Admin: Martin Morgan

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Martin Morgan ♦♦ 22k
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http://bioconductor.org/
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Posts by Martin Morgan

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Comment: C: Rsamtools undefined symbol: gzopen64
... I think the updated line should not have had -L, so PKG_LIBS = ${PKG_LIBS0} /lib64/libz.so.1.2.11   ...
written 1 hour ago by Martin Morgan ♦♦ 22k
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Answer: A: Installing GEOQuery failed with conda
... I think that this is basically a variant of this problem with zlib, where mixing conda and R installation mechanisms fails when there are system libraries in non-standard locations (see also this conda issue). You would instead like to say conda install bioconductor-geoquery ...
written 12 hours ago by Martin Morgan ♦♦ 22k
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Answer: A: Rsamtools undefined symbol: gzopen64
... Thanks for the careful report. I think that there is basically a mis-configuration on your system, with the .so pointing to an old rather than new version of libz. Nonetheless, I think you can work around this by editing Rsamtools/src/Makevars to contain the full path to the libz you'd like to use ...
written 17 hours ago by Martin Morgan ♦♦ 22k
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Comment: C: ExperimentHub wackiness (which breaks packages that depend upon experimentHub-pr
... Looking at this, sessameData() has this in .onAttach > sesameData:::.onAttach function (libname, pkgname) { packageStartupMessage("Loading sesameData.") if (has_internet()) { suppressMessages(log <- capture.output(sesameDataCacheAll())) } } and sesameDataCacheAll() has ...
written 19 hours ago by Martin Morgan ♦♦ 22k
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Answer: A: ExperimentHub wackiness (which breaks packages that depend upon experimentHub-pr
... install("sesameData", localHub=TRUE) seems to be a manufactured command (where did it come from?). I think you're aiming for BiocManager::install("sesameData") And what you're trying to to is to install a plain-old experiment data package, nothing to do with ExperimentHub. ...
written 21 hours ago by Martin Morgan ♦♦ 22k
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Answer: A: Install Bioconductor package locally/temporarily
... use BiocInstaller::biocinstallRepos() to get the correct repositories to be used with standard R package installation commands. (bio)conda expects all packages to be installed by bioconda; if there are packages not available from bioconda or if a recent distribution is important then personally I th ...
written 21 hours ago by Martin Morgan ♦♦ 22k
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Comment: C: ALL dataset, correct syntax using the exprs call?
... You're asking a different question, so ask a new top-level post 'building a linear model' or some such, after of course reading the excellent limma manual. ...
written 2 days ago by Martin Morgan ♦♦ 22k
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Answer: A: Problems with Organism.dplyr
... Thanks Jim For your devel scenario, it's likely that you have duplicate records for the synthetic db, as for mm10 below > library(BiocFileCache); library(tidyverse) > bfc = BiocFileCache() > bfcquery(bfc, "dplyr.") %>% select(rid, rname, fpath) # A tibble: 4 x 3   rid   rname          ...
written 4 days ago by Martin Morgan ♦♦ 22k
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Answer: A: GO.db source obo file?
... Likely the reason for differences is because the version of GO you use for visualization is different from the version used by GO.db. For me with version 3.6.0 of GO.db (same as you), loading the library and printing GO.db gives > GO.db GODb object: | GOSOURCENAME: Gene Ontology | GOSOURCEURL: ...
written 5 days ago by Martin Morgan ♦♦ 22k
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Comment: C: ALL dataset, correct syntax using the exprs call?
... lmFit is in the limma package, so you need to say library(limma) fit <- lmFit(ourData, design) ... or fit <- limma::lmFit(ourData, design) probably the former is better for interactive use. ...
written 6 days ago by Martin Morgan ♦♦ 22k

Latest awards to Martin Morgan

Popular Question 10 weeks ago, created a question with more than 1,000 views. For BioC 2015 Annual Conference
Scholar 10 weeks ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Good Answer 10 weeks 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
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Updated Bioconductor Package Submission Policy
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 10 weeks ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Teacher 10 weeks 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 10 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
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
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Eliminating repetitive calls to ExperimentHub
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: How to get chip information from annotation databases
Scholar 13 months ago, created an answer that has been accepted. For A: about filtering variants in a VCF file
Scholar 13 months ago, created an answer that has been accepted. For A: How to initialize a SummarizedExperiment?
Scholar 13 months ago, created an answer that has been accepted. For A: Extracting sequences from BSgenomeViews object
Scholar 13 months ago, created an answer that has been accepted. For A: Error building R Markdown v2 document
Scholar 13 months ago, created an answer that has been accepted. For A: Warnings messages can not we handles/hidden
Scholar 13 months ago, created an answer that has been accepted. For A: Setting ExperimentHub Cache Location
Scholar 13 months ago, created an answer that has been accepted. For A: annotation: how to use "character" for function 'select()'
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Teacher 13 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 13 months ago, created an answer with at least 3 up-votes. For A: Import gff from character?
Scholar 13 months ago, created an answer that has been accepted. For A: Error with MSA package - could not find symbol "recursive"
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Filtering a BAM file using RSamtools
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Setting ExperimentHub Cache Location

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