Skip to content

[Rcpp-devel] Problem Installing RcppExamples on Mac OS X 10.8.1

6 messages · Dirk Eddelbuettel, Benilton Carvalho, Davor Cubranic

Original
Benilton Carvalho
# 
Hi,

I'm trying to install the RcppExamples packages. I'm running Mac OS X
10.8.1 and R 2.15.1.

I start the installation with:

install.packages('RcppExamples', INSTALL_opts='--merge-multiarch',
type='source')

and everything goes okay until I get the error shown at the end of the message.

Any thoughts on how to proceed?

thank you,

benilton

--

g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG
-I/usr/local/include
-I"/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppClassic/include"
-I"/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/Rcpp/include"
  -fPIC  -g -O2  -c newRcppVectorExample.cpp -o newRcppVectorExample.o
Error in tools:::file_path_as_absolute(base:::system.file(..., package
= "RcppClassic")) :
  file '' does not exist
Calls: <Anonymous> ... RcppClassicLdPath -> RcppClassic.system.file ->
<Anonymous>
Execution halted
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o RcppExamples.so RcppDataFrame.o RcppRNGs.o
classicRcppDateExample.o classicRcppExample.o
classicRcppMatrixExample.o classicRcppParamsExample.o
classicRcppStringVectorExample.o classicRcppVectorExample.o
newRcppDateExample.o newRcppMatrixExample.o newRcppParamsExample.o
newRcppStringVectorExample.o newRcppVectorExample.o
/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/Rcpp/lib/x86_64/libRcpp.a
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
Error in tools:::file_path_as_absolute(base:::system.file(..., package
= "RcppClassic")) :
  file '' does not exist
Calls: <Anonymous> ... RcppClassicLdPath -> RcppClassic.system.file ->
<Anonymous>
Execution halted
installing to /Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so':
  dlopen(/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so,
6): Symbol not found: __Z14copyMessageToRPKc
  Referenced from:
/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so
  Expected in: flat namespace
 in /Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ?/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples?
* restoring previous
?/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples?

The downloaded source packages are in
	?/private/var/folders/sp/_dsm23tj7c1glq1hjgdf53500000gn/T/RtmpMsIbCd/downloaded_packages?
Warning message:
In install.packages("RcppExamples", INSTALL_opts = "--merge-multiarch",  :
  installation of package ?RcppExamples? had non-zero exit status
R version 2.15.1 Patched (2012-09-01 r60533)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] BiocInstaller_1.4.7

loaded via a namespace (and not attached):
[1] tcltk_2.15.1 tools_2.15.1
Dirk Eddelbuettel
#
On 2 September 2012 at 16:55, Benilton Carvalho wrote:
| Hi,
| 
| I'm trying to install the RcppExamples packages. I'm running Mac OS X
| 10.8.1 and R 2.15.1.
| 
| I start the installation with:
| 
| install.packages('RcppExamples', INSTALL_opts='--merge-multiarch',
| type='source')

What happens when you omit the INSTALL_opts argument?
 
| and everything goes okay until I get the error shown at the end of the message.
| 
| Any thoughts on how to proceed?
| 
| thank you,
| 
| benilton
| 
| --
| 
| g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
| -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG
| -I/usr/local/include
| -I"/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppClassic/include"
| -I"/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/Rcpp/include"
|   -fPIC  -g -O2  -c newRcppVectorExample.cpp -o newRcppVectorExample.o
| Error in tools:::file_path_as_absolute(base:::system.file(..., package
| = "RcppClassic")) :
|   file '' does not exist

Something is not right here, and things usually work (witness availability of
RcppExamples on all CRAN platforms, as well as on R-Forge).

I'd try to minimize whatever differences you have in your setup.

Dirk

| Calls: <Anonymous> ... RcppClassicLdPath -> RcppClassic.system.file ->
| <Anonymous>
| Execution halted
| g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
| -undefined dynamic_lookup -single_module -multiply_defined suppress
| -L/usr/local/lib -o RcppExamples.so RcppDataFrame.o RcppRNGs.o
| classicRcppDateExample.o classicRcppExample.o
| classicRcppMatrixExample.o classicRcppParamsExample.o
| classicRcppStringVectorExample.o classicRcppVectorExample.o
| newRcppDateExample.o newRcppMatrixExample.o newRcppParamsExample.o
| newRcppStringVectorExample.o newRcppVectorExample.o
| /Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/Rcpp/lib/x86_64/libRcpp.a
| -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
| -Wl,CoreFoundation
| Error in tools:::file_path_as_absolute(base:::system.file(..., package
| = "RcppClassic")) :
|   file '' does not exist
| Calls: <Anonymous> ... RcppClassicLdPath -> RcppClassic.system.file ->
| <Anonymous>
| Execution halted
| installing to /Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64
| ** testing if installed package can be loaded
| Error in dyn.load(file, DLLpath = DLLpath, ...) :
|   unable to load shared object
| '/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so':
|   dlopen(/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so,
| 6): Symbol not found: __Z14copyMessageToRPKc
|   Referenced from:
| /Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so
|   Expected in: flat namespace
|  in /Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so
| Error: loading failed
| Execution halted
| ERROR: loading failed
| * removing ?/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples?
| * restoring previous
| ?/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples?
| 
| The downloaded source packages are in
| 	?/private/var/folders/sp/_dsm23tj7c1glq1hjgdf53500000gn/T/RtmpMsIbCd/downloaded_packages?
| Warning message:
| In install.packages("RcppExamples", INSTALL_opts = "--merge-multiarch",  :
|   installation of package ?RcppExamples? had non-zero exit status
| > sessionInfo()
| R version 2.15.1 Patched (2012-09-01 r60533)
| Platform: i386-apple-darwin9.8.0/i386 (32-bit)
| 
| locale:
| [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
| 
| attached base packages:
| [1] stats     graphics  grDevices datasets  utils     methods   base
| 
| other attached packages:
| [1] BiocInstaller_1.4.7
| 
| loaded via a namespace (and not attached):
| [1] tcltk_2.15.1 tools_2.15.1
| _______________________________________________
| Rcpp-devel mailing list
| Rcpp-devel at lists.r-forge.r-project.org
| https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
Benilton Carvalho
# 
The error is exactly the same if I run

install.packages('RcppExamples', type='source')

(given the absence of a configure, I wouldnt expect INSTALL_opts to
make a difference)

This is a fresh install of R (the binaries from Simon's website),
installed to the standard location and simply using my home dir to
store the additional packages I choose to use. Installing the Mac
binary version of RcppExamples seems to be okay, but I do have the
preference of installing packages from the source.

b
On 2 September 2012 17:10, Dirk Eddelbuettel <edd at debian.org> wrote:
Dirk Eddelbuettel
#
On 2 September 2012 at 18:01, Benilton Carvalho wrote:
| The error is exactly the same if I run
| 
| install.packages('RcppExamples', type='source')
| 
| (given the absence of a configure, I wouldnt expect INSTALL_opts to
| make a difference)
| 
| This is a fresh install of R (the binaries from Simon's website),
| installed to the standard location and simply using my home dir to
| store the additional packages I choose to use. Installing the Mac
| binary version of RcppExamples seems to be okay, but I do have the
| preference of installing packages from the source.

Could I ask you to investigate with the powers-that-be concerning OS X and
report back?  

I do not have such a machine, and can only state that

   a) CRAN seems to be doing ok with the package per 
      http://cran.r-project.org/web/checks/check_results_RcppExamples.html

   b) R-Forge seems to be doing ok as well per the package page, here is the
      OS X build log:
      http://r-forge.r-project.org/R/?group_id=155&log=build_mac&pkg=RcppExamples&flavor=patched

Sorry for your troubles, but there is nothing more I can do without a
Mac. Maybe some others can pipe in.

Dirk

 
| b
| 
|
| On 2 September 2012 17:10, Dirk Eddelbuettel <edd at debian.org> wrote:
| >
| > On 2 September 2012 at 16:55, Benilton Carvalho wrote:
| > | Hi,
| > |
| > | I'm trying to install the RcppExamples packages. I'm running Mac OS X
| > | 10.8.1 and R 2.15.1.
| > |
| > | I start the installation with:
| > |
| > | install.packages('RcppExamples', INSTALL_opts='--merge-multiarch',
| > | type='source')
| >
| > What happens when you omit the INSTALL_opts argument?
| >
| > | and everything goes okay until I get the error shown at the end of the message.
| > |
| > | Any thoughts on how to proceed?
| > |
| > | thank you,
| > |
| > | benilton
| > |
| > | --
| > |
| > | g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
| > | -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG
| > | -I/usr/local/include
| > | -I"/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppClassic/include"
| > | -I"/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/Rcpp/include"
| > |   -fPIC  -g -O2  -c newRcppVectorExample.cpp -o newRcppVectorExample.o
| > | Error in tools:::file_path_as_absolute(base:::system.file(..., package
| > | = "RcppClassic")) :
| > |   file '' does not exist
| >
| > Something is not right here, and things usually work (witness availability of
| > RcppExamples on all CRAN platforms, as well as on R-Forge).
| >
| > I'd try to minimize whatever differences you have in your setup.
| >
| > Dirk
| >
| > | Calls: <Anonymous> ... RcppClassicLdPath -> RcppClassic.system.file ->
| > | <Anonymous>
| > | Execution halted
| > | g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
| > | -undefined dynamic_lookup -single_module -multiply_defined suppress
| > | -L/usr/local/lib -o RcppExamples.so RcppDataFrame.o RcppRNGs.o
| > | classicRcppDateExample.o classicRcppExample.o
| > | classicRcppMatrixExample.o classicRcppParamsExample.o
| > | classicRcppStringVectorExample.o classicRcppVectorExample.o
| > | newRcppDateExample.o newRcppMatrixExample.o newRcppParamsExample.o
| > | newRcppStringVectorExample.o newRcppVectorExample.o
| > | /Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/Rcpp/lib/x86_64/libRcpp.a
| > | -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
| > | -Wl,CoreFoundation
| > | Error in tools:::file_path_as_absolute(base:::system.file(..., package
| > | = "RcppClassic")) :
| > |   file '' does not exist
| > | Calls: <Anonymous> ... RcppClassicLdPath -> RcppClassic.system.file ->
| > | <Anonymous>
| > | Execution halted
| > | installing to /Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64
| > | ** testing if installed package can be loaded
| > | Error in dyn.load(file, DLLpath = DLLpath, ...) :
| > |   unable to load shared object
| > | '/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so':
| > |   dlopen(/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so,
| > | 6): Symbol not found: __Z14copyMessageToRPKc
| > |   Referenced from:
| > | /Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so
| > |   Expected in: flat namespace
| > |  in /Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples/libs/x86_64/RcppExamples.so
| > | Error: loading failed
| > | Execution halted
| > | ERROR: loading failed
| > | * removing ?/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples?
| > | * restoring previous
| > | ?/Volumes/DataPartition/Users/beniltoncarvalho/Rlibs/2.15/RcppExamples?
| > |
| > | The downloaded source packages are in
| > |       ?/private/var/folders/sp/_dsm23tj7c1glq1hjgdf53500000gn/T/RtmpMsIbCd/downloaded_packages?
| > | Warning message:
| > | In install.packages("RcppExamples", INSTALL_opts = "--merge-multiarch",  :
| > |   installation of package ?RcppExamples? had non-zero exit status
| > | > sessionInfo()
| > | R version 2.15.1 Patched (2012-09-01 r60533)
| > | Platform: i386-apple-darwin9.8.0/i386 (32-bit)
| > |
| > | locale:
| > | [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
| > |
| > | attached base packages:
| > | [1] stats     graphics  grDevices datasets  utils     methods   base
| > |
| > | other attached packages:
| > | [1] BiocInstaller_1.4.7
| > |
| > | loaded via a namespace (and not attached):
| > | [1] tcltk_2.15.1 tools_2.15.1
| > | _______________________________________________
| > | Rcpp-devel mailing list
| > | Rcpp-devel at lists.r-forge.r-project.org
| > | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
| >
| > --
| > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
Benilton Carvalho
# 
Hi Dirk,

will definitely check on this. Please, don't apologise for anything.

b
On 3 September 2012 14:38, Dirk Eddelbuettel <edd at debian.org> wrote:
Davor Cubranic
# 
If you're comfortable using the R debugger, maybe you could set 
"options(error=recover)" and see what's going on?

Or, from the error log you included, it appears that RcppClassicLdPath 
is somehow involved. Can you try calling that directly from the console 
and see whether it succeeds?

Lastly, what happens when you run this from R.app GUI, and choose to 
install RcppExamples into the system library instead of your home directory?

Davor
On 12-09-02 08:55 AM, Benilton Carvalho wrote: