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. 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
