User: ioannis.vardaxis

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New User
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Norway/Trondheim/NTNU
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6 months, 3 weeks ago
Joined:
1 year, 11 months ago
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i***************@ntnu.no

Posts by ioannis.vardaxis

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Disable messages for bplapply when in parallel
... Perfect! Thanks for the help! ...
written 6 months ago by ioannis.vardaxis20
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Comment: C: Disable messages for bplapply when in parallel
... I tried suppressPackageStartupMessages(library(YourPackage)) inside the function I call in parallel but I still get the messages. Link to my package: https://bioconductor.org/packages/devel/bioc/html/MACPET.html Now this version also runs bplapply() but not in a loop (the loop is prepared for ...
written 6 months ago by ioannis.vardaxis20
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Comment: C: Disable messages for bplapply when in parallel
... I am on MAC and I register the snow workers like the following: snow <- BiocParallel::SnowParam(workers = 4, type = 'SOCK', progressbar=FALSE) BiocParallel::register(snow, default=TRUE) I tried bpstart/bpstop but the messages are still printed every time the loop is run. I tested the followin ...
written 6 months ago by ioannis.vardaxis20 • updated 6 months ago by Martin Morgan ♦♦ 22k
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Disable messages for bplapply when in parallel
... Hey, I have a simple question. I am using  the BiocParallel::bplapply in a package I am building, and the function runs in parallel. However every time the function will start running I get the following messages: Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery. ...
biocparallel bplapply written 6 months ago by ioannis.vardaxis20 • updated 6 months ago by Martin Morgan ♦♦ 22k
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Comment: C: BiocParallel NULL value passed as symbol address
... Hey, I did as you suggested. If I source the Rcpp code in the loop it works, but it takes a lot of time and I need to check if it is worth running it in parallel. If on the other hand I place the Rcpp code in my pkg and try to run it this way I get the following error: Error in .Call("_pkg_Testi ...
written 7 months ago by ioannis.vardaxis20
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BiocParallel NULL value passed as symbol address
... Hey, I have written a simple function Rcpp package, the function is the following: #include <Rcpp.h> using namespace Rcpp; //[[Rcpp::export]] SEXP Test(double &i){ double j=std::pow(i,2.0); return Rcpp::wrap(j); } I can source the code and run the function Test. But I want to ...
biocparallel rcpp written 7 months ago by ioannis.vardaxis20 • updated 7 months ago by Martin Morgan ♦♦ 22k
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Answer: A: Reading fastq file after narrowing sequences
... I solved it. I also had to narrow the qualities slot in the fastq file before saving. Now it uploads just fine. ...
written 10 months ago by ioannis.vardaxis20
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Reading fastq file after narrowing sequences
... Hi, I have a fastq file named fastq1 which I upload in R using: StreamFastq1=ShortRead::FastqStreamer(con=fastq1,n=2000000) fastq1yield=ShortRead::yield(StreamFastq1)   I then use the narrow funstion to narrow the reads of fastq1yield:  fastq1yield_narrowed@sread=Biostrings::narrow(fastq1yield ...
shortread fastqstreamer written 10 months ago by ioannis.vardaxis20
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Merge two BAM files into one paired-end file
... Hi,   I was wondering if it is possible to merge two separate BAM files into one paired-end BAM using packages from bioconductor. I know how to do it using external algorithms, but I am writing a package and I need to do it with bioconductor packages. I have two separate BAM files were pair info ...
bam file paired-end reads written 10 months ago by ioannis.vardaxis20
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Problem with BiocParallel::bpiterate
... Hey, I am trying to read a paired-end BAM file in chunks using BiocParallel::bpiterate but the iterations never stop, here is what I do:   bamfile=Rsamtools::BamFile(file="myBamFile",index="myBamFile",asMates=TRUE,yieldSize=1000000) snow <- BiocParallel::SnowParam(workers = 4, type = "SOCK") ...

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Scholar 16 months ago, created an answer that has been accepted. For A: Reading fastq file after narrowing sequences

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