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cytolib fails to build with clang9 #25

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mikejiang opened this issue Dec 17, 2019 · 1 comment
Open

cytolib fails to build with clang9 #25

mikejiang opened this issue Dec 17, 2019 · 1 comment

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@mikejiang
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From: Prof Brian Ripley [email protected]
To: Jiang, Mike [email protected]
Subject: flowWorkspace etc in BioC 3.11 on macOS
Finally this installs on Linux (it is needed for CRAN package flowDiv).

But not on macOS (with clang 9, the likely preferred compiler for R
4.0.0, if not clang 10):

Error: package or namespace load failed for ‘cytolib’:
.onLoad failed in loadNamespace() for 'cytolib', details:
call: dyn.load(cytolib, local = FALSE, now = TRUE)
error: unable to load shared object
'/Users/ripley/R/test-3.7/00LOCK-cytolib/00new/cytolib/libs/cytolib.so':

dlopen(/Users/ripley/R/test-3.7/00LOCK-cytolib/00new/cytolib/libs/cytolib.so,

10): Symbol not found: _ZN5boost10filesystem4pathdVERKS1
Referenced from:
/Users/ripley/R/test-3.7/00LOCK-cytolib/00new/cytolib/libs/cytolib.so
Expected in: flat namespace
in
/Users/ripley/R/test-3.7/00LOCK-cytolib/00new/cytolib/libs/cytolib.so

which demangles to

boost::filesystem::path::operator/=(boost::filesystem::path const&)

@mikejiang
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It succeeds for me , maybe the latest upgrades of boost source fixes it?

clang -v
clang version 9.0.0 (tags/RELEASE_900/final)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin

My R is not the latest though, but I don't think it matters

platform       x86_64-apple-darwin18.2.0                         
arch           x86_64                                            
os             darwin18.2.0                                      
system         x86_64, darwin18.2.0                              
status         Under development (unstable)                      
major          3                                                 
minor          6.0                                               
year           2019                                              
month          03                                                
day            13                                                
svn rev        76230                                             
language       R                                                 
version.string R Under development (unstable) (2019-03-13 r76230)
nickname       Unsuffered Consequences    
> packageVersion("BH")
[1] ‘1.72.0.2> packageVersion("cytolib")
[1] ‘1.9.8

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