On Dec 3, 2012, at 2:58 PM, Dan Tenenbaum <[email protected]> wrote:
> On Mon, Dec 3, 2012 at 11:55 AM, Davor Cubranic <[email protected]> wrote: >> 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. > > > Yes, in fact I just built Rcpp from source immediately before building > rTANDEM. I get the same results after installing the Rcpp binary from > CRAN. In both cases, I build and then attempt to load rTANDEM with the > exact same version of Rcpp. > CRAN version of Rcpp has both x86_64 and i386 libraries - unlike yours. May I suggest someone with the necessary knowledge respond to my initial e-mail before someone gets killed running of the wrong cliff? ;) Cheers, Simon > Dan > > >> >> Davor >> >> On 2012-12-03, at 11:52 AM, Dan Tenenbaum 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 >>> >>> 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
