Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 20k
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20,430
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United States
Website:
http://bioconductor.org/
Last seen:
31 minutes ago
Joined:
12 years ago
Email:
m************@roswellpark.org

Posts by Martin Morgan

<prev • 2,666 results • page 2 of 267 • next >
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Comment: C: ChIPQC Error in .Call2 NCList object is too deep
... Please add the output of sessionInfo(), and be sure to use up-to-date versions of R (3.4.2) and Bioconductor (3.6) with no package conflicts (BiocInstaller::biocValid() returns TRUE). ...
written 18 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Accessing GRangesList rows in Rcpp
... In general terms, R is efficient when it drops to C (most of R and many packages are written in C, not C++) for the implementation. The 'art' is identifying when an operation requires new C / C++ code, versus using convenient, flexible, and TESTED R code. relist() in the GenomicRanges world is 'fas ...
written 18 days ago by Martin Morgan ♦♦ 20k
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Answer: A: Accessing GRangesList rows in Rcpp
... Very roughly, I would write my C++ code to rely on base R vectors as inputs, implement the body using standard C++ data structures, and return the output as a list of base R vectors #include <Rcpp.h> using namespace Rcpp; // [[Rcpp::export]] List orfs( CharacterVector seqname, Inte ...
written 18 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Cannot create SingleCellExperiment object
... Can you provide the output of sessionInfo() after library(SingleCellExperiment), and also BiocInstaller::biocValid() ? ...
written 19 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Upgrade to 3.6 - can't seem to get past Bioconductor 3.5
... Users of R-devel / bioc-devel will experience issues for the next hour or so; windows users of R-devel will need to install from source for the next day or so (at least some CRAN windows binaries seem to be built with R-3.4.2 instead of R-devel). ...
written 19 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Upgrade to 3.6 - can't seem to get past Bioconductor 3.5
... Can you provide some more detail? ...
written 19 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Bioconductor 3.6 release: 3.6 branch created
... Yes, the code repositories need to branch, and then a nightly build run. So today October 31 at about 2:30 Eastern will provide access to 3.6 build products. ...
written 20 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Accessing GRangesList rows in Rcpp
... FWIW, It will not be faster to manipulate a GRanges object in C than in R. If there were some operations I wanted to perform on a GRanges object that were not supported in R (it is challenging to know what these operations are -- I wonder what you are trying to accomplish?) then my strategy would be ...
written 20 days ago by Martin Morgan ♦♦ 20k
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Comment: C: csaw intallation issue: cannot find "lib" in Rhtslib installation
... On windows, it seems like R_ARCH is defined as, e.g, '\x86' and the library is placed in ilb\x86\... Can you verify what, from the command line, R CMD env | grep R_ARCH reports on your system? Can you also indicate how you installed R and Rhtslib? ...
written 23 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Weaknesses with GRanges data type, or just me ?
... tweak that so that unlist() has use.names=FALSE, otherwise the names of the unlisted object are those of the elements of the list, e.g., example(GRangesList) identical(grl, relist(unlist(grl, use.names=FALSE), grl)) # TRUE ...
written 24 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 5 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 6 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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