[R-SIG-Mac] Problem loading a package libraries (Error in dyn.load) on mac environments

Davor Cubranic cubranic at stat.ubc.ca
Mon Dec 3 20:55:42 CET 2012 

Is rTandem built with the same version of Rcpp that is now installed (0.10.1)? The API changed a fair bit over the past few weeks.

Davor

On 2012-12-03, at 11:52 AM, Dan Tenenbaum wrote:

> On Mon, Dec 3, 2012 at 11:13 AM, Davor Cubranic <cubranic at stat.ubc.ca> wrote:
>> Looks like you might not have the 64-bit version of the Rcpp dynamic library installed on the first machine. On the second, check if you have the 32-bit version of both XML and expat's dynamic libraries.
> 
> 
> Thanks. I'm working with Frederic on this.
> On the first machine, both the 32 and 64 bit versions are Rcpp are
> installed (I can library(Rcpp) from both R --arch i386 and R --arch
> x86_64), and the installed Rcpp has these files present:
> 
> pwd
> /Library/Frameworks/R.framework/Versions/Current/Resources/library/Rcpp
> PETTY:Rcpp biocbuild$ ls -lR libs
> total 0
> drwxr-xr-x  3 biocbuild  admin  102 Dec  3 11:40 i386
> drwxr-xr-x  3 biocbuild  admin  102 Dec  3 11:40 x86_64
> 
> libs/i386:
> total 1216
> -rwxr-xr-x  1 biocbuild  admin  619064 Dec  3 11:40 Rcpp.so
> 
> libs/x86_64:
> total 1280
> -rwxr-xr-x  1 biocbuild  admin  651920 Dec  3 11:40 Rcpp.so
> PETTY:Rcpp biocbuild$ ls -lR lib
> total 0
> drwxr-xr-x  4 biocbuild  admin  136 Dec  3 11:40 i386
> 
> lib/i386:
> total 11336
> -rw-r--r--  1 biocbuild  admin  5177484 Dec  3 11:40 libRcpp.a
> -rwxr-xr-x  1 biocbuild  admin   619064 Dec  3 11:40 libRcpp.dylib
> 
> After building rTANDEM against this Rcpp, I then get the same error
> Frederic reports in this thread when trying to library(rTANDEM) on the
> x86_64 architecture. Here it is again with sessionInfo():
> 
>> 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/2.16/Resources/library/rTANDEM/libs/x86_64/rTANDEM.so':
>  dlopen(/Library/Frameworks/R.framework/Versions/2.16/Resources/library/rTANDEM/libs/x86_64/rTANDEM.so,
> 6): Symbol not found: __ZTIN4Rcpp7RObjectE
>  Referenced from:
> /Library/Frameworks/R.framework/Versions/2.16/Resources/library/rTANDEM/libs/x86_64/rTANDEM.so
>  Expected in: dynamic lookup
> 
> Error: package or namespace load failed for 'rTANDEM'
>> sessionInfo()
> R Under development (unstable) (2012-10-31 r61060)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] C
> 
> 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_3.95-0.1
>> 
> 
> I'm not sure if Frederic wants the package source to be posted at this
> point. I'll let him answer that.
> 
> Thanks,
> Dan
> 
> 
>> 
>> Davor
>> 
>> 
>> On 2012-12-03, at 8:34 AM, Frederic Fournier 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!
>>> 
>>> Frederic
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
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