atom feed10 messages in org.r-project.r-sig-macRe: [R-SIG-Mac] Problem loading a pac...
FromSent OnAttachments
Frederic FournierDec 3, 2012 8:34 am 
Simon UrbanekDec 3, 2012 11:11 am 
Davor CubranicDec 3, 2012 11:13 am 
Dan TenenbaumDec 3, 2012 11:51 am 
Davor CubranicDec 3, 2012 11:55 am 
Dan TenenbaumDec 3, 2012 11:57 am 
Simon UrbanekDec 3, 2012 12:03 pm 
Simon UrbanekDec 3, 2012 12:14 pm 
Dan TenenbaumDec 3, 2012 12:18 pm 
Frederic FournierDec 3, 2012 12:35 pm 
Subject:Re: [R-SIG-Mac] Problem loading a package libraries (Error in dyn.load) on mac environments
From:Simon Urbanek (simo@r-project.org)
Date:Dec 3, 2012 11:11:10 am
List:org.r-project.r-sig-mac

Frederic,

do you have the source somewhere so we can test it? It seems like you are not
linking against all libraries you need. You won't see this at link time, because
symbols are only resolved at run time. Make sure you have all necessary
libraries in both 64-bit and 32-bit. Are you using any 3rd party binaries like
MacPorts, Fink, Homebrew or similar? They may cause problems...

Cheers, Simon

On Dec 3, 2012, at 11:34 AM, Frederic Fournier <fred@gmail.com>
wrote:

Hello everyone,

I'm working on a small R package for proteomics analysis, and I am facing
perplexing problems related to the 'dyn.load' function when loading the package
on mac environments. The package relies on two external libraries, expat and pthread, and on three
cran packages: XML, Rcpp and data.table. I have no trouble building, checking or
installing the package. But when I load the package on mac testing environments,
I face various problems related to this error message: "Error in dyn.load(file,
DLLpath=DLLpath, ...): ..." On one machine, the package loads without problem on i386 R, but fails to load
on x64 R; on another machine, things are reversed and the package loads on x64,
but fails to load on i386.

Here is the output from the machinge where the package loads on i386 but fails
on x64 R:

library(rTANDEM)

Loading required package: XML Loading required package: Rcpp Loading required package: data.table data.table 1.8.6 For help type: help("data.table") Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.16new/Resources/library/rTANDEM/libs/ x86_64/rTANDEM.so': dlopen(/Library/Frameworks/R.framework/Versions/2.16new/Resources/library/rTANDEM /libs/x86_64/rTANDEM.so, 6): Symbol not found: __ZTIN4Rcpp7RObjectE Referenced from: /Library/Frameworks/R.framework/Versions/2.16new/Resources/library/rTANDEM/libs/x 86_64/rTANDEM.so Expected in: dynamic lookup

Error: package or namespace load failed for 'rTANDEM'

sessionInfo()

R Under development (unstable) (2012-11-27 r61172) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

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

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

other attached packages: [1] data.table_1.8.6 Rcpp_0.10.1 XML_3.9-4 [4] BiocInstaller_1.9.4

loaded via a namespace (and not attached): [1] tools_2.16.0

Here is the ouput from the machine where the package loads fine on x64 R but
fails on i386:

library(rTANDEM)

Loading required package: XML Loading required package: Rcpp Loading required package: data.table data.table 1.8.6 For help type: help("data.table") Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.16new/Resources/library/rTANDEM/libs/ i386/rTANDEM.so': dlopen(/Library/Frameworks/R.framework/Versions/2.16new/Resources/library/rTANDEM /libs/i386/rTANDEM.so, 6): Symbol not found: _XML_GetErrorCode Referenced from: /Library/Frameworks/R.framework/Versions/2.16new/Resources/library/rTANDEM/libs/i 386/rTANDEM.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/2.16new/Resources/library/rTANDEM/libs/i 386/rTANDEM.so Error: package or namespace load failed for 'rTANDEM'

I am left clueless by this. As anyone faced a similar issue?

Thank you very much for your help!