#x27;tximport',
> 'VariantAnnotation', 'vegan', 'VGAM', 'withr', 'XLConnect',
> 'XLConnectJars',
> 'xml2'
> Update all/some/none? [a/s/n]: n
> > sessionInfo()
> R version 3.3.0 (2016-05-0
ll_github() and thence to
> devtools::install().
>
> Dan
>
>
> - Original Message -
> > From: "Martin Morgan"
> > To: "James W. MacDonald" , "Sean Davis" <
> sdav...@mail.nih.gov>
> > Cc: "bioc-devel"
>
_2.4.2
> [41] ggplot2_2.1.0 digest_0.6.9
> [43] biovizBase_1.20.0 shiny_0.13.2
> [45] tools_3.3.1 bitops_1.0-6
> [47] RCurl_1.95-4.8RSQLite_1.0.0
> [49] dichromat_2.0-0 Formula_1.2-1
> [51] cluster_2.0.4 Matrix_1.2-6
> [53] data.ta
050
> Australia
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environm
r=k93hb-mTY3FnvPobw-XK7YsatsLioMulL2zwAXZNoRo&m=LgNbgBxYv
>>> 1xoQVTZ41uDrgo
>>> XiSE2MpwIrBuyrgPBGQQ&s=_cCwN-6SMimKn17T4EAM9tLSK8ouLKv-GtD9MKPf9_U&e=
>>>
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>&g
>> Pan Du has several packages. Is this an issue for all of those packages
>> or just lumi?
>>
>
> I think that's a reasonable conclusion. Martin
>
I am not sure I follow. What is the reasonable conclusion? That it's just
this one package, or all of the
just trying to find a workable way to add git
functionality for those who prefer to work with git?
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
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Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
[[alt
ges’, ‘GenomicFeatures’, ‘GenomeInfoDb’,
> ‘rtracklayer’, ‘AnnotationHub’, ‘Rsamtools’ are not available for package
> ‘ensembldb’
> * removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/ensembldb’
> ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’,
> ‘SummarizedExperiment’, ‘R
ebody else's package and they are consistently failing you
might contact them and find out if you can help.
Jim
>
> Best,
> Nick Clark
>
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org ma
g him to perform a post-mortem examination: he may be able to say
> what the experiment died of. - Ronald Fisher
>
> [[alternative HTML version deleted]]
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman
gt; Level 4, 4326-WS10, Building 2,
> King Abdullah University of Science and Technology (KAUST),
>
> Thuwal 23955-6900, Kingdom of Saudi Arabia,
> Phone: (+966 12) 808 0614, Mobile: (+966) 5 40375986,
> Email Address: amit.subu...@kaust.edu.sa
>
> [[alternative HTML version deleted]]
>
ia
> >>>>
> >>>> [[alternative HTML version deleted]]
> >>>>
> >>>> ___
> >>>> Bioc-devel@r-project.org mailing list
> >>>> https://stat.et
C_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.26.0
loaded via a namespace (and not attached):
[1] compiler_3.4.0 to
On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> On 04/26/2017 10:00 AM, James W. MacDonald wrote:
>
>> I see the binaries on the respective web pages, but biocLite seems not to:
>>
>
> I'm not 100% sure but can you tr
On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> On 04/26/2017 10:34 AM, James W. MacDonald wrote:
>
>>
>>
>> On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan
>> mailto:martin.mor...@roswellpark.org>>
>>
>
On Wed, Apr 26, 2017 at 11:26 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> On 04/26/2017 11:23 AM, James W. MacDonald wrote:
>
>>
>>
>> On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan
>> mailto:martin.mor...@roswellpark.org>>
>>
significant gene feature
>
> numFeature: number of gene features within the gene
>
>That is to say, to create a a bulleted list without bullets.
>
>Does anyone has idea on how to change settings in test.R file?
>
>
>Thank you,
>
>Aimin
>
27;m new to Bioconductor package maintenance, so I apologize if I'm missing
> anything simple, but I'm really stuck!
>
> [[alternative HTML version deleted]]
>
> _______
> Bioc-devel@r-project.org mailing list
> https://
CGAbiolinks TCGAbiolinksGUI vsn
>>
>>
>> For a little more detail, the problem is manifest as 'unknown' authors in
>> a git commit, e.g., in Biobase from svn user 'jmc'
>>
>> commit b5ae43bc8aae967b80062da13e5085a6a305b274
>> Autho
Never mind. It's all Patrick Aboyoun, for whom I think this should persist.
Jim
On Tue, Aug 22, 2017 at 4:13 PM, James W. MacDonald wrote:
> Hi Martin and Nitesh,
>
>
> On Tue, Aug 22, 2017 at 10:09 AM, Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
>
&g
of Grenoble (BIG)*
> *CEA / Grenoble*
> *17 avenue des Martyrs*
> *F-38054 Grenoble Cedex 9*
> */Tél. : 04.38.78.44.14/*
> */Fax : 04.38.78.50.51/*
>
> http://www.edyp.fr/
>
> [[alternative HTML version deleted]]
>
> _________
ernative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> This email message may contain legally privileged and/or confidential
> information. If you
ced, so it looks
like the GO source date were outdated?
Jim
>
> The files were updated but the rdatadateadded was not updated when I added
> the new files.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Bios
e any other way to install
> the package?
>
>
> Thanks,
>
> Maryam
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-d
devel
> >>
> >
> >
> > This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
chem-bla-ics.blogspot.com/
> PubList: https://www.zotero.org/egonw
> ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
> ImpactStory: https://impactstory.org/u/egonwillighagen
>
> [[alternative HTML version deleted]]
>
> __
ponsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail
(BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) 'pd.hugene.1.0.st.v1'
package 'pd.hugene.1.0.st.v1' is available as a source package but not
as a binary
So maybe you are thinking of an older R installation, from back when we
still made binary versi
AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann http://www.IPB-Halle.DE
> Weinberg 3 http://msbi.bic-gh.de
> 06120 Halle Tel. +49 (0) 345 5582 - 1470
> +49 (0) 345 5582 - 0
>
ying,
> distribution, or use of this email message is prohibited. If you have
> received this 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]]
>
> ___
Ranges_2.17.5
> > [4] S4Vectors_0.21.23Biobase_2.43.1 BiocGenerics_0.29.2
> >
> > loaded via a namespace (and not attached):
> > [1] Rcpp_1.0.1 digest_0.6.18 DBI_1.0.0 RSQLite_2.1.1
> > [5] blob_1.1.1 bit64_0.9-7 bit_1.1-14 compiler_3.7
rch?q=icme&oq=icme&aqs=chrome..69i57j69i60j69i65l3j69i60.1858j0j7&sourceid=chrome&ie=UTF-8#
> >
>
> [[alternative HTML version deleted]]
>
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du I 508.523.0203
>
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>
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Biostatistician
University of Washing
n error if you try
> to access something with a character when you should be using a numeric.
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
; [53] memoise_1.1.0 gridExtra_2.3
> [55] biomaRt_2.41.9stringi_1.4.3
> [57] RSQLite_2.1.2 rlang_0.4.0
> [59] pkgconfig_2.0.3 bitops_1.0-6
> [61] lattice_0.20-38 purrr_0.3.2
> [63] GenomicAlignments_1.21.7 labeling_0.3
>
7833 bytes
> ======
> downloaded 7833 bytes
>
> trying URL 'https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz'
> Content type 'application/x-gzip' length 294967 bytes (288 KB)
>
very of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this ema
>
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>
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>
--
James W. MacDonald, M.S.
Biostatistici
tation to download but I am
> not finding it. Do you have it available?
>
> Thank you,
> Camila
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mail
uld go on but I think the point is clear. This package is full of data
> frames and nested lists and it would be nice to use SE or MAE to tidy up
> the global environment. Is there a way of turning many many data frames/
> nested lists into an SE or MEA object? If there is please
://geneontology.org/docs/download-ontology/) for the downloadable data,
so we should consider switching.
I bring this up because apparently the current release GO.db is missing
terms that were added as far back as 2018.
Best,
Jim
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Further to this point, when comparing to the latest OBO from geneontology,
it looks like the current GO.db has just over 1000 GO IDs that are not in
GO any longer, and almost 500 GO IDs are in the GO OBO file that are not in
GO.db
On Wed, Apr 1, 2020 at 12:11 PM James W. MacDonald wrote:
>
rbird>https://www.box.com/shared/3sj9i3lpkixkq85qar0r
Mozilla Thunderbird <http://www.getthunderbird.com> makes it easy to
share large files over email.
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing lis
version(s) should propagate through the build machines in a day
or so.
Best,
Jim
On 6/16/2014 10:35 AM, James W. MacDonald wrote:
Hi Kristóf,
On 6/16/2014 10:20 AM, Kristóf Jakab wrote:
It seems I can't send attachments, I copy the codes here.
test_plotLocation_affy.R
#!/usr/bin/env Rs
sity of Sydney Camperdown NSW 2050 Australia
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Biostatistician
University of Washington
Environmental and Occupational Health Sciences
42
c-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
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James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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- DESeq2 Home
Cheers,
Andrzej
On Tue, Jul 22, 2014 at 6:26 PM, James W. MacDonald wrote:
Given that we have an ongoing problem with people inadvisedly clicking and
installing things, is there a good rationale for allowing them to do so?
Perhaps the landing page for each package should be
nk I have up to date instalation of all packages.
Vojtech.
[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
Biostatistician
University of Wash
mmary,
-
## AnnotationDb
metadata,
so it appears summary is no longer exported?
Best,
Jim
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
[[alterna
1.24.2
[64] R.utils_1.33.0 scales_0.2.4 sendmailR_1.1-2
[67] splines_3.1.0 stats4_3.1.0 stringr_0.6.2
[70] survival_2.37-7 tools_3.1.0
VariantAnnotation_1.10.5
[73] XML_3.98-1.1 xtable_1.7-3 XVector_0.4.0
[76] zli
Never mind. Installing all of GOstats, Category, AnnotationDbi and
ReportingTools fixed the issue.
Thanks,
Jim
On Tue, Sep 23, 2014 at 1:55 PM, James W. MacDonald wrote:
> Hi Herve,
>
> No joy:
>
>
> > biocLite("ReportingTools")
> BioC_mirror: http://bio
; were using the release. I've no idea how you could get these warnings
> with the release since the changes I made recently to AnnotationDbi,
> Category, and GOstats are in devel only...
>
> H.
>
> On 09/23/2014 11:05 AM, James W. MacDonald wrote:
>
>> Never mind. In
> > If you are still using this service, you should not have to make any
> > changes due to this upgrade.
> >
> > Please reply to the list if you have any questions about this.
> > Dan
> >
> > ___
> >
Thanks Dan!
On Tue, Sep 30, 2014 at 1:19 PM, Dan Tenenbaum wrote:
>
>
> - Original Message -
> > From: "James W. MacDonald"
> > To: "Dan Tenenbaum"
> > Cc: "bioc-devel"
> > Sent: Tuesday, September 30, 2014 10:14:00 AM
&
Medicine Group
> Karolinska Institute
>
>
>
> [BiocStyle]:
>
> http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
>
> [rmarkdown]: http://cran.r-project.org/web/packages/rmarkdown/
>
>
(does that make a difference ?) Or something
> else ?
>
> Yours,
> Steffen
>
>
>
>
>
> ___
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Biostatistici
h/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
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>
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James W. MacDonald, M.S.
Biostatistician
Uni
p://www.bioinformatica.unito.it
>
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>
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>
--
James W. MacDonald, M.S.
Biostatistician
University o
.0.0RSQLite_1.0.0 DBI_0.3.1
> [4] AnnotationDbi_1.29.12 GenomeInfoDb_1.3.12 IRanges_2.1.35
> [7] S4Vectors_0.5.16 Biobase_2.27.1BiocGenerics_0.13.4
> [10] BiocInstaller_1.17.3
>
> loaded via a namespace (and not attached):
> [1] tools_3.2.0
>
> __
irect
> > te informeren door het bericht te retourneren. Het Universitair Medisch
> > Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de
> > W.H.W.
> > (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat
> geregistreerd
> > bij
&
in on the webpage.
>
> --
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
> ___________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/li
x27; argument
2: In .local(name, pos, envir, all.names, pattern) :
ignoring 'envir' argument
3: In .local(name, pos, envir, all.names, pattern) :
ignoring 'all.names' argument
This is going to be a consistent issue going forwar
tating data in an ExpressionSet? Am I
alone in being concerned about this?
Best,
Jim
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
[[alternative HTML version del
for the
> multiVals argument so that you can get back your results in a 1:1 manner.
> And if you don't like any of the options available for the multiVals
> argument, you can make your own function and pass it in.
>
>
> Anyhow please continue to let us know what you think?
>
>
ll represent an acceptable
> compromise.
>
> Marc
>
>
>
> On 06/05/2015 08:37 AM, James W. MacDonald wrote:
>
> I agree that a warning is probably not the way to go, as it does imply
> that there might have been something wrong with either the input or output.
>
100287898
If we now go to NCBI and look at the five IDs for the first gene, they are
all current, and map to DDX11L1, DDX11L9, DDX11L10, DDX11L2, and DDX11L5.
We can certainly choose the first one (and that is what I do for my
collaborators, in general), but is that the right thing to do? If so, why
has been previously removed?
>
> Thanks,
> Sean
>
> [[alternative HTML version deleted]]
>
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>
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James W. MacDon
ust go with what we have. Please speak up if this will
affect you.
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
[[alternative HTML vers
.
> Because of the crazy timing, before I left I build I pushed into devel a
> fresh set of .DB0s and core packages (in late August) just in case it was
> too crazy to do a refresh right now. But it sounds like you won't need
> that.
>
>
> Marc
>
>
>
> On S
b, "smart", res[["smart"]])
Thanks!
Jim
On Mon, Oct 5, 2015 at 10:16 AM, Marc Carlson wrote:
> You need to scroll down that script a ways... Look for 'yeast'.
>
> On Mon, Oct 5, 2015 at 6:11 AM, James W. MacDonald wrote:
>
>> Hi Marc,
&
n
> Ireland
> http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en
>
> [[alternative HTML version deleted]]
>
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--
J
Yes. The original poster 'owns' their post, and they AFAIK are the only one
who can accept an answer.
On Tue, Oct 20, 2015 at 11:34 AM, Kevin Rue-Albrecht <
kevin@ucdconnect.ie> wrote:
> "Original Post(er)" I assume?
>
>
>
> On 20 October 2015 at 16:1
>
> phone: +41 44 633 0473
> cellphone: +41 79 745 8061
> fax: +41 44 633 1532
> e-mail: blattm...@imsb.biol.ethz.ch<mailto:blattm...@imsb.biol.ethz.ch>
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-d
1. Should duplicate keys be allowed, or should duplicates be removed
before querying the database, preferably with a message saying that dups
were removed?
2. If the answer to #1 is yes, then to be consistent, I will just commit
the patch I have made to both devel and release.
an output that is
>> parallel to the input *in general*.
>>
>> It seems that the current philosophy for select() is to emit a note
>> or a warning every time the output is not parallel to the input.
>> Personally I find this too noisy and not that useful.
; a little less noisy i.e. have warnings (and not messages) only when
> the output is not parallel to the input. Also how about having a
> warning that suggests the use of mapIds()? Something like "Hey, your
> output is not parallel to your input! Use mapIds() if that matters
&g
On Jan 5, 2016 7:01 PM, "Tim Triche, Jr." wrote:
>
> 1) this is a support.bioconductor.org question
> 2) don't use .db0 packages, you will rue the day you did
Can you expand on this statement? Right now all of the ChipDb are built
using a db0 package, so it's not clear to me why this might be a p
iew it if the maintainer does not have time?
>
> best
> Witold
>
>
>
>
>
> --
> Witold Eryk Wolski
>
> _______
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>
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James
orward to hearing your thoughts,
> Jesper
>
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>
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>
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Biostatistician
University
__
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>
--
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Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
[[altern
06/09/2016 10:06 AM, James W. MacDonald wrote:
>
>> You should post this on the support site (
>> https://support.bioconductor.org),
>> using the 'News' item description. This bioc-devel is intended for
>> discussion of issues with development of packages, not re
use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
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>
> ___
. Which made me wonder if there are any instances where
anything but the go or go_all tables are used, but I can't find one, which
makes me wonder why we even have these other tables? So maybe the real easy
fix is to just back out the changes that Martin made, and maybe even remove
the subsetted GO t
Hi Gennady,
That information should probably be cleaned up, and the BiMaps that point
to the location data removed. While the OrgDbs do contain position
information, it's been deprecated, which you would find if you tried to
query using select():
> select(org.Dr.eg.db, "30037", "CHR")
'select()'
hought it was as it did not refer to a
> specific genome, unlike TxDb packages, but then I found what I said in my
> previous emails.
>
>
>
> Thank you very much,
>
> Gennady
>
>
>
> *From: *"James W. MacDonald"
> *Reply-To: *"jmac...@u.washi
ersion
I sent the same to c...@r-project.org, which is the email for the
maintainer. So they have been notified, but maybe somebody knows whomever
is actually maintaining RCurl, and can pull a string?
Best,
Jim
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental
s not a slam-dunk for me at the moment. Can the curl package do
> what you need?
>
> On Mon, Nov 23, 2020 at 11:49 AM James W. MacDonald
> wrote:
>
>> FYI, there appears to be a problem with RCurl on Windows, most likely due
>> to building against an old version of
e to the release
> branch?
>
> I'm sure I must be missing something very basic, but any help would be
> appreciated.
>
> Thanks in advance,
> Ted
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-proj
ut not release.
>
> Here are links to the build reports if it's helpful.
>
> devel: https://bioconductor.org/checkResults/3.13/bioc-LATEST/cmapR/
> release: https://bioconductor.org/checkResults/3.12/bioc-LATEST/cmapR/
>
> Thanks again,
> Ted
>
> On Thu, Dec 10,
You also have a commit from yesterday in master that isn't yet reflected on
the build machine, again because it takes time for the build machine to
build stuff. IIRC we are over 24 hours per build, but that may be old news
(FAKE NEWS!).
On Thu, Dec 10, 2020 at 11:09 AM James W. MacDonald
Hi Oleksii,
That function is just a simplification of the negation of overlapsAny:
> getAnywhere("%outside%")
A single object matching '%outside%' was found
It was found in the following places
package:IRanges
namespace:IRanges
with value
function (query, subject)
!overlapsAny(query, subjec
You are looking at the devel version of your package on git, but the release on
the Bioconductor website.
/Rpacks/deltaCaptureC$ grep Version DESCRIPTION
Version: 1.7.1
/Rpacks/deltaCaptureC$ git checkout RELEASE_3_13
Switched to branch 'RELEASE_3_13'
Your branch is up-to-date with 'origin/RELEAS
The release version of your package is 1.8.0, and the devel is on increment
ahead (e.g., 1.9.x). You cannot increment the middle version number of your
release package because that makes it a devel package, hence the pre-release
hook denying your changes.
You should change the version to 1.8.1
Perhaps this helps explain things?
> z <- entrez_search("gtr","muscle_weakness", retmax = )$id
> any(z %in% keys(org.Hs.eg.db))
[1] FALSE
> zz <- entrez_summary("gene", z)
> table(do.call(c,sapply(extract_from_esummary(zz, "organism"),
> function(x) x$scientificname)))
A
Perhaps this helps explain things?
> z <- entrez_search("gtr","muscle_weakness", retmax = )$id
> any(z %in% keys(org.Hs.eg.db))
[1] FALSE
> zz <- entrez_summary("gene", z)
> table(do.call(c,sapply(extract_from_esummary(zz, "organism"),
> function(x) x$scientificname)))
A
Webster lake. Has it been submitted yet? ;-D
-Original Message-
From: Bioc-devel On Behalf Of Steve Lianoglou
Sent: Wednesday, August 25, 2021 12:02 PM
To: Nitesh Turaga
Cc: Russell Bainer ; Hervé Pagès
Subject: Re: [Bioc-devel] Best practices for joint release/update of BioC
packages
Err. check that. Release is 3.13, so you should be checking out RELEASE_3_13
-Original Message-
From: James W. MacDonald
Sent: Friday, September 17, 2021 2:23 PM
To: 'Kort, Eric' ; bioc-devel@r-project.org
Subject: RE: Bioconductor build system using old commit
You are push
You are pushing to the master repo, but then are checking the build results
from the RELEASE_3_14 branch. Are you also checking out the release branch and
making changes/pushing there as well?
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
Best,
Jim
-Origi
It appears that you don't actually want random colors, but instead you want the
same colors each time. Why not just generate the vector of 'random distinct
colors' one time and save the vector of colors?
-Original Message-
From: Bioc-devel On Behalf Of Meng Chen
Sent: Monday, November 2
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