Admin: Dan Tenenbaum
Dan Tenenbaum ♦♦ 8.2k
- Reputation:
- 8,160
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 1 year, 2 months ago
- Joined:
- 8 years, 3 months ago
- Email:
- d*******@fhcrc.org
I was in the Bioconductor group at Fred Hutchinson Cancer Research Center in Seattle, WA, USA.
Posts by Dan Tenenbaum
<prev
• 1,024 results •
page 1 of 103 •
next >
0
votes
2
answers
595
views
2
answers
... 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 21 months ago by
Dan Tenenbaum ♦♦ 8.2k
0
votes
2
answers
595
views
2
answers
... StarCluster is a little old. Look info CfnCluster: https://github.com/awslabs/cfncluster .
...
written 22 months ago by
Dan Tenenbaum ♦♦ 8.2k
0
votes
1
answers
872
views
1
answers
... 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 2.5 years ago by
Dan Tenenbaum ♦♦ 8.2k
0
votes
1
answers
872
views
1
answers
... 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 2.5 years ago by
Dan Tenenbaum ♦♦ 8.2k
0
votes
1
answers
1.3k
views
1
answers
... 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 2.5 years ago by
Dan Tenenbaum ♦♦ 8.2k
0
votes
1
answers
1.4k
views
1
answers
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 2.5 years ago by
Dan Tenenbaum ♦♦ 8.2k
0
votes
1
answers
1.4k
views
1
answers
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 2.5 years ago by
Dan Tenenbaum ♦♦ 8.2k
0
votes
0
answers
580
views
0
answers
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 2.5 years ago by
Dan Tenenbaum ♦♦ 8.2k
0
votes
5
answers
5.6k
views
5
answers
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 2.5 years ago by
Dan Tenenbaum ♦♦ 8.2k
0
votes
0
answers
580
views
0
answers
Comment:
C: Error in loading rsbml
... The build macs use version 5.10.x
...
written 2.5 years ago by
Dan Tenenbaum ♦♦ 8.2k
Latest awards to Dan Tenenbaum
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Bioconductor Git/GitHub Mirrors
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Bioconductor 3.0 is released!
Appreciated
21 months ago,
created a post with more than 5 votes.
For Bioconductor Git/GitHub Mirrors
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Bioconductor 2.13 is released
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Bioconductor 2.13 is released
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Bioconductor 2.13 is released
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For Bioconductor 2.14 is released
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For New Package Submission Process
Teacher
2.6 years ago,
created an answer with at least 3 up-votes.
For A: How to get rid of "Update all/some/none? [a/s/n]:"
Teacher
2.6 years ago,
created an answer with at least 3 up-votes.
For A: "rstudio initialization error: unable to connect to service" after logging in to
Oracle
2.6 years ago,
created more than 1,000 posts (questions + answers + comments).
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For Bioconductor 2.13 is released
Scholar
2.6 years ago,
created an answer that has been accepted.
For A: Package lists and other questions about the site
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: Package lists and other questions about the site
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: How to get rid of "Update all/some/none? [a/s/n]:"
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: best way to terminate a Docker-based bioconductor/RStudio session?
Teacher
2.9 years 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
3.0 years ago,
created an answer that has been accepted.
For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar
3.0 years ago,
created an answer that has been accepted.
For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar
3.0 years ago,
created an answer that has been accepted.
For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar
3.1 years ago,
created an answer that has been accepted.
For A: best way to terminate a Docker-based bioconductor/RStudio session?
Teacher
3.2 years 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
3.2 years ago,
created an answer that has been accepted.
For A: best way to terminate a Docker-based bioconductor/RStudio session?
Scholar
3.2 years ago,
created an answer that has been accepted.
For A: Error updating packages: couldn’t understand kern.osversion
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.2.0
Traffic: 314 users visited in the last hour