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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.
Chee
g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=RBt9k3A-vxuVohDsl55aCS2e531MTyn_iu2qGRh2-qI&s=OO19dRaLUk9SvbPL7BTpB_uWkqIJk-_78VSX_p_SznQ&e=
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview
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
er as long as '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 <mailto:hpa...@fredhut
of cores used)?
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
From: Bioc-devel on behalf of
Kasper Daniel Hansen
Sent: Friday, April 27, 2018 10:29 AM
To: Hervé Pagès
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] build mac
ight happen? Is there something I am missing?
Radu
--
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: hpa...@fredhutch.org
Phone: (206) 667-5791
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1] parallelstats4stats graphicsgrDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicRanges_1.31.23 GenomeInfoDb_1.15.5 IRanges_2.13.28
[4] S4Vectors_0.17.38 BiocGenerics_0.25.3 rJava_0.9-9
[7] rmarkdown_1.9
loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 digest_0.6.1
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Hi Felix,
Please see my answer in the issue you opened on GitHub:
https://github.com/Bioconductor/Biostrings/issues/10
Cheers,
H.
On 04/02/2018 06:07 AM, Felix Ernst wrote:
Dear all,
probably this is for Hervé Pagès:
I tried the following code, which should according to ?AAString not
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Hervé Pagès
Program in Computational Biology
Division of
Hi Zheng,
Thanks for the report. I will look into this and will let you know.
H.
On 04/01/2018 02:38 AM, Zheng Wei wrote:
Dear all,
I find this error if calling library(rJava) before using
BiocGenerics::unique
The code is pasted below.
Thanks,
Zheng
> library(rJava)
> library(GenomicRa
er Bioconductor package. We'll deprecate the old mechanism
(workflowInstall()) at some point in the future.
Thanks to Andrzej, Lori, Nitesh, and Valerie for working on this
migration.
Let us know if you have any question about this.
H.
--
Hervé Pagès
Program in Computational Biology
Divi
ons in
the vignettes. We have one package essentially ready for submission to
bioc, so is the best route forward to submit now or wait until
tensorflow is installed on the build servers?
Many thanks
Kieran
On 28 March 2018 at 15:10, Hervé Pagès wrote:
On 03/28/2018 02:41 PM, Hervé Pagès wrote:
Hi Gordon,
The TIMEOUT that was preventing the Windows binary of GenomicRanges
from propagating has been addressed. The latest version of the package
(1.31.23) is now available for BioC devel users on all platforms via
biocLite().
Cheers,
H.
On 03/19/2018 10:01 AM, Hervé Pagès wrote:
Hi
On 03/28/2018 02:41 PM, Hervé Pagès wrote:
Hi Kieran,
Note that you can execute arbitrary code at load time by defining
an .onLoad() hook in your package. So you *could* put something
like this in your package:
.onUnload <- function(libpath)
{
if (!reticulate::py_module_availa
Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=w2p-VnxwECq9u90RNv_B6yCOpXxDkcIPAjcgcpbEeBE&s=RS0haeXXw_GuGbzVJJuh_ZJKHuYhliDfLjtojgmqKFc&e=
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.
#x27;ll see the error
and some days we won't. Since openPrimeR has not changed between
release and devel, it's possible that we'll sometimes see this error
in devel too.
H.
On 03/22/2018 11:02 AM, Hervé Pagès wrote:
The build system captures the output of the 'R CMD check'
JJKaaPhzWA&m=4dLit0LWO62L2Nbb1SDhPnTyk0HX5yPPi35QNl604X4&s=27EQuRiPmUYDaFi8VIl4UJ2WS43kJT6sHbKhljxra6M&e=
So I'm not sure if adjusting the parallel execution would be a permanent
fix that would ensure that all Bioconductor packages pass the checks
smoothly on Windows. Maybe Mart
problem.
Interestingly, there are no problems for the development version on
tokay2
(https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_openPrimeR_tokay2-2Dchecksrc.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=HjFin7ZZwuYWdlO8wvE3KmoPwj
ender immediately by
e-mail and delete this email message from your computer. Thank you.
--
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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
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Program in Computational Biology
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1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hp
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Program in Computational Biology
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Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N,
the other issue with the build not working in release, that is a
bug in the rentrez (which is on CRAN, not Bioc). I've submitted a PR to
fix that, and we'll see what the response is as to whether I need to
remove that integration or not.
~G
On Tue, Feb 20, 2018 at 10:48 AM, Her
Ranges_2.13.26 S4Vectors_0.17.33 BiocGenerics_0.25.3*
loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0
Best,
~G
--
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Program in Computational Biology
Division of Public Health Sciences
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1100 Fairview Ave. N,
vgfOsNLw&e=>
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El 02/17/2018 a las 04:19 AM, Hervé Pagès escribió:
Hi Bernat,
On 02/15/2018 11:57 PM, Bernat Ge
p;m=Wwl42dL5uGJa8PR0aAcNnIN0t-uut5R2xLKBhl0ynV8&s=z45_PX78N6zLu1Bcn-mYQcyRortvXjNyQcWASriwsr0&e=>
El 02/15/2018 a las 11:19 PM, Hervé Pagès escribió:
On 02/15/2018 01:57 PM, Michael Lawrence wrote:
On Thu, Feb 15, 2018 at 1:45 PM, Hervé Pagès <mailto:hpa...@fredhutch.or
On 02/15/2018 01:57 PM, Michael Lawrence wrote:
On Thu, Feb 15, 2018 at 1:45 PM, Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
On 02/15/2018 11:53 AM, Cook, Malcolm wrote:
Hi,
Can I ask, is this change under discussion in current release or
of the IRanges and GenomicRanges packages.
H.
Thanks!
~malcolm
--
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: hpa...@fre
er.
H.
On Thu, Feb 15, 2018 at 8:30 AM, Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:
Hi Bernat,
Use as(gr, "GRangesList") instead of as.list() on your GRanges objects.
Most of the times (e.g. for passing to lapply() or mclapply()), you
don't need a
thods base
other attached packages:
[1] GenomicRanges_1.31.20 GenomeInfoDb_1.15.5 IRanges_2.13.26
S4Vectors_0.17.32 BiocGenerics_0.25.3
loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0 compiler_3.5.0 XVector_0.19.8
tools_3.5.0 GenomeInfoDbData_1.1.0
[6] RCurl_1
ps://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=PprBTJthrOIxSMiD9GCrT3UpvPflkGUmM65M7FDTevs&e=
--
, those are the versions I
had been using:
other attached packages:
[1] GenomicRanges_1.31.19 GenomeInfoDb_1.15.5 IRanges_2.13.25
[4] S4Vectors_0.17.31 BiocGenerics_0.25.3
And I had pulled them from biocLite...what's going on?
-Nathan
On 02/10/2018 06:19 PM, Hervé Pagès wrote:
Hi
.1.0 RCurl_1.95-4.10
[7] bitops_1.0-6
```
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Matrix_1.2-12
[21] GenomeInfoDbData_0.99.1 ggplot2_2.2.1 codetools_0.2-15
microbenchmark_1.4-2.1
[25] bitops_1.0-6RCurl_1.95-4.10 sandwich_2.4-0
compiler_3.4.3
[29] scales_0.5.0mvtnorm_1.0-6 zoo_1.8-0
(I have also made a benchmark on &q
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t which seems to come from
a rather excessive-looking example in the makeTxDbFromBiomart man page -
that maybe could better live in a vignette, not least for reducing
brittleness? )
Best wishes
Wolfgang
30.1.18 19:00, Hervé Pagès scripsit:
This is done in GenomicFeatures 1.31.6.
No
c4Op-wxmvtyLA&e=
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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
Seattl
.
This morning I fixed the problem in IRanges 2.13.5. This new
version won't be available via biocLite() before tomorrow though.
In the meantime you can grab and install it directly from git.
Sorry for the inconvenience,
H.
--
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Program in Computational Biology
Division of Public H
d out that the change was required on
ensembldb by examining one by one the upstream dependencies or is there
some automatic way to know what package upstream needs to have fixed its
NAMESPACE?
robert.
On 12/20/2017 04:08 AM, Hervé Pagès wrote:
Hi Robert,
Gviz depends on ensembldb which nee
&s=4YrMshnMnZYQexNOs5qmPLZ-7avBU6Ak3aFJxWxV-fI&e=
it seems this is related to the following recent change in Rsamtools:
commit 4c9af13619f8b16955682072da316a0a961a5623
Author: Hervé Pagès
Date: Fri Dec 15 10:07:38 2017 -0800
use new path() generic defined in BiocGenerics instead of ow
on is prohibited. If you are not the intended recipient,
please contact the sender immediately and destroy or permanently delete
all copies of the original message./
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Fred Hutchinson Cancer Research Center
1100
office phone)
<mailto:felix.er...@ulb.ac.be> felix.er...@ulb.ac.be
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Note that if these diagrams are important, then you will probably need
to consider porting your fixes to release. Your regular users use
release, not devel.
Best,
H.
Cheers,
Vlad
On Tue, Nov 28, 2017 at 6:11 PM Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:
Hi Vladimir,
mmh... scm
n rule out that this is a Windows/Linux thing, because the Travis build
error, which pointed to an difference in the first place,
didn‘t occur with bioc-release, just with bioc-devel.
Thanks for any advice and suggestions.
Felix
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fail if built in the package vignette.
Would it be possible to address this issue?
Many thanks,
Vlad
--
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 1902
o Napolitano
wrote:
Il 29/10/2017 22:45, Hervé Pagès ha scritto:
In particular, I'd like to read more about how to create a backend for
DelayedArray. Is there any documentation available beyond the
reference manual?
I'm guilty. I plan to remedy this ASAP. In the mean time I'
mp;d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8qaKmmV2EdC-xaZnriUy443QdJDwRyX20KDCNvz39HQ&s=aTsEAQSOItaNjA9bGc6cVS2MC6X10C1m1JLbwrFVgis&e=
Sean
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hu
altered it
manually. Since the problem was solved, I didn’t send any further email.
Best regards,
Arman Shahrisa
----
*From:* Hervé Pagès
*Sent:* Thursday, November 16, 2017 9:08:47 PM
*To:* Arman Shahrisa; bioc-devel
*Subject:*
-
Isn't that the new file?
H.
http://bioconductor.org/packages/devel/bioc/src/contrib/cbaf_1.1.2.tar.gz
Best regards,
Arman Shahrisa
*From: *Hervé Pagès <mailto:hpa...@fredhutch.org>
*Sent: *Thursday, November 16, 2017 14:53
*To: *Arman Shahrisa <mail
ilman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=btyTSHdxI_K--g8D_jB6Sg_h7_06w1StseJhSqwekZ4&s=BBEbMys1mFJ85V0yPKT_cxqIkrFnO062bAQEhLn1BN4&e=
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Hervé Pagès
Program in Computational Biology
Division of Public H
2 more things:
On 11/07/2017 02:10 PM, Hervé Pagès wrote:
Hi developers,
In this recent thread:
https://stat.ethz.ch/pipermail/bioc-devel/2017-October/012154.html
some of you expressed the desire to be able to have extra/longer unit
tests in their package, with these tests being run on a
f the 'R CMD check' command.
Just to clarify, the daily software packages aren't changed: they
still run the tests located in the tests/ folder and the TIMEOUT
limit is still 40 min.
Feedback/questions/comments are welcome.
Cheers,
H.
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e and data-expriment builds ;-)
Thanks for your patience,
H.
On 11/01/2017 08:21 AM, Hervé Pagès wrote:
Hi Sokratis,
Not sure why but it seems that for some reason the build machines
didn't manage to install pcxn so far. Until only now. I went on
build machine malbec1 to check whether it man
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s
Elm & Carlton Streets
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*From:* Sokratis Kariotis mailto:s.kario...@sheffield.ac.uk>>
*Sent:* Tuesday, October 31, 2017 11:20:39 AM
*To:* Shepherd, Lori
*Cc:* Hervé
i_xfX2OEILrQ3I2u0&e=
Can you please let me know if the page has not been updated for the
packages yet or if I would need to do something at my end to update the
version reported on the page?
Thanks so much
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parallel_3.4.2 compiler_3.4.2
[19] BiocGenerics_0.22.1 AnnotationDbi_1.38.2 memoise_1.1.0
[22] tibble_1.3.4
On 10/27/2017 10:05 AM, Hervé Pagès wrote:
Hi Leonard,
Sorry for missing your earlier posts about this. Will look into it.
Thanks,
H.
On 10/27/2017 09:07 AM, Leonard G
pecific questions and are better asked
on r-help or SO.
Thanks,
H.
I replaced pdf_document2 with pdf_document by the way.
Best,
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help with the c++11 problems I mentioned in the previous email.
My package builds and R-checks (and BiocChecks) with no errors and warning
though. I get some notes from BiocCheck but I don¹t think they are of
immediate importance.
Best,
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On 10/23/2017 02:24 PM, Hervé Pagès wrote:
Hi developers,
The builds completed in time today but the build/check report
couldn't be generated in time. So no updated build/check report
today, sorry!
Some of you might have received an automatic build/check failure
notification today. Please
project!
Cheers,
H.
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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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fa
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On 10/23/2017 01:42 PM, Martin Morgan wrote:
On 10/23/2017 04:40 PM, Hervé Pagès wrote:
Hi Elizabeth,
Thanks for troubleshooting this.
Note that testing with identical()/checkIdentical() is safer than with
'any(sort(colnames1) != sort(colnames2))'. The latter won't do the
ution, or use of this email message is prohibited. If you have received
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Great! Thanks Paolo. H.
On 10/21/2017 09:33 AM, Paolo Martini wrote:
I see,
thanks a lot!
I changed clipper package. The next release should work!
Thanks again.
2017-10-20 17:38 GMT+02:00 Hervé Pagès mailto:hpa...@fredhutch.org>>:
Hi Paolo,
FYI 3 days ago I contacted Ga
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;graphite") in your investigation.
Martin
Anyone has suggestions on how to debug this?
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