Admin: Dan Tenenbaum

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Dan Tenenbaum ♦♦ 8.1k
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I was in the Bioconductor group at Fred Hutchinson Cancer Research Center in Seattle, WA, USA.

Posts by Dan Tenenbaum

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Comment: C: Using AMI with StarCluster - error authenticating
... Since the last time I contributed to this thread, I've become aware of AWS Batch. You might want to look at that. Whatever you do, I'd focus on keeping things simple. If you try to get CfnCluster to work, I'd start by just trying to get a simple cluster to work (with a basic AMI like one of the Ale ...
written 6 months ago by Dan Tenenbaum ♦♦ 8.1k
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Answer: A: Using AMI with StarCluster - error authenticating
... StarCluster is a little old. Look info CfnCluster: https://github.com/awslabs/cfncluster .   ...
written 7 months ago by Dan Tenenbaum ♦♦ 8.1k
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Comment: C: Bioconductor docker images without Rstudio-server?
... That would be a bit tricky as we are trying to base our images on rocker's, so it seems best (from our point of view) to start by depending on their rstudio images, and not add rstudio ourselves at the end. Otherwise we don't get the benefit of the work they have already done. Your Dockerfile can b ...
written 15 months ago by Dan Tenenbaum ♦♦ 8.1k
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Answer: A: Bioconductor docker images without Rstudio-server?
... The docker containers could be based on r-base, but then people might complain that they don't have RStudio.  So I guess it's a question of what is more valuable to more people, being able to use RStudio out of the box with Biooconductor Docker containers, or not having RStudio in order to comply w ...
written 15 months ago by Dan Tenenbaum ♦♦ 8.1k
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Answer: A: Issue Downloading GenomicRanges
... R is not giving you a chance to say whether you want to install packages from source, and then it fails when it can't find the tools (such as 'make') needed to install packages from source. So you have two choices: 1) Tell R to a) either ask you before installing packages from source, or b) to nev ...
written 15 months ago by Dan Tenenbaum ♦♦ 8.1k
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Comment: C: edgeR installation issue
... OK, R is not giving you a chance to say "go ahead and install the binary version even though there is a newer source version". You can change this behavior by doing options(install.packages.compile.from.source="interactive") Before you run biocLite(). Then when it asks you whether to install the ...
written 15 months ago by Dan Tenenbaum ♦♦ 8.1k
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Comment: C: edgeR installation issue
... The easiest way is to install the Mac binary (i.e., don't build from source): source('https://bioconductor.org/biocLite.R') biocLite("edgeR", type="binary") If you need/want to build from source, download and install gfortran-4.2.3.pkg from https://cran.r-project.org/bin/macosx/tools/ If you sti ...
written 15 months ago by Dan Tenenbaum ♦♦ 8.1k
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Comment: C: Error in loading rsbml
... Yeah, something sounds wrong. According to http://sbml.org/Software/libSBML, the latest stable version is 5.13.0.  Please thoroughly remove libsbml and then install version 5.10 from here. ...
written 15 months ago by Dan Tenenbaum ♦♦ 8.1k
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Comment: C: Can't load package "org.Hs.eg.db"
... So do you mean the problem is solved? If so I will mark this thread as answered. ...
written 15 months ago by Dan Tenenbaum ♦♦ 8.1k
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Comment: C: Error in loading rsbml
... The build macs use version 5.10.x ...
written 15 months ago by Dan Tenenbaum ♦♦ 8.1k

Latest awards to Dan Tenenbaum

Appreciated 6 months ago, created a post with more than 5 votes. For Bioconductor Git/GitHub Mirrors
Popular Question 7 months ago, created a question with more than 1,000 views. For Bioconductor 2.13 is released
Popular Question 7 months ago, created a question with more than 1,000 views. For Bioconductor 2.13 is released
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: "rstudio initialization error: unable to connect to service" after logging in to
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to get rid of "Update all/some/none? [a/s/n]:"
Popular Question 17 months ago, created a question with more than 1,000 views. For New Package Submission Process
Popular Question 17 months ago, created a question with more than 1,000 views. For Bioconductor 2.14 is released
Oracle 17 months ago, created more than 1,000 posts (questions + answers + comments).
Popular Question 17 months ago, created a question with more than 1,000 views. For Bioconductor 2.13 is released
Scholar 17 months ago, created an answer that has been accepted. For A: Package lists and other questions about the site
Scholar 17 months ago, created an answer that has been accepted. For A: Package lists and other questions about the site
Scholar 19 months ago, created an answer that has been accepted. For A: How to get rid of "Update all/some/none? [a/s/n]:"
Scholar 19 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: "rstudio initialization error: unable to connect to service" after logging in to
Scholar 21 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar 21 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar 21 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar 23 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Appreciated 23 months ago, created a post with more than 5 votes. For Bioconductor 3.0 is released!
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: how can I access my local files (data, R-scripts) from the *docker* R/Bioconduct
Scholar 23 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar 23 months ago, created an answer that has been accepted. For A: Error updating packages: couldn’t understand kern.osversion
Scholar 23 months ago, created an answer that has been accepted. For A: how can I access my local files (data, R-scripts) from the *docker* R/Bioconduct
Scholar 2.2 years ago, created an answer that has been accepted. For A: What is the best way to get help on Bioconductor packages?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: What is the best way to get help on Bioconductor packages?

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