Hi,
I have an error in the package compilation because of issues accessing a file
from UCSC.
Are you aware of such type of issue? What do I need to do?
Quitting from lines 337-345 [cometwebPlot] (coMET.Rnw)
Error: processing vignette 'coMET.Rnw' failed with diagnostics:
error in evaluating the
Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-9253
Email: tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu>
From: Herv� Pag�s
Sent: Friday, October 20, 2023 12:18 PM
To: Martin, Tiphaine ; bioc-d
Hi,
I have my package that failed to build its vignette because of failing to
obtain 'hguid' cookie.
Could you please tell me how I can solve this?
thanks,
Tiphaine
Tiphaine Martin
Assistant Professor
Department of Oncological
Hi,
I have a question.
I receive an error message for my COMET package, but when I click on the link.
I do not find the error.
Could you advise me what I need to do ?
Thanks
Tiphaine
-Original Message-
From: bbs-nore...@bioconductor.org
Sent: Friday, June 25, 2021 3:15 PM
To: Martin
for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-9253
Email: tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu>
From: Kern, Lori
Sent: Tuesday, May 18, 2021 10:44 AM
To: Martin, Tiphaine ; bioc-devel@r-project.org
S
Hi,
I submitted my update of my package to master Sunday (1.23.1). I did not see a
new update in build/check report
(http://bioconductor.org/checkResults/devel/bioc-LATEST/coMET/)
Did I miss something when I submit it?
Thanks,
Tiphaine
-Original Message-
From: Bioc-devel On Behalf Of
Hi,
This was my previous email.
Please could you put my new email
tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu>
Could you remind me how I can change later if need it.
Thanks,
Tiphaine
From: Nitesh Turaga
Sent: Monday, May 3, 2021 9:07 AM
To: Martin, Tiphaine ; bioc-d
Hi,
I try to submit update of my package comet
I do not remember about my ssh public key
I have this error message and I request it
tiphaine.mar...@mssm.edu is not associated with a maintainer of a Bioconductor
package.
Could you help me please?
Thanks,
Tiphaine
and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-8403
Email: tiphaine.mar...@mssm.edu
From: Shepherd, Lori
Sent: Monday, December 17, 2018 2:41:59 PM
To: Martin, Tiphaine; bioc-devel@r-project.org
Subject: Re: failling to build vignette
Hi,
I need to advise to build my vignette. It seems that my vignette could not
build under Bioconductor 3.9. I try to find where it fails, but I don't find
the bug.
I updated my vignette last February to work with new version of BiocStyle and
it did well for Bioconductor 3.8, but it seems
Great, thanks Lori.
From: Shepherd, Lori <lori.sheph...@roswellpark.org>
Sent: 18 April 2018 17:46:24
To: Martin, Tiphaine; bioc-devel@r-project.org
Subject: Re: incompatibility between logo for build et the version and success
of compilation
This page
Hi,
I updated the dev version of my package,
http://bioconductor.org/packages/3.7/bioc/html/coMET.html
if I am looking the webpage, it seems that my build fails and I can install
only the version 11.3. however, if i am looking at the different compilations,
everything is ok for the version
thanks, I am going to do that.
Best,
Tiphaine
From: Martin Morgan <martin.mor...@roswellpark.org>
Sent: 01 March 2018 20:56:10
To: Martin, Tiphaine; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Questions about tokay2 and import
'grDevices::w
hi,
I have a warning under windows (tokay2) for my devel version of my package
(coMET). I am not sure how to answer it:
* checking whether package 'coMET' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'grDevices::windows' by
Hi,
Could you inform me which modification you did in biomaRt ? or in ENSEMBL ?
Indeed, I have my R package (coMET) use biomaRt to access to data. From the
last update in BiomaRt (12/14/2017), I have a new error message.
Do you change the name of database associated with ENSEMBL ?
This is
Hi,
I tried to push my update to GitHub and Bioconductor.
I succeed to create my fork in my GitHub Id following this page (Pull upstream
changes). I then updated and pushed on GitHub my update, but I cannot for
bioconductor when I follow recommandation on this page (Sync an existing GitHub
Hi,
I tried to push my update to GitHub and Bioconductor.
I succeed to create my fork in my GitHub Id following this page (Pull upstream
changes). I then updated and pushed on GitHub my update, but I cannot for
bioconductor when I follow recommandation on this page (Sync an existing GitHub
Hi,
I tried to push my update to GitHub and Bioconductor.
I succeed to create my fork in my GitHub Id following this page
(http://bioconductor.org/developers/how-to/git/pull-upstream-changes/). I then
updated and pushed on GitHub my update, but I cannot for bioconductor when I
follow
Hi,
I cleaned my gitHub repository to have now the repository coMET in my gitHub as
the fork of coMET from bioconductor.
I followed the directive from
http://bioconductor.org/developers/how-to/git-mirrors/
as I need to correct bug in the current release
but when I try to run
1. git svn
?
* I had a GitHub repository bridged to the 3.0 release branch. Is it ok to
use the same GitHub repository, and use SVN wins during the bridge creation?
That should update GitHub with the new release code, right?
Many thanks,
Kevin
On 17 April 2015 at 11:43, Martin, Tiphaine
tiphaine.mar
Hi Dan,
When I try to access on my package, I have ³Internal Server Error². Maybe
I make a mistake somewhere.
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/
coMET
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coMET
Regards,
Tiphaine
On 17/04/2015
I will commit my fix to coMET and cross fingers that the error doesn't appear
in the build system
Tiphaine
From: Hervé Pagès hpa...@fredhutch.org
Sent: 10 April 2015 20:30
To: Michael Lawrence; Martin, Tiphaine
Cc: bioc-devel
Subject: Re: [Bioc-devel
only for human genome).
It is possible also to extract the correlations between omic features with
their pvalues.
Please let me know of any issues you encounter.
Thanks,
Tiphaine Martin
Tiphaine Martin I PhD Student I TwinsUK
Department of Twin Research, Kings College London,
St
-to/version-numbering/
Dan
Best,
Kasper
On Mon, Mar 16, 2015 at 9:29 PM, Martin, Tiphaine
tiphaine.mar...@kcl.ac.uk wrote:
Dear Dan,
I have 2 naive questions.
I would like to know whether we (developers of a R package currently
only in the development version of Bioconductor
Dear Dan,
I have 2 naive questions.
I would like to know whether we (developers of a R package currently only in
the development version of Bioconductor) need to say that we would like to have
our packages accessible in the next version of Bioconductor or it is automatic
for any packages
Hi Everybody,
Yesterday, I observed that ENSEMBL changed a little their schema of the
dataset hsapiens_gene_ensembl.
In my case, some of my functions were impacted by the change from
external_gene_id to
external_gene_name.
Maybe there are other change in this dataset or other datasets.
Yep you guess well about my colleagues :) sorry.
Thank you for your advices.
Tiphaine
From: Hervé Pagès hpa...@fhcrc.org
Sent: 16 October 2014 19:43
To: Martin, Tiphaine; Michael Lawrence; Dan Tenenbaum
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc
Hi,
I would like to know if I need to add a runnable example for each function that
has keyword either internal or not.
I ask that because with BiocCheck, version 1.0.2, I had a message for function
with keyword internal such as
Checking exported objects have runnable examples...
*
Hi,
I need to create dataset BiomartGeneRegionTrack via Gviz package to run
examples in my packages. But when I run
R CMD check coMET, i have warning message for the checking :
checking data for non-ASCII characters ... WARNING
Warning: found non-ASCII strings
'[alpha cell,acidophil
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