Question

BiocParallel 1.33.12 binary has incorrect library linkage on macOS x86

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Michael Steinbaugh ▴ 90

@mjsteinbaugh

Last seen 5 months ago

Cambridge, MA

I'm seeing a build issue with the current BiocParallel binary on macOS x86:

BiocManager::install("BiocParallel")
# Works in R, but fails in RStudio.
library(BiocParallel)

Error: package or namespace load failed for ‘BiocParallel’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/site-library/BiocParallel/libs/BiocParallel.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/site-library/BiocParallel/libs/BiocParallel.so, 0x0006): Library not loaded: /Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libR.dylib
  Referenced from: <BE9EB1DB-DF61-3612-B689-0B341783A2EC> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/site-library/BiocParallel/libs/BiocParallel.so
  Reason: tried: '/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libR.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libR.dylib' (no such file), '/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, not in dyld cache)

The binary build is attempting to locate libR.dylib in the incorrect place, which should be /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib

Best, Mike

BiocParallel • 1.5k views

ADD COMMENT • link updated 11 months ago by Martin Morgan 25k • written 11 months ago by Michael Steinbaugh ▴ 90

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I don't think 1.33.12 is current -- does BiocManager::valid() report TRUE?

ADD REPLY • link 11 months ago Martin Morgan 25k

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On my Apple Silicon Mac I just tried:

BiocManager::install("BiocParallel")
packageVersion("BiocParallel")
[1] ‘1.33.11’

And this is working inside of RStudio. I'll check on my Intel Mac that installed 1.33.12.

ADD REPLY • link 11 months ago Michael Steinbaugh ▴ 90

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On my Intel Mac, seeing this:

Installing 'BiocParallel' with 'BiocManager::install' in '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/site-library'.
trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-x86_64/contrib/4.3/BiocParallel_1.33.12.tgz'

ADD REPLY • link 11 months ago Michael Steinbaugh ▴ 90

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Aha I see the problem, the binaries are outdated:

> BiocManager::install("BiocParallel", type = "source", force = TRUE)
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Installing package(s) 'BiocParallel'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/BiocParallel_1.34.0.tar.gz'

ADD REPLY • link 11 months ago Michael Steinbaugh ▴ 90

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Here's a temporary fix in case anybody else hits this:

cd /Library/Frameworks/R.framework/Versions
ln -s 4.3-x86_64 4.3

ADD REPLY • link 11 months ago Michael Steinbaugh ▴ 90

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I think this means that your RStudio has a different .libPaths() than your R, probably because of a configuration file, maybe ~/.Rprofile on your system.

ADD REPLY • link 11 months ago Martin Morgan 25k

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> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/site-library"
[2] "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library"

ADD REPLY • link 11 months ago Michael Steinbaugh ▴ 90

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The problem here is that current binaries aren't available on macOS:

http://bioconductor.org/packages/release/bioc/html/BiocParallel.html

Source Package  BiocParallel_1.34.0.tar.gz
Windows Binary  BiocParallel_1.34.0.zip (64-bit only)
macOS Binary (x86_64)   BiocParallel_1.33.12.tgz
macOS Binary (arm64)    BiocParallel_1.33.11.tgz

Safe to close when 1.34.0 is updated in the repo

ADD REPLY • link 11 months ago Michael Steinbaugh ▴ 90

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Yes, thanks the build systems don't (currently... they must have at one point) have Rmpi installed so I've asked to have that corrected.

I'm not sure that this explains differences between R versus RStudio, though, which was your original question. I guess these are actually different R? Or as mentioned earlier different .libPaths() (you only provided one .libPaths() above...)

ADD REPLY • link 11 months ago Martin Morgan 25k

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Sorry should have been clearer -- libPaths are the same in R and RStudio. There's something weird going on between R and RStudio's handling of missing ldpaths.

ADD REPLY • link 11 months ago Michael Steinbaugh ▴ 90

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I moved Rmpi to the 'Enhances' field, so the BiocParallel binary propagated for macOS (actually all platforms).

Does this address the problems you were having, or are there remaining issues?

ADD REPLY • link 11 months ago Martin Morgan 25k