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Error installing bigvis package #28

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jarutis opened this issue Jan 14, 2014 · 3 comments
Closed

Error installing bigvis package #28

jarutis opened this issue Jan 14, 2014 · 3 comments

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@jarutis
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jarutis commented Jan 14, 2014

Hi,

I'm trying to install bigvis package on OS X with R version 3.0.2.
I get the following error:

> devtools::install_github("bigvis")
Installing github repo bigvis/master from hadley
Downloading bigvis.zip from https://github.com/hadley/bigvis/archive/master.zip
Installing package from /var/folders/3f/_zkl_z552jg83n5qcjw6s59h0000gn/T//Rtmpu6fGpR/bigvis.zip
arguments 'minimized' and 'invisible' are for Windows only
Installing bigvis
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL  \
  '/private/var/folders/3f/_zkl_z552jg83n5qcjw6s59h0000gn/T/Rtmpu6fGpR/devtools5bf3f1f792d/bigvis-master'  \
  --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'  \
  --install-tests 

* installing *source* package 'bigvis' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c BigVis.cpp -o BigVis.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c BinnedVector.cpp -o BinnedVector.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c BinnedVectors.cpp -o BinnedVectors.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c Summary2d.cpp -o Summary2d.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c condense.cpp -o condense.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c double-diff-sum.cpp -o double-diff-sum.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c frange.cpp -o frange.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c group.cpp -o group.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c lowerBound.cpp -o lowerBound.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c smooth-nd.cpp -o smooth-nd.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c stats.cpp -o stats.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2  -c summary.cpp -o summary.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o bigvis.so BigVis.o BinnedVector.o BinnedVectors.o RcppExports.o Summary2d.o condense.o double-diff-sum.o frange.o group.o lowerBound.o smooth-nd.o stats.o summary.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/bigvis/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
in method for 'show' with signature '"Rcpp_BinnedVector"': no definition for class "Rcpp_BinnedVector"
in method for 'as.integer' with signature '"Rcpp_BinnedVector"': no definition for class "Rcpp_BinnedVector"
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/bigvis/libs/bigvis.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/bigvis/libs/bigvis.so, 6): Symbol not found: __Z8demangleRKNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEEE
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/bigvis/libs/bigvis.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/bigvis/libs/bigvis.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/bigvis'
Error: Command failed (1)
@hadley
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hadley commented Jan 14, 2014

Can you please reinstall Rcpp from source (install.packages("Rcpp", type = "source")) and try again?

@hadley hadley closed this as completed Jan 14, 2014
@jarutis
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jarutis commented Jan 15, 2014

Works fine, thanks!

@jcarlen
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jcarlen commented Aug 26, 2014

That worked for me too (similar problem, different package). If someone wants to explain why I would much appreciate it.

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