Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 23k
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Website:
http://bioconductor.org/
Last seen:
2 days, 12 hours ago
Joined:
13 years, 5 months ago
Email:
m************@gmail.com

Posts by Martin Morgan

<prev • 3,098 results • page 2 of 310 • next >
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Comment: C: Issue setting up BiocManager due to mgcv / clang?
... Type `R.home("etc/Makeconf")` into the R console, you'll get a path to a plain text file that you can open with any editor, e.g., RStudio. Look for lines containing `-fopenmp`. The simplest solution is to simply say 'no' when asked to install the source version of mgcv. The next simplest solution ...
written 22 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Issue setting up BiocManager due to mgcv / clang?
... Sorry not to read your question closely enough. I think this is an R installation issue rather than Bioconductor (probably `install.packages("mgcv")` fails in the same way...?) but to troubleshoot, I'd guess that the `-fopenmp` flag is present in the file at `R.home("etc/Makeconf")`. Can you verify ...
written 22 days ago by Martin Morgan ♦♦ 23k
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Comment: C: BioC2018 Workshop book not linked from Bioconductor.org?
... We'll get this sorted, thanks ...
written 23 days ago by Martin Morgan ♦♦ 23k
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Answer: A: Issue setting up BiocManager due to mgcv / clang?
... You've opted to install a source package on MacOS, so you need to [install macOS developer tools][1]; the alternative is to install the currently out-of-date binary by answering 'no', or to wait until an up-to-date binary has been produced. [1]: https://r.research.att.com/tools/ ...
written 23 days ago by Martin Morgan ♦♦ 23k
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Answer: A: Convert BAM to FASTQ
... Load Rsamtools and ShortRead library(Rsamtools) library(ShortRead) Create a BamFile that references your file, with a yieldSize (number of records available at one time). Open it bf = BamFile(", yieldSize = 1000000) open(bf) to = "" Write a helper function to read and write o ...
written 23 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Duplicated reads if 'which' has overlapping reads in ScanBamParam
... I added a short comment to `?ScanBamParam` in version 1.99.4, which will be available in 'devel' in the next 24 - 48 hours; the updated documentation will be included in the next release, anticipated at the end of April. Note that the rdocumentation link is for Rsamtools version 1.24.0, so more tha ...
written 27 days ago by Martin Morgan ♦♦ 23k
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Comment: C: GO.db installation problems with BiocManager in R
... The 'annotation' packages are installed from 'source' so have a different extension (`.tar.gz`) than the usual Windows 'binary' packages (extension `.zip`); perhaps that is the reason? Thanks for replying with the diagnosis. ...
written 28 days ago by Martin Morgan ♦♦ 23k
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Comment: C: GO.db installation problems with BiocManager in R
... Try the two-step process of downloading the package download.packages( "GO.db", "C:/Users/Name/Documents", repos = BiocManager::repositories() ) and installing it locally install.packages("C:/Users/Name/Documents/GO.db_3.7.0.tar.gz", repos = NULL) ...
written 28 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Add annotation, biomaRt installation
... Provide the full output of `BiocManager::install("openssl")` ...
written 4 weeks ago by Martin Morgan ♦♦ 23k
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Comment: C: Add annotation, biomaRt installation
... It will help to narrow the problem to the first installation that fails, and to provide additional information. I have > BiocManager::install("openssl") Bioconductor version 3.9 (BiocManager 1.30.4), R Under development (unstable) (2019-03-06 r76203) Installing package(s) 'open ...
written 4 weeks ago by Martin Morgan ♦♦ 23k

Latest awards to Martin Morgan

Appreciated 4 months ago, created a post with more than 5 votes. For Statistics and Computing in Genome Science (CSAMA) Course Material
Scholar 5 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 5 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
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
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
Scholar 6 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
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: Difficulty extending ExpressionSet
Scholar 8 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Teacher 8 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
Popular Question 10 months ago, created a question with more than 1,000 views. For Updated Bioconductor Package Submission Policy
Scholar 10 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 10 months ago, created a question with more than 1,000 views. For BioC 2015 Annual Conference
Teacher 10 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 10 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 10 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Good Answer 10 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 10 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 11 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 11 months ago, created a comment with at least 3 up-votes. For C: Eliminating repetitive calls to ExperimentHub
Teacher 11 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 11 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Scholar 22 months ago, created an answer that has been accepted. For A: about filtering variants in a VCF file

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