On Dec 3, 2012, at 2:52 PM, Dan Tenenbaum <[email protected]> wrote:
> On Mon, Dec 3, 2012 at 11:13 AM, Davor Cubranic <[email protected]> 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 > ^^ --- this is incomplete - you're missing the 64-bit Rcpp library > 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 >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
