Admin: Martin Morgan

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Martin Morgan ♦♦ 22k
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Posts by Martin Morgan

<prev • 3,008 results • page 2 of 301 • next >
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Comment: C: edgeR package fails to load after install
... It would probably help to include the full transcript of the attempt to install edgeR, and to include the output of sessionInfo(). ...
written 8 days ago by Martin Morgan ♦♦ 22k
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Answer: A: Recommended way to use BiocInstaller / BiocManager in packages on CRAN?
... I believe, though it would be more effective to communicate with CRAN directly, that the intention was to alert you to a problem that your R-devel users will experience when BiocInstaller is no longer available, with the recommendation to handle the situation gracefully rather than with an error. ...
written 8 days ago by Martin Morgan ♦♦ 22k
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Answer: A: problems regarding installing TEQC package
... The warning in this code > config <- "https://bioconductor.org/config.yaml" > readLines(config) Error in file(con, "r") : cannot open the connection to 'https://bioconductor.org/config.yaml' In addition: Warning message: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': ...
written 11 days ago by Martin Morgan ♦♦ 22k
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Comment: C: problems regarding installing TEQC package
... The underlying problem is like from config <- "https://bioconductor.org/config.yaml" readLines(config) Do those lines work for you? Can you also report the result of packageVersion("BiocManager")   ...
written 12 days ago by Martin Morgan ♦♦ 22k
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Comment: C: Rhtslib - install error
... f you were not using conda, the standard method of installation would work or would be remedied by installing libz. You are using conda, so this is a conda error and needs to be reported to them. The Bioconductor approach is not finding libz and headers, because they are installed in a location kno ...
written 12 days ago by Martin Morgan ♦♦ 22k
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Comment: C: unable to load rsbml for piano reporter metabolite analysis
... My suggestion was to use bioconda, since you've opted for that for other packages. bioconda is responsible for managing libraries (I guess it is the main use case) and does so in a way that does not play well with 'native' installations. The worst case scenario is to report to bioconda that their rs ...
written 12 days ago by Martin Morgan ♦♦ 22k
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Comment: C: Initial List of Deprecated Package Bioc 3.9
... I did move this to https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014301.html ...
written 14 days ago by Martin Morgan ♦♦ 22k
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Comment: C: unable to load rsbml for piano reporter metabolite analysis
... Are you using bioconda to install rsbml as well? A consequence of this might be restriction to the previous Bioconductor release, at least in the short term. ...
written 14 days ago by Martin Morgan ♦♦ 22k
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Comment: C: Recommended way to use BiocInstaller / BiocManager in packages on CRAN?
... BiocManager actually has a second component, the Bioconductor BiocVersion package. As you know, Bioconductor has two releases per year, whereas CRAN has only one. There is therefore a need to store the version of Bioconductor in use, from the two available for R, in a particular R session. This is t ...
written 14 days ago by Martin Morgan ♦♦ 22k
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Comment: C: dmrseq installation failed
... If you're using github and the release branch, be sure to add the argument ref = "RELEASE_3_8" to the install command. Likewise, be sure to git checkout RELEASE_3_8 in the git clone. ...
written 14 days ago by Martin Morgan ♦♦ 22k

Latest awards to Martin Morgan

Scholar 7 weeks ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Teacher 7 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 7 weeks ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 7 weeks ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
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: Difficulty extending ExpressionSet
Good Answer 5 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
Scholar 5 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Popular Question 5 months ago, created a question with more than 1,000 views. For Updated Bioconductor Package Submission Policy
Scholar 5 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 5 months ago, created a question with more than 1,000 views. For BioC 2015 Annual Conference
Teacher 5 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 5 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Teacher 5 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
Scholar 6 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 6 months ago, created a comment with at least 3 up-votes. For C: Eliminating repetitive calls to ExperimentHub
Teacher 6 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 6 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Scholar 16 months ago, created an answer that has been accepted. For A: about filtering variants in a VCF file
Scholar 16 months ago, created an answer that has been accepted. For A: How to initialize a SummarizedExperiment?
Scholar 16 months ago, created an answer that has been accepted. For A: Extracting sequences from BSgenomeViews object
Scholar 16 months ago, created an answer that has been accepted. For A: Error building R Markdown v2 document
Scholar 16 months ago, created an answer that has been accepted. For A: Error with MSA package - could not find symbol "recursive"
Scholar 16 months ago, created an answer that has been accepted. For A: Warnings messages can not we handles/hidden
Scholar 16 months ago, created an answer that has been accepted. For A: Setting ExperimentHub Cache Location

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