 680 bytes
Why wouldn't object.size() look at the content of environments?
Thanks,
H.
--
Hervé Pagès
P
=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=2j-XqMgkHFiUdQuOv_PEqQ9KrpllNoZTuWR7_nklpRg=XzqMAcuqzJrQgjYmNrFXftlr_eMfox7d-OEiiOLNS3c=
--
Hervé Pagès
Program in Computational Biology
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
=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=yOswU0969aOLHa3jBIrzVj8fAiukIOoj9_7XnCcbRqI=zbtkDPRVf5duX0qU9xSZy3MqdeBSIo3Bpl7L6zEdNBE=
--
Hervé Pagès
Program in Computational Biology
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
Hi Paul,
I can reproduce this on my laptop. See full output below (it's big!).
Make sure to use a recent version of R devel (I updated mine 3 days
ago). The error seems to occur in MotIV's C/C++ code (in
/home/hpages/R/R-4.0.r78037/library/MotIV/libs/MotIV.so on my machine).
2 unrelated
45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=I5byLUAug01hPl-C-VbCCk-t7h7gPtd9rcxv5fK3NHk=vL4MJYsNa8_56NxXoYbZEYYHZk9-HJku2hLUuZLDwqw=
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N,
Excellent. Thank you! H.
On 3/20/20 23:55, Tomas Kalibera wrote:
On 3/18/20 6:11 PM, Hervé Pagès wrote:
Thanks Tomas. Any chance the old version of the error message could be
restored? It would definitely be more helpful than the current one.
It's confusing to get an error and be told
Did it work?
On 3/18/20 15:41, Egon Willighagen wrote:
Thanks, in going to try your suggestion tomorrow!
On Wed, Mar 18, 2020, 23:22 Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
mmh.. for some reason the original post in this thread is only showing
up now in my mailbox
that Egon was using
download.file() but this was not working on Windows 10 so he switched to
the RCurl solution. And the RCurl solution works on Windows 10 but now
fails on our Windows builders (Windows Server 2012 R2 Standard). Do I
get the situation right?
H.
On 3/18/20 14:53, Hervé Pagès wrote
meWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=6ZUwYkvqkDVxUXnwM4Ny0c26DHiOZSSZMb3TcjTEhTU=IIwoUM7vnfvLY_e0j7jr4Vd3-EFsgGD1khuegLj83KI=
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19
PM, Hervé Pagès wrote:
Using --with-pcre1 to configure the latest R 4.0 (revision 77988) on
an Ubuntu 14.04.5 LTS system gives me the following error:
...
checking if lzma version >= 5.0.3... yes
checking for pcre2-config... no
checking for pcre_fullinfo in -lpcre... yes
checking pcre.h usabil
eaders are required, or use --with-pcre1
Maybe the real problem is that the PCRE version on this OS is 8.31?
The error message is not particularly helpful.
Thanks,
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fa
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