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Error installing velocyto.R #30
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Please install pcaMethods and h5 packages.
Also, are you using the latest version (on github)? These packages should have been added during the installation procedure as they’re specified in the Imports section.
Best,
-peter.
… On Jun 15, 2018, at 16:11, cynthiazhou1005 ***@***.***> wrote:
Anyone can help me with these errors?
ERROR: dependencies ‘pcaMethods’, ‘h5’ are not available for package ‘velocyto.R’
Thanks!
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I tried in the docker system but keeps getting this error: Build an image from a Dockerfile R version 3.4.2 (2017-09-28) -- "Short Summer" R is free software and comes with ABSOLUTELY NO WARRANTY. R is a collaborative project with many contributors. Type 'demo()' for some demos, 'help()' for on-line help, or
Any advice please? Thank you! |
@pkharchenko @cynthiazhou1005 I suspect this might be the same problem I'm having, which has also been reproduced by @vagnec here as an issue with The problem seems to boil down to the installation of Is there any plan to update the dependency to the new Thanks! |
It should be quite straightforward to switch to hdf5r … unfortunately I’d be able to get to it in next couple of weeks ... if someone can test/submit patch, I’ll gladly accept it.
It’s used in only two functions: read.loom.matrices() and read.gene.mapping.info().
… On Oct 15, 2018, at 11:59 AM, Alejandro Barrera ***@***.***> wrote:
@pkharchenko <https://github.com/pkharchenko> @cynthiazhou1005 <https://github.com/cynthiazhou1005> I suspect this might be the same problem I'm having, which has also been reproduced by @vagnec <https://github.com/vagnec> here <mannau/h5#72> as an issue with h5.
The problem seems to boil down to the installation of h5, now deprecated. Is there any known solution to this problem?
Is there any plan to update the dependency to the new hdf5r package? This has already been asked in #42 <#42>, but I want to reflect that at least in my case, the request would be motivated by the issues installing velocyto.R with the current h5 package as a dependency.
Thanks!
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Since my issue happened to be No. 42, I felt 'obligated' to make it happen. 😄 The PR (#43) hopefully works. |
pcaMethods is a Bioconductor dependency, which |
Does this work: if (!requireNamespace("BiocManager", quietly = TRUE)) |
Anyone can help me with these errors?
ERROR: dependencies ‘pcaMethods’, ‘h5’ are not available for package ‘velocyto.R’
Thanks!
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