Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 22k
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Website:
http://bioconductor.org/
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12 years, 11 months ago
Email:
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Posts by Martin Morgan

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Comment: C: Indexing large chromosomes (like wheat) bam files in Rsamtools
... Actually Rsamtools is based on an old code base; it is being updated to htslib this release. ...
written 1 day ago by Martin Morgan ♦♦ 22k
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Comment: C: New computer won't install DESeq2
... Go after the first hint of trouble, and try to install / troubleshoot the installation of RcppArmadillo. ...
written 5 days ago by Martin Morgan ♦♦ 22k
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Comment: C: Reason: image not found Error: package GenomeInfoDb could not be loaded
... I probably didn't read the error message carefully enough. It looks like your conda environment doesn't have libintl.9.dylib. It isn't obvious from google how to install this in conda, other than through indirectly through some other package. Probably more help available in conda forums. Sorry for m ...
written 5 days ago by Martin Morgan ♦♦ 22k
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Answer: A: Reason: image not found Error: package GenomeInfoDb could not be loaded
... Did you use biocLite() or BiocManager::install() to install packages in your conda installation? I think that you must opt fully for conda (and live with outdated versions and perhaps some packages that are not available) or fully for installation 'by hand' for the reasons described at https://githu ...
written 5 days ago by Martin Morgan ♦♦ 22k
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Comment: C: DESeq2 install problem
... Have you restarted your R session? Can you use get available.packages() to work on the rstudio url, perhaps with the argument ignore_repo_cache = TRUE? ...
written 6 days ago by Martin Morgan ♦♦ 22k
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Comment: C: bam2CTSS function error from CAGEr package
... I have > packageVersion("CAGEr") [1] ‘1.22.3’ Somehow you seem to have had a 'stale' version of the class definition. Maybe you were saving the environment of your previous session, or just needed to restart R? At any rate I think the key was to restart a _clean_ session. ...
written 7 days ago by Martin Morgan ♦♦ 22k
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Comment: C: bam2CTSS function error from CAGEr package
... It's confusing to mark this with a check mark. The check mark means that this answer solves your problem. But you say that you still have a problem... ...
written 7 days ago by Martin Morgan ♦♦ 22k
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Comment: C: bam2CTSS function error from CAGEr package
... In a new session, I have > library(CAGEr) > CAGEexp class generator function for class “CAGEexp” from package ‘CAGEr’ function (...) new("CAGEexp", ...) <bytecode: 0x7faf493f3b78> <environment: namespace:CAGEr> > getClass("CAGEexp") Class "CAGEexp" [package "CAGEr"] Slots: N ...
written 7 days ago by Martin Morgan ♦♦ 22k
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Comment: C: Error while installing Phyloseq using biocLite
... I believe the error is coming when R tries to download the file http://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/PACKAGES (which exists) via the equivalent of fl = "http://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/PACKAGES" dest = tempfile() download.file(fl, dest ...
written 8 days ago by Martin Morgan ♦♦ 22k
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Comment: C: bam2CTSS function error from CAGEr package
... Please confirm that you are updating packages using BiocInstaller::biocLite(), and that your package installation is correct based on BiocInstaller::biocValid(). Please also start a new R session and load only the packages required for the commands that you are trying to execute, to simplify the si ...
written 8 days ago by Martin Morgan ♦♦ 22k

Latest awards to Martin Morgan

Scholar 10 weeks ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Teacher 10 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 4 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Popular Question 4 months ago, created a question with more than 1,000 views. For BioC 2015 Annual Conference
Scholar 4 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Good Answer 4 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 4 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 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: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Popular Question 4 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
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Eliminating repetitive calls to ExperimentHub
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
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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