Cannot install dplyr about dplyr HOT 34 CLOSED

Which of the two options described on http://www.rstudio.com/ide/docs/packages/prerequisites did you try?

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Professor Wickham,

Thanks for getting back to me on this. I tried the first option. I already had Xcode downloaded and the command line tools installed but I uninstalled Xcode and reinstalled it with the command line tools through preferences>downloads.

Thanks,

Cyrus

On Sep 20, 2013, at 7:25 AM, hadley wickham [email protected] wrote:

Which of the two options described on http://www.rstudio.com/ide/docs/packages/prerequisites did you try?

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Hmmm, that's strange. If you open the terminal, what happens if you type which llvm-g++-4.2?

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Ahhh -I don't think i have 'llvm'

When I type which g++ i get a file path suggesting that compiler is installed on my OS (probably from the command line tools in Xcode) but "which llvm-g++-42" gives me "-bash: llvm-g++-4.2: command not found". Is llvm another compiler? If so where can I download it, github?

Thank you so much for all your help thus far!

Best,
Cyrus

On Sep 23, 2013, at 5:09 AM, hadley wickham [email protected] wrote:

Hmmm, that's strange. If you open the terminal, what happens if you type which llvm-g++-4.2?

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llvm is installed as part of recent xcode installs - which version of xcode do you have?

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I have version 5.0 (5A1413)

Thanks

Sent from my iPhone

On Sep 23, 2013, at 2:03 PM, hadley wickham [email protected] wrote:

llvm is installed as part of recent xcode installs - which version of xcode do you have?

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Hmm, that didn't help as much as I thought it might because I don't have xcode installed ;) Maybe just try installing the command line tools?

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I hade the same problem on Mac OS 10.8.5 and the Xcode 5.0. It seems that with the latest version of Xcode llvm-g++-4.2 is not used as compiler any more. I solved this problem by folowing development version of "R Installation and Administration" manual and particulary chapter on installing of additional packages on OS X.

You need to changes seetings in the file /Library/Frameworks/R.framework/Resources/etc/Makeconf by replacing existing lines with:

CC=clang
CXX=clang++

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Thanks for your response. I tried replacing the following in my makeconf file:
CC=clang
CXX=clang++
that alone did not work so I applied the following changes as well

CFLAGS="-mtune=native -g -O2 -Wall -pedantic -Wconversion"
CXXFLAGS="-mtune=native -g -O2 -Wall -pedantic -Wconversion"
but that didn't help either, in the manual it says there are two ways to use other compilers -either by editing the makeconf file or in a file such as ~/.R/Makevars

But I wasn't sure if the makevars file is an existing one that needs to be edited or a new file that needs to be saved in the same directory. Also, the manual suggests "Entries which may need to be changed include ‘CC’, ‘CXX’, ‘FC’, ‘F77’, ‘FLIBS’ and the corresponding flags, and perhaps ‘CXXCPP’, ‘DYLIB_LD’, ‘MAIN_LD’, ‘SHLIB_CXXLD’, ‘SHLIB_FCLD’ and ‘SHLIB_LD’." Did you replace these other other entries as well?

Thanks for your help

Cyrus

On Sep 25, 2013, at 9:38 PM, Didzis Elferts [email protected] wrote:

I hade the same problem on Mac OS 10.8.5 and the Xcode 5.0. It seems that with the latest version of Xcode llvm-g++-4.2 is not used as compiler any more. I solved this problem by folowing development version of "R Installation and Administration" manual and particulary chapter on installing of additional packages on OS X.

You need to changes seetings in the file /Library/Frameworks/R.framework/Resources/etc/Makeconf by replacing existing lines with:

CC=clang
CXX=clang++

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Thank you for all your help I just figured out a solution -I uninstalled Xcode and then installed the command line tools directly from the apple's website and it just loaded properly.

Again thank you for all your help with this

Cheers,

Cyrus

On Sep 25, 2013, at 9:38 PM, Didzis Elferts [email protected] wrote:

I hade the same problem on Mac OS 10.8.5 and the Xcode 5.0. It seems that with the latest version of Xcode llvm-g++-4.2 is not used as compiler any more. I solved this problem by folowing development version of "R Installation and Administration" manual and particulary chapter on installing of additional packages on OS X.

You need to changes seetings in the file /Library/Frameworks/R.framework/Resources/etc/Makeconf by replacing existing lines with:

CC=clang
CXX=clang++

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Thanks for the update - exactly which command line tools did you install? The problem is the xcode 5 came out on September 18 and it no longer includes the compilers that R used to use (which is why I'd never seen this problem before). I think you can install an older version of the command line tools (which maybe you did), or you can override the default compiler setting by creating a file called ~/.R/Makevars which contains

CC=clang
CXX=clang++

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I did indeed download an older version of the command line tools that was released in April -which solved the problem -so I suppose there 3 ways to fix it.

Sent from my iPhone

On Sep 26, 2013, at 5:56 AM, hadley wickham [email protected] wrote:

Thanks for the update - exactly which command line tools did you install? The problem is the xcode 5 came out on September 18 and it no longer includes the compilers that R used to use (which is why I'd never seen this problem before). I think you can install an older version of the command line tools (which maybe you did), or you can override the default compiler setting by creating a file called ~/.R/Makevars which contains

CC=clang
CXX=clang++
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Hi

I've just got a new iMac with Mavericks. I installed the command line tools (from bash ) but not full Xcode.

I do have exactly this ~/.R/Makevars configuration file already.

I think my problem is different??? I don't actually understand the error.

Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/dplyr/libs/dplyr.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/dplyr/libs/dplyr.so, 6): Symbol not found: __ZNSoD0Ev
Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/dplyr/libs/dplyr.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/dplyr/libs/dplyr.so
Error: loading failed
Execution halted
ERROR: loading failed

• removing '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/dplyr'
  Error: Command failed (1)

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Did you try a clean install?

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I'm not sure what you mean?

R CMD INSTALL --clean ...

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Hi
I got the same error after downloading source and trying

R CMD INSTALL --preclean --no-multiarch --with-keep.source dplyr

I have not previously had dplyr installed on this computer (plyr is installed).

Stephen

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I just had this problem too, after upgrade to mavericks. You need to reinstall Rcpp, and possibly other packages - I ended up deleting all my installed packages and starting from scratch.

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I'm having trouble with other Rcpp related packages too... maybe related or possibly not. Are you suggesting deleting installed then installing 1. dplyr, 2. Rcpp then the rest?

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In doubt, do what hadley did and reinstall all of them.

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Hmm.....no luck. I deleted /Users/rmgzshd/Library/R/3.0/library and then the whole R.Framework then reinstalled with just base packages

I installed devtools and tried:

devtools::install_github("assertthat")
devtools::install_github("dplyr")

but to no avail I get exactly the same gnostic (to me) error message as every time previously:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/dplyr/libs/dplyr.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/dplyr/libs/dplyr.so, 6): Symbol not found: __ZNSoD0Ev
Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/dplyr/libs/dplyr.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/dplyr/libs/dplyr.so
Error: loading failed
Execution halted

You say it worked for you after deleting/removing packages?

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Did you install Rcpp from source ?

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This is typical compiler mismatch:

$ c++filt  __ZNSoD0Ev
std::basic_ostream<char, std::char_traits<char> >::~basic_ostream()

My guess is that you used a precompiled Rcpp (so compiled presumably on cran with llvm-g++ and you compiler dplyr with clang.

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Ahhh... OK that makes sense to me. Thanks
I'll try that tomorrow.

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Had the same problem after upgrading to Mavericks - installing Rcpp from source worked for me. Thanks for the advice.

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For closure. I might have an idea about changing Rcpp so that does not happen. Not trivial though.

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I think this is just a transient problem, and at least we know the resolution (install Rcpp from source) now

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install.packages("Rcpp",type="source")

didn't help for me.

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@alexbbrown can you be a bit more specific, what happened when you tried ?

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I'm running mavericks, on which the compiler llvm-g++-4.2 does not exist.

R 3.0.2 was built using llvm, so /Library/Frameworks/R.framework/Resources/etc contains llvm-g++-4.2 and friends.

editing that file to use clang and clang++ seems to fix it (but is a little scary)

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That's when you make the ~/.R/Makevars file containing e.g.

CXX=clang++
CC=clang
CXXFLAGS=-g -O3

Hopefully we'll have better guidelines when the next version of R (3.1.0) is released.

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I tried that with no success - it still uses llvm-4.2 if I do that

On 7 January 2014 10:59, Romain François [email protected] wrote:

That's when you make the ~/.R/Makevars file containing e.g.

CXX=clang++
CC=clang
CXXFLAGS=-g -O3

Hopefully we'll have better guidelines when the next version of R (3.1.0)
is released.

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I doubt that as this is what I use all day, every day. Is the Makevars file mispelled perhaps ?

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That particular test was done on the makeovers file in plyr. I can try
again in a bit

On 7 January 2014 11:20, Romain François [email protected] wrote:

I doubt that as this is what I use all day, every day. Is the Makevarsfile mispelled perhaps ?

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Hi,
I also tried to install 'dplyr' in kali linux. But could not install it success fully The ERROR I'm getting is as follows. If anybody can helpally it`s re appriciated.
install.packages("/root/SoftwareCollection/R/tiq-test/dplyr_0.3.tar",repos=NULL,type="source")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)

• installing source package ‘dplyr’ ...
  ** package ‘dplyr’ successfully unpacked and MD5 sums checked
  ** libs
  clang++ -I/usr/share/R/include -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
  In file included from RcppExports.cpp:4:
  In file included from ./../inst/include/dplyr.h:134:
  ../inst/include/dplyr/JoinVisitorImpl.h:175:13: error: cannot initialize a member subobject of type 'int ' with an rvalue of type 'const_iterator' (aka 'const int *')
  left_ptr(left.begin()),
  ^ ~~~~~~~~~~~~~
  ../inst/include/dplyr/JoinVisitorImpl.h:236:13: error: cannot initialize a member subobject of type 'int *' with an rvalue of type 'const_iterator' (aka 'const int *')
  right_ptr(right_.begin()),
  ^ ~~~~~~~~~~~~~~
  2 errors generated.
  /usr/lib/R/etc/Makeconf:137: recipe for target 'RcppExports.o' failed
  make: *_* [RcppExports.o] Error 1
  ERROR: compilation failed for package ‘dplyr’
• removing ‘/usr/local/lib/R/site-library/dplyr’
  Warning in install.packages :
  installation of package ‘/root/SoftwareCollection/R/tiq-test/dplyr_0.3.tar’ had non-zero exit status

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