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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Program in Com
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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*From:* Ahmed Mohamed
*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]]
> >
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> >
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you soon.
Juan
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Fax:(206) 667-1319
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Program in Computational Biology
Division of Public Health Sciences
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P.O. Box 19024
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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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Program in Computation
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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+47 41 80 80 25
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5ctHOQ2Hjw49pX7VAGBn7-u5l3mAqH1rt9tFNnZM=A7jGEFF5ehz2Hsxmlr_vGmPSX3Xy2SwZErgyi1mPIuw=
If anyone has seen something like this before then I'd appreciate some
help. Thank you!
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+47 41 80 80 25
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Program in Computational Biology
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Fred Hutchinson Cancer Research Cente
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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Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
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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Program in Computational Biology
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Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
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.
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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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/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.
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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:
g mailing list
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E
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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=
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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=
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eWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iEfGQDmbJr0Dp78RIYxXPcyoSMXMo31SAqDdWvOcdxI=q-0nEguTQCQNv04U4nju5HMBn6l8GmC_yCd7KSemIU8=
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Sea
fqt84VtBcfhQ=BK7q3X
eAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=stHSi8EN5PUgMEVus6KdL2z7-DfGz
ikck8btNROFUx0=dSXLn6y8wJtjg6ukcpOpGbSHfXqqsH97r9fuSJkakGo=
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P.O
be a reasonable
substitute, especially if it can spit out a VRanges somehow
--t
On Thu, Oct 11, 2018 at 10:14 AM Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
Sounds good.
I should also mention that Rsamtools has pileup() that is available
on all platforms. Don't know how easy
iZvSXAJJKaaPhzWA=zy-TmtsjB4a5Mwg313kvmlN0-6yO-6JDYZsT1nV6cCw=5WZzTZGK1jX2QI5fKn_INmjLYyv876INVFqftwFxlT4=
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P.O. Box 19024
Seattle, WA 98109-1
, platform agnostic. This should work.
--t
On Oct 11, 2018, at 1:41 AM, Hervé Pagès wrote:
And of course: the whole trick I described below only makes sense
if MTseeker doesn't rely on gmapR for its core functionality, that
is, if not having gmapR installed still allows the user to accomplish
on Windows
but Windows users won't be able to accomplish anything meaningful
with it. In that case, marking the package as unsupported on Windows
would be preferable.
Hope this makes sense,
H.
On 10/10/2018 10:26 PM, Hervé Pagès wrote:
Hi Tim,
No platform-specific dontrun capabilities AFAIK
WYiZvSXAJJKaaPhzWA=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18=rzPUqLBge6xE1TymeYxIxJxkiiOHefbSgzPOLYEhvrM=
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1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hp
my function for the slot definition. And I
don’t think the user sees this generally. But given that we’re coming up on a
release I thought I would ask if there’s anything I can do to get rid of this
warning! Or can I go with my first instinct and safely ignore it?
Thanks,
Elizabeth Purdom
0.058 0.006 0.065
Presumably the mcols()$<- copies/rewrites a lot of data needlessly?
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Program in Computational Biology
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E-mail: h
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.
On 09/07/2018 10:25 AM, Bo Wen wrote:
Yes.
Bo
On Fri, Sep 7, 2018 at 12:24 PM Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
Hi Bo,
Are you saying you cannot push changes to your package?
H.
On 09/07/2018 09:55 AM, Bo Wen wrote:
> Hi,
> I'
=-qRky554yTDVN2u7XQ0xlXDcnNdMzg93wm5J1Z0dAd8=8KSj7P_s3AiHvIUqkGETwbJeuTqxb0ptt1zRCEzYMbE=
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=k4gMuekxpPsqOqqUSi0uHUPWOMOjAVWbvHVFbq-rMYA=
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Program in Computational Biology
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Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
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On 08/28/2018 11:46 AM, Hervé Pagès wrote:
On 08/27/2018 11:01 PM, Martin Morgan wrote:
On 08/28/2018 12:19 AM, Charles Plessy wrote:
Dear Bioconductor developers,
In the CAGEr package, I created a "CAGEexp" class that extends
"MultiAssayExperiment" without adding
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nterest that y' may
have more or less features than y.
I will explore a bit using the solutions you've laid out.
Now that I think about it, the start-position based solution that I
was thinking about will break if two features in y share the same
start position, so that's not good.
On Mon, Aug 13,
start(y.boot.1)[runValue(y.boot.1) == 1],
width=runLength(y.boot.1)[runValue(y.boot.1) == 1])
I'm interested in building a function that takes in IRanges and
outputs these shuffled set of IRanges.
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PM, Samsiddhi Bhattacharjee wrote:
OK...1.98.0 and 1.99.0 sounds good. Shall do that.
Is it necessary to convey the reasons for the change e.g. NEWS file ?
That's my last question...I hope !
On Tuesday, June 12, 2018, Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
Ah ok. Y
? It should
probably have been 1.19.1 ?
On Monday, June 11, 2018, Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
Hi,
Having a package that is known to be broken in release is not
really an option.
How about replacing all the files in the RELEASE_3_7 branch
wi
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provide links to the other packages (as a comment
in the issue tracker) after you submit the first package. This
will provide some context to the review.
Thanks,
H.
Thanks a lot
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Fred Hutchi
Yes the .tar.gz file. Thanks! H.
On 05/14/2018 11:37 AM, Jose Die wrote:
Hi Hervé,
You mean the .tar.gz file?
Sorry, first time I’m doing this.
Jose
El 14/5/2018, a las 1:33, Hervé Pagès <hpa...@fredhutch.org> escribió:
Hi Jose,
Contributed BSgenome packages get added to the repo
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Fre
er fix can be hard to figure out even if it's simple.
BTW, before the fix, the 'envir' argument was ignored so I wonder if
a static code analysis tool couldn't have detected this...
H.
On 04/30/2018 03:26 PM, Michael Lawrence wrote:
I just pushed it to the 3.5 branch.
On Mon, Apr 30, 2018
is thread. I will look into this and hopefully fix it.
On Sun, Apr 29, 2018 at 6:12 PM, Hervé Pagès <hpa...@fredhutch.org> wrote:
Hi,
I made progress on this. This has actually nothing to do with Java.
You get the same thing with the flexmix package. What rJava and flexmix
have in common is tha
kage and potentially other things. So you
could define a parent class of 'matrix' using setClassUnion() and then
use setIs() to establish further derivations:
setClassUnion("MatrixLike", "matrix")
setIs("DelayedMatrix", "MatrixLike")
Michael
On Mon, Apr 30
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1100
you get when running the code in scmeth
vignette. The build system will pick-up the latest version
of HDF5Array so scmeth should go green again on the build
report tomorrow.
H.
On 04/30/2018 10:21 AM, Hervé Pagès wrote:
Hi Divy,
I will take care of this. You don't need to do anything.
Cheers,
H
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ils datasets
[8] methods base
other attached packages:
[1] IRanges_2.13.29 S4Vectors_0.17.44 BiocGenerics_0.25.3
[4] rJava_0.9-9
loaded via a namespace (and not attached):
[1] compiler_3.5.0
On 04/14/2018 03:11 AM, Hervé Pagès wrote:
Hi Zheng,
I can totally reproduce this on my Ubuntu lap
x' derives
from GRangesList. Doing class(x) == "CompressedGRangesList" will be
FALSE if 'x' is another GRangesList derivative and that is probably not
what you want.
Cheers,
H.
Radu
On Fri, Apr 27, 2018 at 8:11 PM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.
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From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of
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