User: becker.gabriel

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Posts by becker.gabriel

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
... Sorry, I misread your question when posting my previous answer, though I'll leave it up in the hopes perhaps it is useful to someone. switchr can also install exact historical versions of packages. Make sure you have switchr version 0.12.9 (currently only available from http://github.com/gmbecker/s ...
written 14 months ago by becker.gabriel10
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Comment: C: Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
... switchr can also install exact, old sets of R packages if that's what you need to do (I don't recommend installing a single historical package version on top of an otherwise modern package library in most cases ). See our paper in JSS https://www.jstatsoft.org/article/view/v082i01 and the package vi ...
written 14 months ago by becker.gabriel10
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Comment: C: Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
... James, You can use switchr to more easily get back to exact package versions if you need to. It has the crawl git/SVN/CRAN webarchive functionality built in so you don't have to worry about it. Best, ~G ...
written 14 months ago by becker.gabriel10
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Answer: A: Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
... Hi all, My switchr package  (on CRAN) has functionality to do this. To create a new switchr library which uses Bioc 3.4, you can do: > library(switchr) > switchTo("bioc3.4test", seed = BiocVers("3.4")) trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/BiocInstaller_1.24.0.t ...
written 14 months ago by becker.gabriel10
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Answer: A: ReportingTools Segmentation fault
... This is strange. ReportingTools does not have any C or C++ code in it at all, so it is difficult to imagine the segfault being due to our code. I'm also not able to reproduce this when installing from source on OS X El Capitan in R 3.4.4 patched.  I will try to look into this more but I'm not sure ...
written 18 months ago by becker.gabriel10
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Answer: A: genbankr fails when reading GBK file
... Monther, Apologies for not responding sooner. I'm not familiar with this error. I haven't seen it before. Can you provide me the gbk file in question so I can do some debugging? Thanks, ~G ...
written 18 months ago by becker.gabriel10
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Answer: A: problem with genbankr
... Hi, Sorry for the delay getting back to you. The issue here was not a bug in genbankr, per se, but rather a but introduced in a new version of the underlying rentrez package. This has now been fixed in both release and devel and you should no longer get this error. Best, ~G ...
written 18 months ago by becker.gabriel10
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Answer: A: Importing genbank entries for synthetic constructs
... Thomas, Thanks for the report. Ideally, genbankr is intended to support anything (reasonable) provided in the GenBank (or GenPept) format. I will look into this and should be able to get it fixed.  I will comment again when there is news. Best, ~G ...
written 2.8 years ago by becker.gabriel10

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