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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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problem loading phyloseq #1677

Open sclknowles opened 1 year ago

sclknowles commented 1 year ago

Hi there, I'm having an issue loading phyloseq, which seems to be caused by the package rhdf5filters. I've tried uninstalled and reinstalling rhdf5filters. Perhaps it's just a path issue that is general, but I'm not sure how to resolve it so any help greatly appreciated. Many thanks.

sessionInfo() R version 4.3.0 (2023-04-21) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.5.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_4.3.0 tools_4.3.0

BiocManager::install("phyloseq", force=T) 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21) Installing package(s) 'phyloseq' trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-x86_64/contrib/4.3/phyloseq_1.44.0.tgz' Content type 'application/x-gzip' length 6764042 bytes (6.5 MB)

downloaded 6.5 MB

The downloaded binary packages are in /var/folders/bs/pb3knlgj32xbjr5nncz50d1w0000gr/T//RtmpU4vUea/downloaded_packages Old packages: 'rhdf5filters' Update all/some/none? [a/s/n]: a trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-x86_64/contrib/4.3/rhdf5filters_1.11.2.tgz' Content type 'application/x-gzip' length 822510 bytes (803 KB)

downloaded 803 KB

The downloaded binary packages are in /var/folders/bs/pb3knlgj32xbjr5nncz50d1w0000gr/T//RtmpU4vUea/downloaded_packages

library(phyloseq) Error: package or namespace load failed for ‘phyloseq’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rhdf5filters/libs/rhdf5filters.so': dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rhdf5filters/libs/rhdf5filters.so, 0x0006): Library not loaded: '/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libR.dylib' Referenced from: '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rhdf5filters/libs/rhdf5filters.so' Reason: tried: '/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libR.dylib' (no such file), '/usr/local/lib/libR.dylib' (no such file), '/usr/lib/libR.dylib' (no such file)

ycl6 commented 1 year ago

Hi @sclknowles

It looks like a problem with R and MacOS, not specific to phyloseq.

Two things you can try, first is to re-install the rhdf5filters package, which seems to be the cause of the problem when it didn't install properly when you did the update. You might encounter the same error message on libR.dylib where it says it is not found in the lib paths. The second thing you can try is to re-install R, as suggested here.