On Mon, Dec 3, 2012 at 12:15 PM, Simon Urbanek <[email protected]> wrote: > > 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? ;)
Hi Simon, you're right. If Rcpp is removed and then installed from CRAN (binary version), the installed package then has both x86_64 and i386 libraries, and rTANDEM then installs on both architectures. Thanks for your help, sorry for the noise. Dan > > 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
