dear GenomicRanges developers,
my package qpgraph is breaking in devel due to the following behavior of
GenomicRanges:
library(GenomicRanges)
gr <- GRanges(seqnames=rep("1", 10), IRanges(1:10, width=1))
mcols(gr)
DataFrame with 10 rows and 0 columns
mcols(gr) <- cbind(mcols(gr), DataFrame(test
Thanks but that didn’t clarify why users should install the dev version.
Why the package is not on the page
http://bioconductor.org/packages/release/BiocViews.html#___Software
Sorry this is first time I submitted a package to bioconductor and I am not so
familiar with instructions.
> On Sep 11
I think this was fixed in S4Vectors a couple of days ago but I forgot
to bump the version (just did). Sorry.
On Tue, Sep 12, 2017 at 12:06 AM, Robert Castelo wrote:
> dear GenomicRanges developers,
>
> my package qpgraph is breaking in devel due to the following behavior of
> GenomicRanges:
>
> l
Bioconductor has a release version and a devel version. Releases happen twice
a year (The next occurring at the end of October). All new packages accepted
will remain in the devel version of Bioconductor until the next schedule
release. The package for that time, will only be available on the
From http://bioconductor.org/developers/package-submission/
Following acceptance of a package:
Packages accepted on the tracker repository are added to the ‘devel’
branch of the Bioconductor SVN repository, with the current version
number of the accepted package.
Packages are then built by the Bi
Thanks.
Everything is clear to me now.
> On Sep 12, 2017, at 9:08 AM, Shepherd, Lori
> wrote:
>
> Bioconductor has a release version and a devel version. Releases happen
> twice a year (The next occurring at the end of October). All new packages
> accepted will remain in the devel version
Dear all,
Our DeepBlueR package is currently not passing R CMD check in devel because
of a class cache issue:
http://bioconductor.org/checkResults/devel/bioc-LATEST/DeepBlueR/tokay1-checksrc.html
Found more than one class "file" in cache; using the first, from
namespace 'BiocGenerics'
Also defin
yep, i've cloned, built and installed the latest S4Vectors and then
qpgraph builds and checks cleanly. thanks
robert.
On 09/12/2017 03:06 PM, Michael Lawrence wrote:
I think this was fixed in S4Vectors a couple of days ago but I forgot
to bump the version (just did). Sorry.
On Tue, Sep 12
Begin forwarded message:
From: ni41435_ca
mailto:nitesh.tur...@roswellpark.org>>
Subject: Re: [Bioc-devel] Hook declined on a branch
Date: September 12, 2017 at 7:33:00 AM EDT
To: Samuel Wieczorek mailto:samuel.wieczo...@cea.fr>>
You cannot create branches on upstream.
The only ones allowed
Hi Simina,
Please try again now.
The issue was you didn’t submit your SVN ID “s.boca”. This is needed for people
who have been maintainers before the Git transition, to associate your key to
the package.
For new packages this issue doesn’t apply, because we just collect their Github
IDs.
Ho
Let's consider loading the `bods` object via `data` from the pathview
package.
I guess you can either use
> bods <- get(data("bods", package="pathview"))
or
> bods <- NULL
> data("bods", package="pathview")
to make this note go away.
> "Consider clarifying how 6 object(s) are initialized"
>
Hi,
I would just ignore that note.
H.
On 09/12/2017 07:19 AM, Ludwig Geistlinger wrote:
Let's consider loading the `bods` object via `data` from the pathview
package.
I guess you can either use
bods <- get(data("bods", package="pathview"))
or
bods <- NULL
data("bods", package="pathview"
Your key is in our system. It starts with,
ssh-rsa
B3NzaC1yc2EDAQABAAACAQD4+kbkP7J0rkIGy81r9fO+4tCgHzQXfkthRu/MFPE7AMvZy7SeNf9WuxPQtMeOjAl
It is associated with the correct package “pathview” and also “gageData”.
Please give me more information to help you. Show me the exact commands y
Hi Markus,
The class cache issue is just a warning here and is distracting.
What seems to break deepblue_liftover() is a recent
change to rtracklayer::import.chain. Looks like commit
a3c4308d928290700c6326eabda8dea4a96146e3 from Sep 4 might
be the culprit.
Cheers,
H.
On 09/12/2017 06:29 AM, Ma
the following the are commands I used and output:
luo$ git clone g...@git.bioconductor.org:packages/pathview
Cloning into 'pathview'...
key_load_public: invalid format
Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
Hi Dario,
I wasn't able to reproduce this error on my version of Ubuntu. (see below)
Please kindly post any future package inquiries at
support.bioconductor.org.
Best,
Marcel
---
> ExperimentList()
ExperimentList class object of length 0:
> BiocInstaller::biocValid()
* sessionInfo()
R v
What name did you store your key under? “id_rsa” or something else?
Nitesh
> On Sep 12, 2017, at 12:11 PM, Luo Weijun wrote:
>
> the following the are commands I used and output:
>
> luo$ git clone g...@git.bioconductor.org:packages/pathview
> Cloning into 'pathview'...
> key_load_public: inva
Hi Laurent,
The 2 Ontology,character methods defined in AnnotationDbi and
rols do very different things. The 1st one expects a vector of
GO IDs and returns the GO sub-ontologies that they belong to:
> Ontology(c("GO:009", "GO:012", "GO:006"))
GO:009 GO:012 GO:006
"M
The original file name was id_rsa.pub.pub.
I changed it to id_rsa.pub or id_rsa now. It stops complaining about the
invalid format, but still have permission problem.
##id_rsa.pub
luo$ git clone g...@git.bioconductor.org:packages/pathview
Cloning into 'pathview'...
Permission denied (publickey).
http://bioconductor.org/developers/how-to/git/faq/
You need point#16 on the FAQ section.
Change your permissions.
> On Sep 12, 2017, at 12:35 PM, Luo Weijun wrote:
>
> The original file name was id_rsa.pub.pub.
> I changed it to id_rsa.pub or id_rsa now. It stops complaining about the
> inv
Well, I modified the file acces by:
chmod 400 ~/.ssh/id_rsa
it goes further, but the passphrase I stored seems not work (as below). I
couldn’t change passphrase either due to the same problem. Can I remove the old
ssh key, regenerated/resubmit a new key? What’s the best way to proceed?
luo$ git
Please regenerate a new key and submit.
> On Sep 12, 2017, at 1:26 PM, Luo Weijun wrote:
>
> Well, I modified the file acces by:
> chmod 400 ~/.ssh/id_rsa
>
> it goes further, but the passphrase I stored seems not work (as below). I
> couldn’t change passphrase either due to the same problem.
Hi Herve,
I understand that there is a clash between the two identical methods.
Both packages seem to have good reasons to implement their own
`Ontology,character`. Such clashes are relatively frequent.
My issue really is that when unloading AnnotationDbi's namespace,
`Ontology,character` is rem
I think I'm going to vote for the policy that methods with identical
signatures are currently unsupported by the methods package. It's
tough to imagine how they might work in any reliable and natural way,
and they totally break the methods package currently.
In the grand scheme of things, generics
For this particular problem, it may be worth noting that
http://geneontology.org/page/ontology-structure
describes CC, MF, BP as "sub-ontologies" of GO. AnnotationDbi might replace
its Ontology() with subontology() to acquire those tokens.
On Tue, Sep 12, 2017 at 4:28 PM, Michael Lawrence wrot
Dear Andrzej,
BiocStyle2 is a great piece of work and the new vignettes look really nice!
Thank you!
However, I am having a problem with the widefigure (figure*) environment,
which apparently only holds for my local installation, as the same
vignette builds fine here:
http://bioconductor.org/che
Hi Ludwig,
thank you! This sounds like an issue with your LaTeX distribution, in
particular the package 'marginfix'. Please make sure that all the packages
listed in the BiocStyle vignette under Appendix B "Attached LATEX packages"
are installed, and possibly the up-to-date.
Best,
Andrzej
On Tue
On 09/12/2017 01:58 PM, Vincent Carey wrote:
For this particular problem, it may be worth noting that
https://urldefense.proofpoint.com/v2/url?u=http-3A__geneontology.org_page_ontology-2Dstructure&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECJZN8XlNzgWTqEBb
Good day,
Whatever the problem is, it's gone with R Under Development and all packages
installed from the development branch of Bioconductor.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
___
B
Good day,
Subsetting a MultiAssayExperiment object fails if the column data has one
column but not 2 or more columns. Perhaps drop = FALSE is missing for the
DataFrame subsetting. A minimal example is:
rowColNames <- list(paste0("Gene", 1:10), paste0("Person", 1:10))
aTable <- matrix(rnorm(100)
Hey guys,
I love the org.Hs.eg.db package (and similar others for other organisms).
I work a lot with LCMSMS proteomics data, and I have always missed a similar
org.Hs.uniprot.db package, so I am thinking of creating that (and then sharing
it on BioC, to benefit fellow proteomics R users).
Wou
Hi Aditya,
you could check the more recent ensembldb EnsDb databases to see if
there is something in them you might need/want.
I've added protein annotations to them (as provided by Ensembl). They
contain the Ensembl protein domains, the AA sequence, all protein domain
families (as defined/linked
Hi Johannes,
Thanks for your feedback!
I tried ensembl based maps earlier, but I loose many features.
In LCMS proteomics the unit of identification and quantification is a uniprot
accession, so annotation mappings would benefit from a uniprot-centric database
object.
Cheers,
Aditya
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