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: 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 6 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 6 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 6 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 7 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 7 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 7 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 7 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 7 months ago by Dan Tenenbaum ♦♦ 8.1k
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Comment: C: Can't load package "org.Hs.eg.db"
... Actually this is not the same problem. The original poster's problem had to to with firewalls and installing the package. You are able to install it but not load it.  As a side note, you should use biocLite() to install Bioconductor packages, then you won't have to worry about getting the wrong ver ...
written 7 months ago by Dan Tenenbaum ♦♦ 8.1k
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Comment: C: Severe problems with bioc installation of source packages (R 3.3 epel)
... How did you install/build R? DId you check it out from Subversion? If so did you run  tools/rsync-recommended  after checking it out? If not please do that. ...
written 7 months ago by Dan Tenenbaum ♦♦ 8.1k

Latest awards to Dan Tenenbaum

Scholar 9 months ago, created an answer that has been accepted. For A: Package lists and other questions about the site
Scholar 9 months ago, created an answer that has been accepted. For A: Package lists and other questions about the site
Scholar 11 months ago, created an answer that has been accepted. For A: How to get rid of "Update all/some/none? [a/s/n]:"
Scholar 11 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Teacher 12 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 12 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar 12 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar 13 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar 15 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar 15 months ago, created an answer that has been accepted. For A: Error updating packages: couldn’t understand kern.osversion
Appreciated 15 months ago, created a post with more than 5 votes. For Bioconductor 3.0 is released!
Scholar 15 months ago, created an answer that has been accepted. For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar 15 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
Teacher 15 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 18 months ago, created an answer that has been accepted. For A: What is the best way to get help on Bioconductor packages?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: What is the best way to get help on Bioconductor packages?
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: What is the best way to get help on Bioconductor packages?
Appreciated 19 months ago, created a post with more than 5 votes. For Recent course materials now easily searchable
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: BiocCheck: REQUIRED: vignette sources in vignettes/ directory (for custom vignet
Scholar 19 months ago, created an answer that has been accepted. For A: ChemmineOB cannot find installed open-babel
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: BiocCheck: REQUIRED: vignette sources in vignettes/ directory (for custom vignet
Guru 19 months ago, received more than 100 upvotes.
Appreciated 19 months ago, created a post with more than 5 votes. For Recent course materials now easily searchable
Scholar 19 months ago, created an answer that has been accepted. For A: ChemmineOB cannot find installed open-babel
Scholar 20 months ago, created an answer that has been accepted. For A: ChemmineOB cannot find installed open-babel

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