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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Read10Xfunction not available in R v 4.1.0 #4574

Closed kstriedinger closed 3 years ago

kstriedinger commented 3 years ago

I downloaded from cran hdf5r and rhdf5 packages. however the hdf5r is not loading upon calling on library(hdf5r) after multiples install and trial efforts and it keeps producing an Error: "Error in Read10X_h5(filename = "/Volumes/LaCie/ihg-client.ucsf.edu/pomerantzj/201123_A00269_0437_AHVH7MDRXX_fastqs_analysis/HVH7MDRXX/outs/filtered_peak_bc_matrix.h5") : could not find function "Read10X_h5"

I am using: Version 1.4.1106 R studio R version 4.1.0 (2021-05-18) -- "Camp Pontanezen" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) MacOS Big Sur 11.4

samuel-marsh commented 3 years ago

Hi,

Not member of dev team but hopefully can be helpful. So the error you posted is not associated with the hdf5r package as Read10X_h5 is from Seurat not hdf5r. Have you loaded Seurat in your R session? Could you post the results of sessionInfo()?

Best, Sam

timoast commented 3 years ago

I'm going to close this now, the issue is almost certainly because you haven't loaded the Seurat package

kstriedinger commented 3 years ago

Hi, To fix the issue of not been able to read h5 after loading Seurat, I had to install the hdf5 in a shell because of my mac OS operating system, more info here: https://hhoeflin.github.io/hdf5r/ Close all programs, reinstall all packages. not a trivial thing. thanks,

Katharine

kstriedinger commented 3 years ago

Hi, To fix the issue of not been able to read h5 after loading Seurat, I had to install the hdf5 in a shell because of my mac OS operating system, more info here: https://hhoeflin.github.io/hdf5r/ Close all programs, reinstall all packages. not a trivial thing. thanks,

Katharine

From: Tim Stuart @.> Sent: Friday, June 4, 2021 11:49 AM To: satijalab/seurat @.> Cc: Striedinger Melo, Katharine @.>; Author @.> Subject: Re: [satijalab/seurat] Read10Xfunction not available in R v 4.1.0 (#4574)

I'm going to close this now, the issue is almost certainly because you haven't loaded the Seurat package — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. ‍ ‍ ‍ ‍ ‍ ‍ ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd

I'm going to close this now, the issue is almost certainly because you haven't loaded the Seurat package

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