one: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.4.0 tools_4.4.0
--
Shraddha Pai, PhD
Principal Investigator
Adaptive
Hello BioC community,
What’s the Java version installed on Merida1?
I have a package failing build specifically on that macOS machine (has worked
with older versions of BioC) and I suspect it’s got a newer version of Java,
but want to rule out other possibilities.
Thanks,Shraddha
--
Shraddha
rew install gcc" (this is OS X). This is getting
too complicated for your average user.
Is there a way I could precompile needed packages and just make them
available to my users? Are there instructions for how to do this somewhere?
I can host the compiled version on a lab server.
Thanks,
g")
> > lengths(deps)
> > #' netDx
> > #'109
> > ```
> >
> > This number is not matching up with the value listed in the badge. Hervé
> > is currently looking into it
> > and will have an update soon.
> >
> > Best
dependencies?
Thank you,
Shraddha
On Tue, Sep 21, 2021 at 5:35 PM Shraddha Pai
wrote:
> Hi Michael,
> Thanks! Looks like the package trying to load 'rtracklayer' was
> 'TCGAutils' (see graph from Zugang above, generated using pkgndep - looks
> to be quite useful). T
tor.org. I have also
added a webhook to issues.bioconductor.org.
Is there anything else I need to do to ensure that this repo becomes the
official one for BioC? Thinking especially of the upcoming release and
version change.
Thanks,Shraddha
--
*Shraddha Pai, PhD*
Principal Investigator, OICR
you could remove the rtracklayer import
> and run functions in that package to identify the symbol-level
> dependencies. The output is a bit noisy though.
>
> Btw, using @importFrom only allows you to be selective of symbol-level
> dependencies, not package-level.
>
> Michae
etting up my package so that a github push triggers a Github
Action to build and test the package on bioc-devel, followed by
building and pushing a Docker image with the package installed.
SO looking forward to not having to do this manually anymore!
Best,Shraddha
On Mon, Sep 20, 2021 at 12:17 PM
st.pdf
>
> Cheers,
> Zuguang
>
>
> On Mon, 20 Sept 2021 at 20:37, Shraddha Pai
> wrote:
>
>> Hello again,
>> I'm trying to simplify the dependencies for my package "netDx", make it
>> easier to install. It's currently got over 200(!)
uot; 1 13 7.69 0.01 1
"MultiAssayExperiment" 4 46 8.7 0.22 1
"foreach" 2 23 8.7 0.02 0
"graphics" 8 87 9.2 0.01 0
"GenomicRanges" 15 106 14.15 0.08 0
"rappdirs" 1 7 14.29 0.01 0
"reshape2" 1 6 16.67 0.05 0
"RColorBrewer" 1 4 25
ting up triggers for each?
Thanks very much,
Shraddha
--
*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
*Ontario Institute for Cancer Research*
MaRS Cent
ype = "Article",
>
>---
>
>> c(bibentry(bibtype = "Article",
>
>43c43
>
>< )
>
>---
>
>> )
>
>\ No newline at end of file
>
>
> So it looks like you've managed to get the file right in de
key = "netDx-methods",
title = "{netDx: interpretable patient classification using
integrated patient similarity networks}",
author = c(
person("Shraddha", "Pai"),
person("Shirley", "
lattice_0.20-41
> [55] ps_1.6.0 pillar_1.6.1
> [57] futile.options_1.0.1 glue_1.4.2
> [59] BiocVersion_3.12.0 lambda.r_1.2.4
> [61] remotes_2.3.0 vctrs_0.3.8
> [63] httpuv_1.6.1 gtable_0.3.0
> [65] purrr_0.3.
rkdown_2.8 Rtsne_0.15
[147] clusterExperiment_2.10.1 shiny_1.6.0
[149] ggbeeswarm_0.6.0 tinytex_0.31
--
*Shraddha Pai, PhD*
Principal Investigator
shraddhapai.com; @spaiglass on Twitter
*Ontario Institute for Cancer Research*
MaRS Centre, 661 University Avenue, Suite 510, Toronto, O
#x27;ve upgraded R to R 4.1 alpha on machv2, and made a tweak to the
> setup, so hopefully these errors will be gone on tomorrow's report.
>
> Best,
> H.
>
> On 4/30/21 2:46 PM, Shraddha Pai wrote:
> > Hello BioC community,
> > My package netDx is building correctly
s solution. Was this change a mistake?
Any thoughts would be appreciated.
Thanks,
Shraddha
--
*Shraddha Pai, PhD*
Independent Investigator
shraddhapai.com; @spaiglass on Twitter
*Ontario Institute for Cancer Research*
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G
0A3
t;
> Building vignette index
>
> >
>
>
>
> so can’t really help further…?
>
>
>
> *From: *Shraddha Pai
> *Date: *Monday, November 23, 2020 at 12:14 PM
> *To: *Martin Morgan
> *Subject: *Re: [Bioc-devel] Running vignettes one at a time works but
> build_vignett
n built and
the second is just named.
But running the vignettes one at a time leads to them all running smoothing.
Any thoughts as to what could be causing the problem would be appreciated.
Thanks,Shraddha
--
Shraddha Pai, PhD
http://shraddhapai.com ; @spaiglass on Twitter
Post-doctoral Fellow
.3.1 which is in Bioc-devel release.
Thanks,Shraddha
--
Shraddha Pai, PhD
http://shraddhapai.com ; @spaiglass on Twitter
Post-doctoral Fellow, http://baderlab.org
The Donnelly Centre for Cellular and Biomolecular Research
University of Toronto
---
On bioc-devel Docker:
$ R CMD build netDx
Hello BioC community,
Our package build fails specifically on merida, the OS X machine.
I suspect the issue is due to Java version incompatibility for that
machine (based on the nature of the error message and ongoing Java-related
issues).
https://bioconductor.org/checkResults/3.12/bioc-LATEST/ne
==|
> 100%
>
> > path <- bfcrpath(bfc, url)
> >
>
> where the first time 'url' is used (as a unique key) the resource is
> downloaded to the cache; the second time it is simply accessed from the
> cache.
>
> It might be necessary to manual
Hello BioC-devel team,
Any idea why netDx 1.1.4 fails on the bioc devel build system?
This is the error:
--- re-building 'Predict_CaseControl_from_CNV.Rmd' using knitr
Quitting from lines 173-195 (Predict_CaseControl_from_CNV.Rmd)
Error: processing vignette 'Predict_CaseControl_from_CNV.Rmd' fail
6
[67] RCy3_2.8.0 DBI_1.1.0
[69] curl_4.3reshape2_1.4.4
[71] bigmemory_4.5.36R6_2.4.1
[73] knitr_1.29 dplyr_1.0.0
[75] bit_1.1-15.2shape_1.4.4
[77] stringi_1.4.6 Rcpp_1.0.4.6
[79] vctrs_0.3.1 t
cer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Shraddha Pai
> *Sent:* Friday, June 12, 2020 10:32 AM
> *To:* Bioc-devel ; Shepherd, Lori
>
> *Subj
Forgot to cc the group.
Also, this is the correct link:
http://download.baderlab.org/netDx/supporting_data/refGene.hg18.bed
Hosting it on our end isn't an issue.
S
-- Forwarded message -
From: Shraddha Pai
Date: Fri, Jun 12, 2020 at 10:24 AM
Subject: Re: [Bioc-devel]
"source("Predict_CaseControl_from_CNV.R"). And it ran through
successfully.
What am I missing? Is it that the snapshot date it from June 10 but the
build page is from June 11 so I need to wait for the changes to kick in?
I'm also getting errors with the devel branch, s
> cd /tmp
> git clone path/to/updated/repo
> R CMD build repo
> R CMD check repo_x.y.z.tar.gz
>
> or similar, depending on your development system.
>
> If there are obscure errors then one might visit
>
> http://bioconductor.org/developers/how-to/troubles
t, because the builder is
> heavily used, and a better strategy is usually to tackle more modest
> analyses in examples.
>
> Martin
>
> On 2/21/20, 2:43 PM, "Bioc-devel on behalf of Shraddha Pai" <
> bioc-devel-boun...@r-project.org on behalf of shraddhapai.ne..
addha
--
--
Shraddha Pai, PhD
http://shraddhapai.com ; @spaiglass on Twitter
Post-doctoral Fellow, http://baderlab.org
The Donnelly Centre for Cellular and Biomolecular Research
University of Toronto
[[alternative HTML version deleted]]
___
Bioc-de
to submit our package to BioC? It would be great to
increase community adoption of our package via the BioC system.
Thanks,Shraddha
--
Shraddha Pai
Post-doctoral Fellow, http://baderlab.org
The Donnelly Center, University of Toronto
@spaiglass on Twitter
[[alternative HTML version deleted
t;
> Once everything is ready, don't forget to bump the version in order to
> trigger a new build by the Single Package Builder. Thanks!
>
> H.
>
>
> On 6/14/19 16:43, Shraddha Pai wrote:
> > Hi,
> > Ok thank you.
> > I should probably comment out some time-con
:58, Shraddha Pai wrote:
> > Hi,
> >
> > Thanks Herve. I have actually spent weeks making sure my packages passed
> > check and build following guidelines. So I am actually doing my best and
> > your snarky remark is not appreciated.
>
> OK maybe. But please note th
t;# Line starting 'The method converts ...' is malformed!
>
> How about making sure that your package is valid before submitting?
>
> H.
>
> On 6/14/19 15:14, Shraddha Pai wrote:
> > Hello BioC dev community,
> >
> > I just submitted a package t
https://stat.ethz.ch/pipermail/bioc-devel/
My apologies if these are trivial questions.
Thanks very much,
Shraddha
--
Shraddha Pai
Post-doctoral Fellow, http://baderlab.org
The Donnelly Center, University of Toronto
@spaiglass on Twitter
[[al
tml
>
>
> https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#submitting-related-packages
>
> Best,
>
> Nitesh
>
> > On Jun 13, 2019, at 2:45 PM, Shraddha Pai
> wrote:
> >
> > Hello BioC devel community,
> >
> > I am preparing two
,
Shraddha
----
Shraddha Pai
Post-doctoral Fellow, http://baderlab.org
The Donnelly Center, University of Toronto
@spaiglass on Twitter
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/lis
Hi Martin,
Ah, thank you for pointing out the build report page and the typo at the
top of the vignette.
I'll bookmark the page for quick checking in the future.
Best,Shraddha
On Thu, Feb 1, 2018 at 4:42 PM, Martin Morgan wrote:
>
>
> On 02/01/2018 11:09 AM, Shraddha Pai wrote:
&
Jan 2017.
I've followed the steps from here:
https://bioconductor.org/developers/how-to/git/push-to-github-bioc/
What else do I need to do to sync updates to BioC?
Here is the github repo: https://github.com/shraddhapai/IdeoViz
Thanks,Shraddha
Shraddha Pai
Post-doctoral Fellow, htt
:32 PM, Hervé Pagès wrote:
> Hi Shraddha,
>
> On 10/26/2016 11:12 AM, Shraddha Pai wrote:
>
>> Hello BioC developers,
>>
>> I'm not sure why the nightly build of my package IdeoViz is reporting this
>> error on tokay (see message below). It seems to me that
emoving
'C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/Rtmpu0feNb/Rinst1230396730de/IdeoViz'
-------
ERROR: package installation failed
---
Thanks for your time,
Shraddha
Shraddha Pai
Post-doctoral Fellow, http://baderlab.org
The Donnelly Center, University of Toronto
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