The (very popular) safe package breaks due the quite disruptive class(matrix)
update in R-4.0.0 which I could easily fix if given access.
Marcel and I contacted the maintainer of the safe package (William T Barry),
but received the following automatic notice.
"AUTOMATIC NOTICE: Please note
Great, thanks for the update!
From: Interdonato, Kayla
Sent: Thursday, February 27, 2020 2:40 PM
To: Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: EXTERNAL: Re: [Bioc-devel] List of Deprecated Packages Bioc 3.11
When generating
Why will org.At.tair.db be deprecated and by what will it be replaced? It's the
org package for Arabidopsis and thus central for gene ID mapping when working
with Arabidopsis data ...
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
Department of Epidemiology and Biostatistics
CUNY School of Public
Cc: Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10
Hi Ludwig,
Thank you for volunteering to take over as maintainer for PathNet and
PathNetData.
You should now have access to both packages as the maintainer. They should show
Yes, I could do that if needed.
From: Shepherd, Lori
Sent: Wednesday, December 4, 2019 1:28 PM
To: Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: Final List of Deprecated Packages for Bioc3.10
***ATTENTION: This email came from an external source. Do
Hi Lori,
Is it possible to undeprecate the "PathNet" package?
I just checked, the problem is a failing unit test, causing the otherwise well
working package to fail R CMD check.
I fixed this here on a local clone of
https://git.bioconductor.org/packages/PathNet and could push these minor
> What is your experience with pkgdown?
>>
>> > Martin
>>
>> > On 9/25/19, 9:44 AM, "Bioc-devel on behalf of Laurent Gatto"
>>
>> wrote:
>>
>> > I think this would be very useful. This is one of the
Dear Bioc-Team,
I repeatedly wondered whether it would be possible to display the reference
manual
as HTML instead of PDF on a package's landing page. This is already possible
for vignettes.
HTML reference manuals have at least two advantages:
1. links to functions of other package in the
Hi,
According to
http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html
all SPB machines run different snapshots of R-devel with the most recent one
(2019-01-22 r76000,
already >1 month outdated) installed on celaya2.
I observe two things:
1. My package builds on celaya2,
esn't seem to have an internet connection?
Thank you,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
From: Bioc-devel on behalf of Shepherd, Lori
Sent: Tuesday, January 22, 2019 9:26 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel]
> Having said that, I'll note that specifying R as a dependency, and a version
> of R as a criterion for your package, is really a mis-nomer for a
> Bioconductor package -- of course it uses R, and the version of R in use
> determines the Bioconductor version(s) that can be used! So a rational
While this might be obvious to most of us, it seems to be less clear to others.
In particular, those who worked out their first package and wonder what's the
difference between having a package available on Github, CRAN, or Bioconductor.
I wonder whether it would be helpful for the Bioc
o realize this within my code, i.e. checking whether the
code is currently subject to R CMD check (and accordingly reducing the number
of cores used)?
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
From: Bioc-devel <bioc-devel-boun...@r
,
Deadline for packages passing ��R CMD build�� and ��R CMD check�� without
errors or warnings).
Best,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
From: Shepherd, Lori <lori.sheph...@roswellpark.org>
Sent: Monday, March 26, 2018 8
Hi Lori,
Yes I would take over maintenance.
Anything particular that I need to take care of?
Otherwise I would just follow:
https://bioconductor.org/developers/how-to/git/maintain-github-bioc/
to accordingly set this up.
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public
here serial) computation is carried out?
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
in over again, as it is likely that
some datasets of the compendium share the corresponding annotation db.
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
From: Martin Morgan <martin.mor...@roswellpark.org>
Sent: Friday, Janu
mpiler_3.4.1pillar_1.1.0 Biostrings_2.46.0 XML_3.98-1.9
[25] pkgconfig_2.0.1
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Martin Morgan
<martin.mor..
on AnnotationDbi, and
AnnotationDbi itself, before sending the job to the workers (and reload all of
them after the job has finished?)
Thanks a lot,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
[[alternative HTML version deleted
to obtain something similar using BiocParallel?
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.1
Matrix products: default
BLAS:
/Library
Great! Thanks for resolving this so fast. Ludwig
From: Shepherd, Lori <lori.sheph...@roswellpark.org>
Sent: Friday, December 15, 2017 1:48 PM
To: Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: GSE62944, empty EH164 and EH165
Thank you for br
Hi Lori,
I would be willing to take over maintenance of
ToPASeq
in case maintainers remain unresponsive.
Best,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Sh
t;package")
[1] "SummarizedExperiment"
> str(x)
Formal class 'SummarizedExperiment0' [package "SummarizedExperiment"] with 0
slots
Named list()
It would be great if this could be updated.
Thanks a lot,
Ludwig
--
Dr. Ludwig Geistlinger
CUNY School of Public Health
Yes, I am experiencing the same problem for the EnrichmentBrowser package.
The release package landing page holds all the new stuff, but the vignette
is still the one of the old release.
Best,
Ludwig
--
Dr. Ludwig Geistlinger
eMail: ludwig.geistlin...@bio.ifi.lmu.de
> Dear,
>
>
warnings:
Warning: no function found corresponding to methods exports from
Organism.dplyr for: supportedFilters
See
/home/biocbuild/bbs-3.6-bioc/meat/EnrichmentBrowser.Rcheck/00install.out
for details.
I am not quite sure how to deal with that.
Any advice?
Thanks,
Ludwig
--
Dr. Ludwig
n the BiocStyle vignette under Appendix B "Attached LATEX
> packages"
> are installed, and possibly the up-to-date.
>
> Best,
> Andrzej
>
> On Tue, Sep 12, 2017 at 11:03 PM, Ludwig Geistlinger <
> ludwig.geistlin...@bio.ifi.lmu.de> wrote:
>
>> Dea
r your understanding and cooperation.
>
> Kind regards,
> Andrzej OleÅ
>
> [1]
> http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle2.pdf
>
> [[alternative HTML version deleted]]
>
>
_
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Dr. Ludwig Geistlinger
eMail: ludwig.geistlin...@bio.ifi.lmu.de
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
't an eSet coercion method be preferable because it would
> cover ExpressionSet as well as all the classes that extend eSet?
>
> [[alternative HTML version deleted]]
>
> ___________
> Bioc-devel@r-proj
;>>>>>> clnanno = sub(".db", "", annotation(z))
>>>>>>> stopifnot(require(paste0(annotation(z), ".db"),
>>>>>>> character.only=TRUE) )
>>>>>>>
seems to have built without problems.
What is the problem here?
Thanks,
Ludwig
--
Dr. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München
Tel.: 089-2180-4067
eMail
of the package?
Thx,
Ludwig
> On 07/18/2016 04:27 AM, Ludwig Geistlinger wrote:
>> Hi,
>>
>> I am trying to access the devel page of my package
>>
>> https://www.bioconductor.org/packages/devel/bioc/html/EnrichmentBrowser.html
>>
>> but I am obtaining
>
Hi,
I am trying to access the devel page of my package
https://www.bioconductor.org/packages/devel/bioc/html/EnrichmentBrowser.html
but I am obtaining
Page Not Found
The page you were looking for was not found.
What is the reason for that?
Thx,
Ludwig
--
Dr. Ludwig Geistlinger
Lehr- und
FYI
That works for me, but maybe this is also of interest for others, so I
wonder if somebody of the Bioc annotation/experiment team (Sonali,
Valerie, Martin?) could update this accordingly for ExperimentHub?
Best,
Ludwig
--
Dr. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
ults in the observed discrepancies with the above description,
indicating that this is an outdated version of the dataset.
Is it possible to
(1) update it accordingly
(2) include a varLabel, i.e. pData column indicating whether this is a
tumor or an adjacent normal sample for the respective cancer ty
implementation of the desired
functionality?
Thx & Best,
Ludwig
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München
Tel.: 089-2180-4067
eMail: ludwig.geis
RNINGs that appeared in the latest build
persist, for example
* checking for code/documentation mismatches ... WARNING
just issues a warning with any further details.
Thx,
Ludwig
>
>
> On 05/02/2016 11:11 AM, Ludwig Geistlinger wrote:
>> I encounter the same issue w
;>>
>>
>>
>> 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 her
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München
Tel.: 089-2180-4067
eMail: ludwig.geistlin...@bio.ifi.lmu.de
& Best,
Ludwig
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München
Tel.: 089-2180-4067
eMail: ludwig.geistlin...@bio.ifi.lmu.de
> BioC dev
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München
Tel.: 089-2180-4067
eMail: ludwig.geistlin...@bio.ifi.lmu.de
__
of the page (--> Package Archives).
How to resolve this?
Thx,
Ludwig
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München
Tel.: 089-2180-4067
eM
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München
Tel.: 089-2180-4067
eMail: ludwig.geistlin...@bio.if
) slot in ExpressionSet was to
> include the microarray chip identifier, so that one references this when
> translating from probeset to gene identifiers.
>
> Martin
> ____________
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig
&g
at one references this when
> translating from probeset to gene identifiers.
>
> Martin
> ____________
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig
> Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de]
> Sent: Thursday, Decem
the organism
under investigation in a convenient format also for non-Biocs.
I have not found something similar in existing packages and I am wondering
whether this could be something of general interest.
Best,
Ludwig
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Hi,
I am experiencing troubles installing "Hmisc", especially its dependency
"acepack", via
> biocLite("acepack")
in R-devel installed from the "R-devel-mavericks-signed.pkg" downloaded
from https://r.research.att.com/.
The error reads:
BioC_mirror: https://bioconductor.org
Using
d
>>
>> https://stat.ethz.ch/pipermail/r-sig-mac/2015-October/011641.html
>>
>> which points to the R-admin manual and especially
>>
>> https://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X
>>
>> From the discussion (especially the posts b
I agree with Martin, I would love to see something like that.
Especially if this would not be restricted to chromatin interactions, but
also allows to represent protein-protein, transcriptionFactor-targetGene,
miRNA-mRNA etc (e.g. via suitably tailored subclasses).
This might nicely work together
a developer's best practice is on that - ignoring the
notes, adding all Biobase/ExpressionSet functionality via imports, or
indeed depending on both packages.
Best,
Ludwig
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians
work better??
http://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v79.html
-Robert
On Wed, Jun 3, 2015 at 7:04 AM Ludwig Geistlinger
ludwig.geistlin...@bio.ifi.lmu.de wrote:
Dear Bioc annotation team,
Querying TxDb.Hsapiens.UCSC.hg38.knownGene for gene coordinates
/data/annotation/html/EnsDb.Hsapiens.v79.html
-Robert
On Wed, Jun 3, 2015 at 7:04 AM Ludwig Geistlinger
ludwig.geistlin...@bio.ifi.lmu.de wrote:
Dear Bioc annotation team,
Querying TxDb.Hsapiens.UCSC.hg38.knownGene for gene coordinates, e.g.
for
BRCA1; ENSG0012048; entrez:672
via
of biomaRt, but I want to explicitely use the Bioc annotation
functionality).
Thanks!
Ludwig
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München
/).
Sorry for the inconvenience!!
Best,
Ludiwg
Hi,
On Thu, Apr 9, 2015 at 10:27 AM, Ludwig Geistlinger
ludwig.geistlin...@bio.ifi.lmu.de wrote:
Error in file(con, r) : cannot open the connection
In addition: Warning message:
In file(con, r) : unable to resolve 'annotationhub.bioconductor.org
AnnotationDbi_1.29.17
[23] htmltools_0.2.6 interactiveDisplayBase_1.5.1
Please provide sessionInfo()
The class is defined in AnnotationHub in devel. Perhaps it is not
suitably
exported.
On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger
ludwig.geistlin
samples from The
Cancer Genome Atlas of class ExpressionSet; reason:
ExpressionSetResource is not a defined class
Did I do something wrong?
Thank you for your help,
Ludwig
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig
are expected to come into the game.
So how to resolve this - am I overseeing something?
Thanks Best,
Ludwig
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333
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