It's busted. I think Lori said something about it, but I can't find that now.
You could put in an issue
https://github.com/Bioconductor/support.bioconductor.org/issues
-Original Message-
From: Bioc-devel On Behalf Of Hooiveld,
Guido via Bioc-devel
Sent: Wednesday, March 26, 2025 3:54 A
I don't think anybody needs to help Luca. It's simple enough to unsubscribe
here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
-Original Message-
From: Bioc-devel On Behalf Of Hervé Pagès
Sent: Tuesday, March 25, 2025 2:18 PM
To: Luca Lepore
Cc: bioc-devel@r-project.org
Subject: Re:
You are looking at the build report for 1.32.0. You will have to wait for
1.32.1 to propagate, and should check the build report after that has happened.
Best,
Jim
-Original Message-
From: Bioc-devel On Behalf Of Alexander Blume
Sent: Monday, March 3, 2025 1:19 PM
To: bioc-devel@r-proj
Hi Tulip,
You have incremented the version for the release branch, but not for the devel
branch.
Best,
Jim
From: Tulip Nandu
Sent: Thursday, December 5, 2024 12:42 PM
To: Kern, Lori ; James W. MacDonald
; Mike Smith
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] groHMM package
You need to commit your changes to g...@git.bioconductor.org, which you
apparently have not done as yet (you should have g...@git.bioconductor.org set
up as a remote which you can see by doing git remote -v). The last commit is
Jennifer Wokaty bumping the version for the last release:
/groHMM$
You could just grab Sean's version from his GEOquery GitHub and put the
function in your package.
https://github.com/seandavi/GEOquery/commit/b3f81349f937870ae030757b454a02fa759b4da7
Best,
Jim
-Original Message-
From: Bioc-devel On Behalf Of Zhu, Jack
(NIH/NCI) [E] via Bioc-devel
Se
As I already noted on the support site, you need to use makeOrgPackage, which
has a help page, and a vignette
https://bioconductor.org/packages/release/bioc/vignettes/AnnotationForge/inst/doc/MakingNewOrganismPackages.html
-Original Message-
From: Bioc-devel On Behalf Of KABILAN S
Sent:
You are trying to use a release version number on a devel package. See here:
https://contributions.bioconductor.org/versionnum.html
-Original Message-
From: Bioc-devel On Behalf Of Brian Roberts
via Bioc-devel
Sent: Thursday, August 22, 2024 4:53 PM
To: bioc-devel@r-project.org
Subject:
.37.1
[4] S4Vectors_0.41.5 Biobase_2.63.0 BiocGenerics_0.49.1
These new packages are still on the builder, and have to be transferred over to
the download repository, which I imagine will happen sometime next week.
Best,
Jim
From: Anatoly Sorokin
Sent: Thursday, April 18, 2024 11:01 PM
There was an error in the scripts used to generate the organism packages that
excluded (among other genes) GRPEL1. We have rectified the error and are
re-running. The updated packages should be available early next week.
-Original Message-
From: Bioc-devel On Behalf Of James W
We have to re-generate these packages - there was an error that excluded 65
genes (total) from nine of the species. They will be available early next week.
Sorry for the delay!
Best,
Jim
-Original Message-
From: Bioc-devel On Behalf Of Kern, Lori via
Bioc-devel
Sent: Thursday, Marc
It is the wrong place to send the request. This listserv is for package
developers. If you want support please use support.bioconductor.org.
-Original Message-
From: Bioc-devel On Behalf Of Anatoly Sorokin
Sent: Thursday, April 18, 2024 12:40 AM
To: bioc-devel@r-project.org
Subject: [Bio
an I have tried many
(many) times to get affy removed in lieu of oligo, to no avail.
From: Tim Triche, Jr.
Sent: Thursday, March 28, 2024 10:40 AM
To: James W. MacDonald
Cc: Vincent Carey ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now
available
As well as
> subsetByOverlaps(transcripts(Homo.sapiens), GRanges("chrM:1-16569"))
'select()' returned 1:1 mapping between keys and columns
GRanges object with 37 ranges and 2 metadata columns:
seqnames ranges strand | TXIDTXNAME
|
[1] chr
It depends on your OS. If you are on a Linux derivative not named macOS, you
can get the sources here: https://cran.r-project.org/src/base-prerelease/ You
want R-devel with the latest date. If you are on Windows, you can get the
installer here https://cran.r-project.org/bin/windows/base/rdevel.h
Are you subscribed to the bioc-devel mailing list?
-Original Message-
From: Bioc-devel On Behalf Of Marek
Gierlinski (Staff)
Sent: Thursday, January 25, 2024 5:51 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] BiocCheck error
When running BiocCheck::BiockCheck() on my package, it
It's not clear from your screenshot that you checked out the release branch,
made the fix, and then tried to push? You don't want to push your devel branch
onto the release branch.
https://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel
-Original Messag
geneAnnotation <- createGeneAnnotation(TxDb = tx, OrgDb = org.Hs.eg.db)
Best,
Jim
From: Christian Arnold
Sent: Tuesday, December 12, 2023 9:35 AM
To: Vincent Carey ; James W. MacDonald
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects
Dear Vincent
I don't believe a different OrgDb is required. The OrgDb package is meant to
provide annotations for genes such as gene symbol or GO term, etc, which are
orthogonal to the sequence of the genome, so the current version should suffice.
-Original Message-
From: Bioc-devel On Behalf Of Vin
Hi Stephanie,
I didn't add the tags to the original post, but I did edit the post to
highlight the code, and then I responded. I guess it's possible that either
action caused the email to be generated?
Best,
Jim
-Original Message-
From: Bioc-devel On Behalf Of Stephanie
Gogarten
S
See here
https://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel
-Original Message-
From: Bioc-devel On Behalf Of Michael Shapiro
Sent: Wednesday, April 19, 2023 8:32 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] maintenance question
I recen
You have this in line 1093-1094
```{r}
samp_frac = out$samp_frac
And yet it appears that there is no 'out' object ever generated. There is an
'output' object, that perhaps you meant to use?
Also, the vignette building is skipped for Windows and MacOS, which is why it
is passing check on those
That looks like you have the wrong RSA key. You should be able to check which
key you are using by logging in here:
https://git.bioconductor.org/BiocCredentials/login/
-Original Message-
From: Bioc-devel On Behalf Of Gabriel Odom
Sent: Thursday, February 9, 2023 1:56 PM
To: bioc-devel@r
It appears that you don't actually want random colors, but instead you want the
same colors each time. Why not just generate the vector of 'random distinct
colors' one time and save the vector of colors?
-Original Message-
From: Bioc-devel On Behalf Of Meng Chen
Sent: Monday, November 2
You are pushing to the master repo, but then are checking the build results
from the RELEASE_3_14 branch. Are you also checking out the release branch and
making changes/pushing there as well?
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
Best,
Jim
-Origi
Err. check that. Release is 3.13, so you should be checking out RELEASE_3_13
-Original Message-
From: James W. MacDonald
Sent: Friday, September 17, 2021 2:23 PM
To: 'Kort, Eric' ; bioc-devel@r-project.org
Subject: RE: Bioconductor build system using old commit
You are push
Webster lake. Has it been submitted yet? ;-D
-Original Message-
From: Bioc-devel On Behalf Of Steve Lianoglou
Sent: Wednesday, August 25, 2021 12:02 PM
To: Nitesh Turaga
Cc: Russell Bainer ; Hervé Pagès
Subject: Re: [Bioc-devel] Best practices for joint release/update of BioC
packages
Perhaps this helps explain things?
> z <- entrez_search("gtr","muscle_weakness", retmax = )$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$scientificname)))
A
The release version of your package is 1.8.0, and the devel is on increment
ahead (e.g., 1.9.x). You cannot increment the middle version number of your
release package because that makes it a devel package, hence the pre-release
hook denying your changes.
You should change the version to 1.8.1
You are looking at the devel version of your package on git, but the release on
the Bioconductor website.
/Rpacks/deltaCaptureC$ 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
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 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
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,
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
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
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
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
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()'
. 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
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]]
>
> ___
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:
>
://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
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
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
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
James W. MacDonald, M.S.
Biostatistici
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
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)
>
; [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
>
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
>
du I 508.523.0203
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washing
rch?q=icme&oq=icme&aqs=chrome..69i57j69i60j69i65l3j69i60.1858j0j7&sourceid=chrome&ie=UTF-8#
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/
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
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]]
>
> ___
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
>
(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
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
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> e-mail
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]]
>
> __
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,
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
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
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
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]]
>
> _________
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
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
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://
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
>
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>>
>>
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 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
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
ia
> >>>>
> >>>> [[alternative HTML version deleted]]
> >>>>
> >>>> ___
> >>>> Bioc-devel@r-project.org mailing list
> >>>> https://stat.et
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]]
>
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
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
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
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
[[alt
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
>> 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
r=k93hb-mTY3FnvPobw-XK7YsatsLioMulL2zwAXZNoRo&m=LgNbgBxYv
>>> 1xoQVTZ41uDrgo
>>> XiSE2MpwIrBuyrgPBGQQ&s=_cCwN-6SMimKn17T4EAM9tLSK8ouLKv-GtD9MKPf9_U&e=
>>>
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>&g
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
_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
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"
>
#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
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
__
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
[[altern
orward to hearing your thoughts,
> Jesper
>
> [[alternative HTML version deleted]]
>
> ___
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James W. MacDonald, M.S.
Biostatistician
University
iew it if the maintainer does not have time?
>
> best
> Witold
>
>
>
>
>
> --
> Witold Eryk Wolski
>
> _______
> Bioc-devel@r-project.org mailing list
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>
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James
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
; 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
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.
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.
>
> 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]]
>
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> Bioc-d
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
n
> Ireland
> http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en
>
> [[alternative HTML version deleted]]
>
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J
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,
&
.
> 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
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
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has been previously removed?
>
> Thanks,
> Sean
>
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James W. MacDon
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
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