Admin: Hervé Pagès
Hervé Pagès ♦♦ 14k
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- Joined:
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Posts by Hervé Pagès
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... Not sure what's going on exactly but the fact that you have
```
seqs_srcdir:/ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/
```
in your seed file does not look good. As explained in the vignette, the `seqs_srcdir` folder must be local:
> So we assume that you've downloaded the _seq ...
written 2 days ago by
Hervé Pagès ♦♦ 14k
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... Just set the seqnames of all the ranges in the query and subject to the same value. This can be done with something like:
```
library(GenomicRanges)
example(GRanges)
GRanges("A", ranges(gr), strand(gr))
# GRanges object with 10 ranges and 0 metadata columns:
# seqnames ranges strand
# ...
written 8 days ago by
Hervé Pagès ♦♦ 14k
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... FYI this `R CMD check` bug has been fixed in R-devel: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17613 ...
written 15 days ago by
Hervé Pagès ♦♦ 14k
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... Problem with using `dependencies=c("Depends", "Imports", "LinkingTo", "Suggests","Enhances")` is that it tends to install way to many packages, and many of them are actually never used/needed by the package that you're trying to install (in this case maEndToEnd). This is the case for statnet. It's n ...
written 18 days ago by
Hervé Pagès ♦♦ 14k
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... Hi,
2 problems with your post:
1. The tag you used (software error) is too general. Please use a package specific tag (GenomeInfoDb in this case). This will help other users of the support site find questions/answers about the package and will notify the GenomeInfoDb maintainers that a questions ...
written 18 days ago by
Hervé Pagès ♦♦ 14k
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... The tag you used (software error) is too general and the Rgraphviz maintainers won't necessarily pay attention to a post with such a general tag. Since this is about an installation error with the Rgraphviz package, I'd suggest you tag your post with Rgraphviz. ...
written 19 days ago by
Hervé Pagès ♦♦ 14k
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... Rhtslib 1.16.2 is now available: https://bioconductor.org/packages/3.9/Rhtslib
Cheers,
H. ...
written 25 days ago by
Hervé Pagès ♦♦ 14k
0
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... Rhtslib 1.16.2 is now available: https://bioconductor.org/packages/3.9/Rhtslib
Cheers,
H. ...
written 25 days ago by
Hervé Pagès ♦♦ 14k
0
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Comment:
C: Rhtslib - install error
... Rhtslib 1.16.2 is now available: https://bioconductor.org/packages/3.9/Rhtslib
Also please make sure that you have libbz2 + liblzma + header files on your system. On a Debian-based Linux system like Ubuntu these can be installed with `sudo apt-get install libbz2-dev liblzma-dev`.
Cheers,
H. ...
written 25 days ago by
Hervé Pagès ♦♦ 14k
1
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565
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... I backported the fix yesterday to Rhtslib 1.16.2. Rhtslib 1.16.2 should become available via `BiocManager::install()` in the next 24h or so.
Best,
H. ...
written 29 days ago by
Hervé Pagès ♦♦ 14k
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For C: Error in GRanges: could not find symbol "recursive" in environment of the generi
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