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 <dtenenba@fhcrc.org> wrote:

> On Mon, Dec 3, 2012 at 12:15 PM, Simon Urbanek
> <simon.urbanek@r-project.org> wrote:
> >
> > On Dec 3, 2012, at 2:58 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
> >
> >> On Mon, Dec 3, 2012 at 11:55 AM, Davor Cubranic <cubranic@stat.ubc.ca>
> 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 <cubranic@stat.ubc.ca>
> 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
> >>
> >>
> >
>

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