User: james.dalgleish

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Posts by james.dalgleish

<prev • 22 results • page 1 of 3 • next >
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Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
... NIPTeR is experiencing new warnings when loading Biostrings. I have the exact same warnings with my package, CNVScope. I would post sessionInfo(), but this occurs only on the check debian servers. It doesn't happen on windows 10 or Ubuntu (zero problems there). I realize that one response will prob ...
biostrings written 6 days ago by james.dalgleish30 • updated 6 days ago by Martin Morgan ♦♦ 24k
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Answer: A: GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
... Here's what I did to solve it: ``` remotes::install_github("Bioconductor/BiocGenerics") remotes::install_github("Bioconductor/S4Vectors") remotes::install_github("Bioconductor/IRanges") remotes::install_github("Bioconductor/GenomicRanges") ``` GenomicRanges now loads. ``` > library(BiocGenerics) ...
written 9 weeks ago by james.dalgleish30
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Comment: C: GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
... The remainder of the BiocManager::valid() output is below (it was over 5000 characters). ``` Bioconductor version '3.9' * 5 packages out-of-date * 140 packages too new create a valid installation with BiocManager::install(c( "affycoretools", "airway", "AllelicImbalance", "AnnotationFilt ...
written 9 weeks ago by james.dalgleish30
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Comment: C: GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
... Here's the requested output in the comment. ``` > BiocManager::valid() * sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /usr/local/intel/compilers_and_libraries_2019.1.144/linux/mkl/li ...
written 9 weeks ago by james.dalgleish30
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GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
... So, this may be pretty big problem that may affect many packages, including mine. I hope others are not having the same issue, but I cannot get GenomicRanges to load because it wants a newer version of S4Vectors than exists on Bioconductor(see https://bioconductor.org/packages/release/bioc/html/S4Ve ...
genomicranges s4vectors biocmanager written 9 weeks ago by james.dalgleish30
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Comment: C: "Packages required but not available." rtracklayer in OSX is not available to CR
... Might be an idea for the future. My code is fairly well documented and has good vignettes at this point. It took a LOT of work to get CRAN to take it, though. I imagine the process for getting accepted on Bioconductor is very difficult, like CRAN. Thanks for the insights into the mechanics. That's p ...
written 4 months ago by james.dalgleish30
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"Packages required but not available." rtracklayer in OSX is not available to CRAN, resulting in errors for downstream dependencies.
... So, I'm attempting to update my CRAN package and it depends on several other packages. What I notice is that many packages fail with errors on OSX checks due to Bioconductor packages not being visible when CRAN checks are run. I guess I'm posting first to Bioconductor because I know that the communi ...
variantannotation rtracklayer genomicranges s4vectors summarizedexperiment written 4 months ago by james.dalgleish30 • updated 4 months ago by Steve Lianoglou12k
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Comment: A: Old jmosaics working package
... Is there a replacement that does something similar? I've never seen anything quite like it previously. ...
written 20 months ago by james.dalgleish30
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Old jmosaics working package
... I've had a hard time finding it, but is there a jmosaics package that is version 1.1.0? I've been trying to find it and had old code that required it's use for chipseq. http://www.bioconductor.org/packages//2.13/bioc/html/jmosaics.html The package binary (zip) listed here doesn't actually contain a ...
jmosaics written 20 months ago by james.dalgleish30

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