Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 20k
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http://bioconductor.org/
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Posts by Martin Morgan

<prev • 2,666 results • page 1 of 267 • next >
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Answer: A: Error in file.choose() : file choice cancelled
... Questions about package development should be directed to the bioc-devel mailing list. file.choose() implies user interaction, so obviously cannot be evaluated by a vignette. You don't provide enough detail, but if this were a function you wrote. Usually the file that the vignette is supposed to p ...
written 6 days ago by Martin Morgan ♦♦ 20k
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Answer: A: error displaying bam files
... Usually this type of error occurs when packages are out of sync. Does the result of BiocInstaller::biocValid() suggest any problems? Does the simpler example example(readGAlignments) work? ...
written 6 days ago by Martin Morgan ♦♦ 20k
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Comment: C: How to set 'strandMode' with summarizeOverlaps()
... GenomicFiles::reduceByYield() might be a wrapper around some of this. Is there a bug in SummarizedExperiment, along the lines Jim indicated of not passing strandMode correctly? If so, perhaps an issue and / or pull request on https://github.com/Bioconductor/SummarizedExperiment would be appropriate. ...
written 6 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Rstudio session aborts when using read.celfiles()
... Try to narrow down the culprit by reducing the number of non-essential pieces, e.g., at the command line (i.e., no RStudio) start a vanilla R session (i.e., no unnecessary packages) and recreate the problem $ R --vanilla > library(oligo) > CELfiles<-list.celfiles() > raw_data <- rea ...
written 7 days ago by Martin Morgan ♦♦ 20k
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Answer: A: How to filter all column using Loop
... Create a data.frame directly. Using cbind() causes the numeric values to be represented as character vectors, which is not desired. o value in using data.table in the current example e = data.frame(a,b,c,d) A data.frame is a list of vectors, so iterate over the columns that you're interested in, i.e ...
written 7 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Bioconductor installing pakage error, R 3.4.2, Ubuntu 17.10
... It is the same story, a missing system library, to be installed via apt-get or to configure R without. A different route through this is to install R itself via apt, following relevant instructions here https://cran.r-project.org/bin/linux/ and installing the -devel flavor. This will also install th ...
written 9 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Bioconductor installing pakage error, R 3.4.2, Ubuntu 17.10
... You can either install readline ,I think sudo apt-get install readline-common or configure R not to use readline ../R-patched/configure --with-readline=no The former is the better solution, although the package (readline-common) is only a guess. ...
written 9 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Bioconductor installing pakage error, R 3.4.2, Ubuntu 17.10
... I usually build 'out-of-source'. Also best practice is to reserve use of sudo for the essential steps tar zxvf R-patched.tar.gz mkdir R-3-4-2-patched cd R-3-4-2-patched ../R-patched/configure make -j R-3-4-2/bin/R should be executable; sudo make install if you want to install as root, though a ...
written 10 days ago by Martin Morgan ♦♦ 20k
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Answer: A: Bioconductor installing pakage error, R 3.4.2, Ubuntu 17.10
... See this where a solution is to install the patched version of R. But it is still interesting to understand what the particular features of your setup-are that trigger this. A diagnostic step is provided here; it would be very helpful to provide some additional information about your particular setu ...
written 11 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Bioconductor version too old
... Your BiocInstaller is too old and needs to be updated following these instructions. If that fails, please copy and paste your attempts at removal and installation into a comment. ...
written 15 days ago by Martin Morgan ♦♦ 20k

Latest awards to Martin Morgan

Scholar 4 months ago, created an answer that has been accepted. For A: BiocParallel: messages shown only when processes finished
Teacher 5 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
Scholar 5 months ago, created an answer that has been accepted. For A: BiocParallel: messages shown only when processes finished
Scholar 5 months ago, created an answer that has been accepted. For A: BiocParallel: messages shown only when processes finished
Scholar 5 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 5 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 6 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Good Answer 6 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
Appreciated 6 months ago, created a post with more than 5 votes. For Statistics and Computing in Genome Science (CSAMA) Course Material
Scholar 6 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 6 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 7 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Appreciated 7 months ago, created a post with more than 5 votes. For BioC 2015 Annual Conference
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Scholar 7 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 7 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 7 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Appreciated 8 months ago, created a post with more than 5 votes. For BioC 2015 Annual Conference
Scholar 8 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 8 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Scholar 8 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 9 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()

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