The problem seems to originate in the BioMart service itself:
library(biomaRt)
mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
attributes1 <- c("ensembl_transcript_id", "ensembl_exon_id")
df1 <- getBM(attributes1, mart=mart)
dim(df1)
# [1] 1150974 2
subs
The "Re:" in the title of this e-mail? I add an "Re:" to all my titles,
and I assume that the mailing list dispatcher adds the "[Bioc-devel]"
tag (cleverly inserting it between the "Re:" and the actual title).
Just looked it up - apparently it stands for "in re" in Latin. I guess I
learn something
Thanks Aaron I'll follow up on the support site.
Can you clarify where the 'Re:' came from in the title? I can't find a
previous post with similar title.
Martin
On 10/27/2017 05:42 AM, Aaron Lun wrote:
Dear list,
It seems that there is an issue with Rhtslib::pkgconfig() regarding the
identi
Hi Nitesh,
I started merging and updating package rcellminerData following the
instructions here :
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
I have conflict merge in step 7:
git merge --allow-unrelated-histories upstream/master
warning: Cannot merge binary file
We have the following public key in our system
ssh-rsa
B3NzaC1yc2EDAQABAAACAQDvWK0YKmx/h5uYfJjIwWBwsoZkVPZsWeIA7kGKfXK8K4omYzH8eq/7Q0cDQdN/ySJbu6yRvip8k+CUdNT7UDwZjYuj6qKNqCxCm0pBeJSyB4f9Ff60OLCz/4roiRCZYz49Z95Lrj/y3b2Xc9HatRrhaQrxRLxPjty6K9nr8E8lwVoE0FlENKdpfy0mR3NFClUNkIsOBwc/whXdfZxKzT
Thanks Lori. The problem still persists.
$ git remote add upstream
g...@git.bioconductor.org:packages/IntramiRExploreR.git
$ git fetch upstream
Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exis
On 10/27/2017 11:42 AM, Ioannis Vardaxis wrote:
Hey,
I think the problem might be coming from the command
"file.path(path.expand('~'),'Desktop’)” on line 77 on MACPET.rmd file. I
just want to find the desktop path for creating a folder there for the
vignette and the examples. This seems to work
Hey,
I think the problem might be coming from the command
"file.path(path.expand('~'),'Desktop’)” on line 77 on MACPET.rmd file. I
just want to find the desktop path for creating a folder there for the
vignette and the examples. This seems to work on MAC, but not on the other
platforms, how can I
Hey,
Here is the report:
bioconductor.org/spb_reports/MACPET_buildreport_20171027135637.html
I get a warning for Warning: No Rd macros in package ‘Rdpack’, for which I
can’t find any solution in the internett. But I am guessing that the warning
might come from a special norwegian character Ø i
Make sure your webhook is set up as described
https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#adding-a-web-hook
You will need to bump the version in the description file each time you would
like a new build report so please make the bump from 0.99.0 to 0.99.1. Thank
Hey,
One quick question. When I push again now, do I need to change the version
from 0.99.0 to 0.99.1 or does it change automatically?
Best,
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 27/10/2017, 19:03, "Hervé Pagès" wrote:
>Adding 'SystemRequirements: C++11' works for me (I'm on Linux):
Hey,
Ok, I have made the changes to the DESCRIPTION file adding the c++11 you
suggested, and also fixed the Rd files. I will try to push the package
again soon and see what I get.
Thanks,
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 27/10/2017, 19:03, "Hervé Pagès" wrote:
>Adding 'SystemR
Hi Leonard,
Sorry for missing your earlier posts about this. Will look into it.
Thanks,
H.
On 10/27/2017 09:07 AM, Leonard Goldstein wrote:
Dear bioc-devel,
I noticed exonsBy is dropping a lot of genes when run on a TxDb object
created with makeTxDbFromBiomart (see below). Please also see rel
Adding 'SystemRequirements: C++11' works for me (I'm on Linux):
hpages@latitude:~/MACPET$ git diff
diff --git a/DESCRIPTION b/DESCRIPTION
index d8238b6..061d692 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -7,6 +7,7 @@ Author: Ioannis Vardaxis
Maintainer: Ioannis Vardaxis
Description: The MAC
Hey again,
I think I have fixed the \insertRef macro problem now. However I still
need 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
Dear bioc-devel,
I noticed exonsBy is dropping a lot of genes when run on a TxDb object
created with makeTxDbFromBiomart (see below). Please also see related post
on the Bioconductor support site:
https://support.bioconductor.org/p/101951/#102160
Thanks for your help.
Leonard
--
> tx <- makeTx
Hi Lori,
It looks like there are additional locations:
> .libPaths()
[1] "/home/mikemorgan/R/x86_64-pc-linux-gnu-library/3.4"
"/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library" "/usr/lib/R/library�
I�ve switched to just a single local library path by setting R_LIBS_SITE in my
.Renvir
Hi guys,
On 10/27/2017 05:50 AM, Obenchain, Valerie wrote:
Hi Sokratis,
I added the .BBSoptions file to pcxn when it should have been added to
pcxnData. The .BBSoptions file should be put in the package that 'Suggests'
(not 'Depends') on the other. In this case it's pcxnData that needs the
.
Are there any other locations where BiocInstaller might already be installed?
.libPaths()
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: B
I find it really, really hard to write classic unit testing for analytical
/ methods functions. Unit testing works well and goes a long way for the
part of our stack which is infrastructure and basic classes. I am
concerned about to what extent our analytic stack actually gets tested
well, even w
Hi, Nate.
Yes, the auto-invite app is not as robust as we would like. I went ahead
and invited you directly.
Sean
On Fri, Oct 27, 2017 at 10:27 AM, Nathan Olson
wrote:
> Hi, When I recently tried to join the community-bioc slack channel using
> the following link, https://bioc-community.herok
Hey,
Thanks for the answer. Sorry for not including the link!
For the references part: I am using roxygen2 to create the Rd formats and
the \insertRef{link to bib reference file} should work for that. It looked
like:
#' @references \insertRef{macpetcite}{MACPET}
However I followed your suggesti
Hi, When I recently tried to join the community-bioc slack channel using
the following link, https://bioc-community.herokuapp.com/, I received a
`missing_scope` error message. I quick google search indicated the message
indicates an OAuth error. Does anyone know if someone is working on fixing
this
Dear Bioc-Developers,
I am trying to switch to Bioc Devel (R version 3.4.2). There is a
versioning issue with Bioconductor:
> source("https://bioconductor.org/biocLite.R";)
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> useDevel()
Error: 'devel' version already in use
We do similar testing (mostly upstream of package building) for GEOmetadb
and SRAdb. I have been thinking of this problem as "integration testing"
rather than "unit testing".
https://stackoverflow.com/questions/5357601/whats-the-difference-between-unit-tests-and-integration-tests
The build system
Hello all,
The complete set of OrgDb packages have been added to AnnotationHub as well as
the newly added TxDb. They will be immediatly available following the release
and using the release Bioc 3.6.
The following example:
> library(AnnotationHub)
> hub = AnnotationHub()
updating metadata:
Hi Sokratis,
I added the .BBSoptions file to pcxn when it should have been added to
pcxnData. The .BBSoptions file should be put in the package that 'Suggests'
(not 'Depends') on the other. In this case it's pcxnData that needs the
.BBSoptions. Sorry for the mix up, this has been fixed.
The da
Hello,
It looks like when you submitted your package we were still in svn and had
provided a svn id that was associated with your package. This was the id that
we would have originally requested in the form for rsa keys.
We have changed the id on our system to match your github id and you sho
Dear list,
It seems that there is an issue with Rhtslib::pkgconfig() regarding the
identification of the location of the shared library on some systems:
https://support.bioconductor.org/p/102248/
To summarize: on this system, R is putting the shared library in lib64/,
while pkgconfig() looks f
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