al is October 12. I will get to it much
sooner.
Regards,
Marcel Ramos
Bioconductor Core Team
On Fri, Sep 30, 2016 at 9:50 AM Lukas Weber wrote:
Hi,
I submitted a new package last week, which passed all the checks, but I
haven't heard anything else back since then.
I wanted to confirm how t
Hi Lukas,
You will be receiving SVN credentials soon for upload.
Please expect a message from Martin Morgan.
Regards,
Marcel
On Sat, Oct 15, 2016 at 10:02 AM Lukas Weber wrote:
> Hi,
>
> Is there anything we need to do to set up the svn repository and git mirror
> for new packages accepted las
https://stat.ethz.ch/mailman/listinfo/bioc-devel
<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
--
Marcel Ramos
Bioconductor Core Team Member
Roswell Park Cancer Institute
This email message may contain legally privileged and/or...{{dropped:4}}
__
Hi Sam,
This is a pertinent issue to shiny app development and there are continuing
efforts to create unit tests for shiny applications.
At the moment, there is a package dedicated to providing tests for shiny
applications but it has not been published.
See: https://github.com/rstudio/shinytest
T
"0.9-8" "3.2.3" "0.9-8"
> Repository
> rJava "https://cran.rstudio.com/src/contrib";
>
> update with biocLite()
>
> Error: 1 package(s) out of date
>
> The same example works on another computer using Windows operating syste
Hi Dario,
You're using a different version of MultiAssayExperiment which might make
the original problem less reproducible.
I was not able to reproduce the error on the release version of
MultiAssayExperiment. If you do find the issue again. Please let me know.
As a side note, we are using the
d packages:
> [1] S4Vectors_0.15.7BiocGenerics_0.23.1
> MultiAssayExperiment_1.3.34
>
> --
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
>
> ________
Hi Maarten,
It appears that your vignette is pointing to a package that doesn't
exist in the build system.
Please reference `package = "brgedata"` instead.
Regards,
Marcel
On 12/13/2017 02:09 PM, Maarten van Iterson wrote:
> Dear all,
>
> Our new package, omicsPrint, has been accepted and add
Hi Maarten,
It appears that your vignette is pointing to a package that doesn't
exist in the build system.
Please reference `package = "brgedata"` instead.
Regards,
Marcel
*Note. Apologies if you've received this email twice.
On 12/13/2017 02:09 PM, Maarten van Iterson wrote:
> Dear all,
>
>
s_0.22.1 GenomicRanges_1.28.6
> [41] RaggedExperiment_1.0.0 SummarizedExperiment_1.6.5
> [43] mime_0.5 xtable_1.8-2
> [45] colorspace_1.3-2 httpuv_1.3.5
> [47] stringi_1.1.6 RCurl_1.95-4.8
>
Hi Kornel,
I downloaded your package from our git repo and ran check locally on
Windows 7.
It seems like there are some issues with the `data.table` (version
1.10.4-3) package.
Here is my result for the `i386` architecture:
>>> R CMD check --force-multiarch --no-vignettes amplican_1.1.6.tar.gz
[t
Hi Kevin,
Being that I am unable to fully reproduce the issue, I can only say that
I have been successful in running the steps in the Wercker build for a
different package.
Please do a *clean* pull of the Bioconductor image from docker hub by
removing any stale images
first.
Here is the wercker.
vel
> mailing list? That would be odd, I sent it from my bioc-devel
> registered email address :/
>
> Kind regards,
> Kevin
>
> On Tue, Mar 20, 2018 at 5:03 PM, Marcel Ramos
> mailto:marcel.ra...@roswellpark.org>>
> wrote:
>
> Hi Kevin,
>
> Bei
Hi Dario,
Gabe is right, you shouldn't be building within the package directory.
Although AFAIK, you should be able to do so. Perhaps if you point us
to your package, we might be able to see the issue...
Regards,
Marcel
On 03/21/2018 06:15 PM, Gabe Becker wrote:
Dario,
Does this ever happen
Hi Vivek,
Make sure you are using the appropriate version of R.
Your appveyor code says you're using 3.4.4.
https://ci.appveyor.com/project/vivekbhr/icetea#L22
Add a chunk like:
```
environment:
global: ...
matrix:
- R_VERSION: devel
```
after your "global:" tag under the "environmen
Hi Kenneth,
I was unable to reproduce the issue that you described in your original
email with a different package (without access to your package).
I ran `devtools::build_vignettes` on the `RaggedExperiment` package
and the vignettes were built without a problem (with pandoc installed):
> devt
Hi Ryan,
Thanks for pointing this out.
I'm not sure what you mean by "structured" or "format". We do have
public facing citations
which can be found at:
http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/citation.html
(Thanks Lori for locating these pages!)
And even with a web-b
Hi Shijia,
I am assigned to the submission and will be reviewing your package soon.
Please send further correspondence as comments to the issue on GitHub.
Best regards,
Marcel
On 04/18/2018 08:31 PM, Shijia Zhu wrote:
> Hi Everyone,
>
> My package just passed the check, without errors or wa
Hi Christian,
It looks like you have to do
*git pull upstream master *
according to your `git remote -v`.
Regards,
Marcel
On 05/14/2018 04:21 PM, cstrato wrote:
> Dear Nitesh,
>
> Thank you for your fast reply. Here is what I tried now,
> including using 'git pull':
>
> $ cd /Volumes/T3Data
Dear bioc-devs,
A month ago we notified you about our "next generation" changes to
BiocInstaller.
Thanks to all beta testers and those who provided feedback and
suggestions for a new package name.
I am pleased to inform you that BiocManager is now on CRAN:
https://cran.r-project.org/web/packag
nding packages:
https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653
Best regards,
Marcel
Bioconductor Core Team
Roswell Park Cancer Institute
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263
On 06/20/2018 12:23 PM, Marcel Ramos wrote:
D
code to support the use of `BiocManager`”
> specifically entails. Would you mind expanding on what criteria, other
> than usage of BiocInstaller or biocLite in the vignette, that might
> cause packages to appear in your gist?
>
> Kind Regards,
> Jason Serviss
>
>
>
> Is there guidance on how to handle this issue?
>
> Thanks,
> ~G
>
> On Sun, Jul 15, 2018 at 10:53 AM, Marcel Ramos
> <mailto:marcel.ramospe...@roswellpark.org>> wrote:
>
> Hi Jason,
>
> Please check all of your package files and not
16, 2018 at 1:06 PM Gabe Becker wrote:
Ah, of course. I should have realized that. Makes sense. I'll get that
fixed in devel soon.
Thanks and sorry for the noise.
~G
On Mon, Jul 16, 2018 at 9:37 AM, Marcel Ramos
wrote:
Hi Gabe,
Please note that we are only making changes to packages
/packages/devel/bioc/html/RaggedExperiment.html
Best regards,
Marcel
--
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263
On 07/13/2018 05:11 PM, Marcel Ramos wrote:
> Dear bioc-devs,
>
> Ab
Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263
On 08/31/2018 01:28 PM, Marcel Ramos wrote:
> Dear bioc-devs,
>
> Thank you to all maintainers who have made appropriate changes to their
> packages *in devel*.
>
> This is an ongoing effort to replace
Hi Valentino,
You will have to provide more details concerning the issue.
It may be as simple as removing the dashes with `gsub` before using
`featureCount`.
Please review the posting guidelines for a better idea on how to get help:
https://bioconductor.org/help/support/posting-guide/
And cons
Hi Charles,
Thank you for your post and for providing a reproducible example.
I was able to reduce the example to behavior from the coerce method on
`list`/`ANY` objects to `SimpleList`.
Here is the reduced example:
``` r
suppressPackageStartupMessages({
library(SummarizedExperiment)
})
exa
Hi Stefano,
I'm no roxygen expert either but you could try using the
`usethis::use_pipe(export = TRUE)`
functionality developed by actual roxygen experts ;)
Best,
Marcel
On 2/13/20 2:28 AM, Felix Ernst wrote:
> Hi,
>
> I am certainly not a roxygen expert, but if \code{\link{\%>\%}} is to
> impl
Hi Francesco,
Please wait at least 24 hours before seeing an effect on the build report.
We should have a build report with your changes later today.
Check around 2 PM EST or https://everytimezone.com/s/3eab3407
Best regards,
Marcel
On 2/14/20 11:32 AM, Francesco Del Carratore wrote:
> Dear sup
advance for your help.
P.S. GitHub Repository: https://www.github.com/vjcitn/biocMultiAssay
Regular check is passing.
Regards,
Marcel Ramos
sessionInfo()
R Under development (unstable) (2015-11-25 r69695)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.04
locale:
[1] LC_CTYPE=e
Hi Lara,
I often recommend the use of the `Authors@R` field in the DESCRIPTION file
which will give you more control:
```
Authors@R: c(
person(given = "Lara", family = "Selles Vidal", ...),
...
)
```
Best,
Marcel
On 4/22/20 4:00 PM, Selles Vidal, Lara wrote:
> Dear Bioconductor te
fo/bioc-devel
---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263
This email message may contain legally privileged and/or...{{dropped:2}}
___
fected your use cases
of not specifying the sampleMap. I've opened an issue at
https://github.com/waldronlab/MultiAssayExperiment/issues/291.
---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton
not read from remote repository.
>>
>> Please make sure you have the correct access rights
>> and the repository exists.
>> error: Could not fetch upstream
>>
>> Thanks,
>> Krithika
>> kb...@georgetown.edu
>>
&g
d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032050928%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Jc5VJ3OtF73XPxF86RvZ%2FKjuJdCaabu4SC6aMnTIOwA%3D&reserved=0
> --
> Robert Castelo, PhD
> Associate Professor
> Dept. of
> Papenfuss Laboratory
>
> The Walter Eliza Hall Institute of Medical Research
>
> +61 (0)466452544
>
> [[alternative HTML version deleted]]
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bio
; Victoria University, Footscray Park Campus, VIC 3011 Australia
> *Email*: sarah.voisin.ae...@gmail.com
> *Office phone*: +61 3 9919 5744
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing li
London
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FI
secure-web.cisco.com/1lBSXrH5hVjuH3-oc2I8NYekmxreCRjMdBCESkhqsfPrcWfc8Ab0kjvn_Z_XrrywP-PCmcemZQIcG9qS5MN2iEXcHw16ZoAOf-To94IhLrODOlwxcAI8b36l90cL8uTmDa7F2eBjvSqKN49SkTyST48O4qon7Zqy5URTI0-Wo8ieqL1l5jMEgIt1yMIlo_9vSl6CuEpz30Ypcz6_LoGl-amdxx7WVeqaqDzUC3_f5UcFZHsqCQnQ8BWkaLyZdedEwzoQZsecXMJK-HyQv6dVV
1] scuttle_1.0.4 pkgconfig_2.0.3
>>>> [73] XML_3.99-0.6 R.methodsS3_1.8.1
>>>> [75] dbplyr_2.1.1 locfit_1.5-9.4
>>>> [77] utf8_1.2.1RJSONIO_1.3-1.4
>>>> [79] howmany_0.3-1
mailing list if you have any question or need help.
>>>>
>>>> This is very problematic. If no action is taken over the next few weeks
>>>> we will begin the deprecation process for your package. We appreciate your
>>>> assistance on pushing changes
es on disk, should I skip such tests on Windows?
> Thank you
> Giulia Pais
>
> [[alternative HTML version deleted]]
>
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
---
Mar
> we provide justification for it?
>
> Thank you,
> Kelsey
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
---
Marcel Ramos
Bioconductor
ote? Or is there another mistake I am making?
>
> -Eric
>
>
>
>
> [[alternative HTML version deleted]]
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
---
Marcel Ramo
l/fCCAC.html>
>
>
> Could you please advice?
>
> Thanks,
> Pedro
>
>
---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263
ML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Care
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 1
jAzMisLM3y392gW-Fvhmv3_njfTB6cjrfeX38csHrTAKwwurEo15wRDhq_rOrwp33T8CokQiEgjwzIn3UJ9cucpAVJihGYoA421tb1gd0dzqTnh8xDoFEsfdm__83oKghIe5TH3Wb1EqBAzuf3eSdTcBgK6bl0bR9lGQGLfQzzGfxpN8FWGLFcrqhL6VV_fHwQpfRZ267LbpkMTJ0BNTwHkI00LJmMuq-7m2YvCs1NyxzR8ls2M5q/https%3A%2F%2Fgithub.com%2Fmartaint%2FInterCellar
ai, PhD*
>>>> Principal Investigator, OICR
>>>> Assistant Professor, Department of Molecular Biophysics, University of
>>>> Toronto
>>>> shraddhapai.com; @spaiglass on Twitter
>>>> https://pailab.oicr.on.ca
>>>>
>>>>
>>>> *Ontario Institute fo
> *Shraddha Pai, PhD*
>>> Principal Investigator, OICR
>>> Assistant Professor, Department of Molecular Biophysics, University of
>>> Toronto
>>> shraddhapai.com; @spaiglass on Twitter
>>> https://pailab.oicr.on.ca
>>>
>>>
>>> *Ont
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinfor
gna
>> Pol.S.Orsola-Malpighi, via Massarenti 9,
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
ioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
---
Marcel Ramos
Bioconductor Core
Specifically, the instructions can be found here:
http://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel
I always cherry-pick commit /hashes/ from the main branch into the
RELEASE_3_XX branch.
This method ensures good practice by requiring atomic commits
(sep
Hi Giulia,
Are you using a recent version of BiocCheck?
If so, check the bottom of the BiocCheck::BiocCheck():
---
See the .BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
---
Can you provide more details, e.g., the repository of the package?
Thanks.
Best reg
not on Biconductor
> after the build.
>
> Just for reference the package is ISAnalytics and the BiocCheck
> version is the latest one.
>
> Thanks again,
>
> Giulia
>
> *From: *Bioc-devel on behalf of
> Marcel Ramos
> *Date: *Wednesday, 2022October5 at 23:48
Hi Sarvesh,
The error has something to do with an interaction between internal base
R code
and checking for dependencies in BiocCheck with `loadNamespace`.
Either way, this check in BiocCheck is redundant with R CMD check.
It will soon get removed but for now, you can disable it by running:
Bioc
Hi Teemu Daniel,
Those packages were developed before ExperimentHub.
Please follow the current standard for experiment data packages at
https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html
You may want to take a look at curatedTCGAData as an example
Hi Teemu Daniel,
Those packages were developed before ExperimentHub.
Please follow the current standard for experiment data packages at
https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html
You may want to take a look at curatedTCGAData as an example
Thank you.
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!LRXxDv2l!WNSkzT46H5_u0xvGUQjr-PyZWdSinodtB2tjp
ing list
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!LRXxDv2l!R1UBbqc4BHJec6ZHNELX8IUi15Kbh_AubbZAfATDL6GXHAx_0JPPkdwBP017w0_6_roNAS1s0HU-6nhdnP3MBxp76WNcIw$
*Marcel Ramos, MPH*
Sr. Data Scientist
CUNY Graduate School of Public Health &
is.
>
> Best,
>
> Lluís
>
> PS: .Rprofile is a standard .R file, I'm not sure which relation it
> has with a specific IDE. But even IDE's specific files might be a
> choice of the maintainers of the package to enable and encourage
> community participatio
M, Tulip Nandu wrote:
> Hi,
>
> Yes, I haven't change the master package. What is the solution? Also
> the link below is not working.
>
> Regards,
>
> Tulip.
>
> ----
> *From:* Marcel Ramos
Hi Tulip,
Are you sure? It looks like `edgeR` has deprecated / defunct that
function. See this commit:
https://code.bioconductor.org/browse/edgeR/commit/bdd73bc0c6a0a710838f77ad419bdc2cf21ed357
Best regards,
Marcel
On 10/24/24 5:56 PM, Tulip Nandu wrote:
> * This email originates from a sende
Hopkins Bloomberg School of Public Health
> 855 N. Wolfe St., Room 382
> Baltimore, MD 21205
> lcolladotor.github.io
> lcollado...@gmail.com
>
> ___
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