BiocParallel 1.33.12 binary has incorrect library linkage on macOS x86
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@mjsteinbaugh
Last seen 8 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 • 1.7k views
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I don't think 1.33.12 is current -- does BiocManager::valid() report TRUE?

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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.

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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'
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Aha I see the problem, the binaries are outdated: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'
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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
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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.

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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"
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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

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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...)

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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.

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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?

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