Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 22k
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Website:
http://bioconductor.org/
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1 day, 13 hours ago
Joined:
12 years, 10 months ago
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m************@gmail.com

Posts by Martin Morgan

<prev • 2,941 results • page 2 of 295 • next >
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Comment: C: Segfault error when loading WGCNA
... One possibility is that it is not WGCNA at all, but a stale dependency. You could try trace(loadNamespace,   tracer=quote(print(package)),   exit=quote(print(paste("leaving", package))),   print=FALSE ) ​library(WGCNA) it'll print the package names as each is loaded; the output is a bit co ...
written 17 days ago by Martin Morgan ♦♦ 22k
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Answer: A: Cannot install flowViz package because dependency flowCore cannot be found, howe
... I think that .libPaths() has more than one entry, and that flowCore is installed in, e.g., the second entry. Try removing flowCore from all locations, and installing it again. Then try to install flowViz. ...
written 17 days ago by Martin Morgan ♦♦ 22k
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Answer: A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
... When I use devtools::install_bioc() I get a very old version of Rhtslib -- it does a checkout from (our no longer current) svn and installs > packageVersion("Rhtslib") [1] '1.9.2' whereas the current version of Rhtslib (from https://bioconductor.org/packages/Rhtslib) is 1.12.1. I reported this ...
written 22 days ago by Martin Morgan ♦♦ 22k
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Comment: C: Problem installing Bioconductor
... Sorry, I won't really be any more help than googling; what happens when you follow the link in a browser? ...
written 4 weeks ago by Martin Morgan ♦♦ 22k
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Answer: A: Problem installing Bioconductor
... Try using the https: url directly source("https://bioconductor.org/biocLite.R") ...
written 4 weeks ago by Martin Morgan ♦♦ 22k
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Answer: A: Problem installing ChAMP package.
... It looks like you're using R 3.3, which is quite old and problematic, since if there is a fix to be had it won't be made available for that version. So the first step is to update to the current version of R (R-3.5.1) and then to install ChAMP again. If there is still a segfault, start R-3.5.1 and m ...
written 4 weeks ago by Martin Morgan ♦♦ 22k
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Answer: A: How to parse supplementary (not secondary) alignments
... Thanks, its surprising that this hasn't come up before, and that it has not been implemented. This will be available via a flag isSupplementaryAlignment in Rsamtools version 1.32.3 (Bioconductor version 3.7) / 1.33.4 (devel) in the next day or so; it can also be installed using BiocManager::install( ...
written 4 weeks ago by Martin Morgan ♦♦ 22k
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Comment: C: DEXUSResult as.data.frame doesn't work well if topGO is loaded
... BiocGenerics defines an S4 generic as.data.frame that has as it's default method base::as.data.frame. The effect is to either handle the S4 object, or if the object is not an S4 object / does not have an S4 as.data.frame method to let base::as.data.frame do it's job. Thus BiocGenerics implements S4 ...
written 4 weeks ago by Martin Morgan ♦♦ 22k
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Comment: C: annotationhub: data update
... The core team will come up with a strategy for updating these resources as part of our regular work flows. ...
written 5 weeks ago by Martin Morgan ♦♦ 22k
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Answer: A: R says include dir is empty, but it's not.
... Remember that you are using a conda installation, so that the correct way to install Bioconductor packages is to use conda install, NOT biocLite. This is a conda issue, and should be reported there (readers of this forum are not in a position to fix it). ...
written 5 weeks ago by Martin Morgan ♦♦ 22k

Latest awards to Martin Morgan

Scholar 6 weeks ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 3 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Popular Question 3 months ago, created a question with more than 1,000 views. For BioC 2015 Annual Conference
Scholar 3 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Error in GRanges: could not find symbol "recursive" in environment of the generi
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 3 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Popular Question 3 months ago, created a question with more than 1,000 views. For Updated Bioconductor Package Submission Policy
Scholar 4 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Eliminating repetitive calls to ExperimentHub
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 4 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Scholar 15 months ago, created an answer that has been accepted. For A: about filtering variants in a VCF file
Scholar 15 months ago, created an answer that has been accepted. For A: How to initialize a SummarizedExperiment?
Scholar 15 months ago, created an answer that has been accepted. For A: Extracting sequences from BSgenomeViews object
Scholar 15 months ago, created an answer that has been accepted. For A: Error building R Markdown v2 document
Scholar 15 months ago, created an answer that has been accepted. For A: Warnings messages can not we handles/hidden
Scholar 15 months ago, created an answer that has been accepted. For A: Setting ExperimentHub Cache Location
Scholar 15 months ago, created an answer that has been accepted. For A: annotation: how to use "character" for function 'select()'
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Scholar 15 months ago, created an answer that has been accepted. For A: Error with MSA package - could not find symbol "recursive"
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Error in GRanges: could not find symbol "recursive" in environment of the generi
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Import gff from character?

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