Many thanks to all of you! Those were very well-focused answers! The problem seems to be solved on the bioc build machine, and I now know where to look to fix similar problems on the other machines I used for testing. Thanks again! Frederic On Mon, Dec 3, 2012 at 3:18 PM, Dan Tenenbaum wrote: > On Mon, Dec 3, 2012 at 12:15 PM, Simon Urbanek > wrote: > > > > On Dec 3, 2012, at 2:58 PM, Dan Tenenbaum wrote: > > > >> On Mon, Dec 3, 2012 at 11:55 AM, Davor Cubranic > 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 > 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@r-project.org > >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >>>>> > >>>>> _______________________________________________ > >>>>> R-SIG-Mac mailing list > >>>>> R-SIG-Mac@r-project.org > >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >>> > >> > >> _______________________________________________ > >> R-SIG-Mac mailing list > >> R-SIG-Mac@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >> > >> > > > [[alternative HTML version deleted]]