Can't install on Mac

[Goiageshiketa]

I have been tried to install Rpath on Mac (10.12.6) with Xcode and Command Line Tools installed.
Typing "devtools::install_github('slucey/RpathDev/Rpath', ref = 'Public', build_vignettes = TRUE)"
on Rstudio returns,

---

Downloading GitHub repo slucey/RpathDev@Public
from URL https://api.github.com/repos/slucey/RpathDev/zipball/Public
Installing Rpath

In file included from ecosim.cpp:2:
./ecosim.h:33:4: error: no matching function for call to 'transform'
std::transform(base.begin(), base.end(),
^~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/algorithm:1932:1: note: candidate template ignored: couldn't infer template argument '_BinaryOperation'
transform(_InputIterator1 __first1, _InputIterator1 __last1, _InputIterator2 __first2,
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/algorithm:1922:1: note: candidate function template not viable: requires 4 arguments, but 5 were provided
transform(_InputIterator __first, _InputIterator __last, _OutputIterator __result, _UnaryOperation __op)
^
1 error generated.
make: *** [ecosim.o] Error 1
ERROR: compilation failed for package ‘Rpath’

• removing ‘/Users/takeshigeaigo/Library/R/3.3/library/Rpath’
  Error : Command failed (1)

---

Does anyone help this?
Thank you.

[Goiageshiketa]

It solved. I changed CXX in Makevars.
Thanks

[slucey]

Great...I was doing some research to figure it. It looked like an issue with your compiler not having the right c++ libraries. Sean

…

On Thursday, October 12, 2017, Goiageshiketa ***@***.***> wrote: It solved. I changed CXX in Makevars. Thanks — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFUeDqbgV7K30BI5Gq1N8EeRarQccKNkks5srbuOgaJpZM4P0_7k> .

-- Sean M. Lucey Fisheries Biologist Ecosystem Dynamics and Assessment Branch U. S. Dept. of Commerce/NOAA/NMFS Northeast Fisheries Science Center 166 Water Street, Woods Hole, MA 02543 508-495-2011 (voice) 508-495-2232 (fax)

[VirginieRam]

Hello, I get the exact same error as above, though hard time in understanding the solution. Could anyone be a little more specific on how to solve the problem? That would highly appreciated. Thanks!
Virginie

Typing:
"devtools::install_github('slucey/RpathDev/Rpath', ref = 'Public', build_vignettes = TRUE)"

returns:
In file included from ecosim.cpp:2:
./ecosim.h:33:4: error: no matching function for call to 'transform'
std::transform(base.begin(), base.end(),
^~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/include/c++/v1/algorithm:1932:1: note: candidate template ignored: couldn't infer template argument '_BinaryOperation'
transform(_InputIterator1 __first1, _InputIterator1 __last1, _InputIterator2 __first2,
^
/Library/Developer/CommandLineTools/usr/include/c++/v1/algorithm:1922:1: note: candidate function template not viable: requires 4 arguments, but 5 were provided
transform(_InputIterator __first, _InputIterator __last, _OutputIterator __result, _UnaryOperation __op)
^
1 error generated.
make: *** [ecosim.o] Error 1
ERROR: compilation failed for package 'Rpath'

• removing '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rpath'
  Installation failed: Command failed (1)

[Goiageshiketa]

HI, below is my Makevars environment.

CC=clang
CXX=/opt/local/bin/c++-mp-4.6

It works macOS 10.12.6.
Makevars is found in ~/.R
I hope this help you.

[raerickson]

@Goiageshiketa As a work around, I was able to install RPath inside a Docker image on my Mac. I used this tutorial. However, I got an error message unless I turned off the building vignettes.

[leomarameo7]

#4 (comment)
Hi Goiageshiketa ,
I don't understand how to change the Makevars environment ...
Can you explain step by step how it is working...

Thank you very much

Leonardo

[Goiageshiketa]

Hi, Leonardo

1. Move directory to ~/.R using shift + command + g.
2. Yo will find Makovars file, and open it text editor.
3. Add
   CC=clang
   CXX=/opt/local/bin/c++-mp-4.6
   to Makevars.
4. Retry installing Rpath.
   Note that CC and CXX options depend on your environment and install XCODE and command line tools before try above.

Hope this help you.

[leomarameo7]

Thank you very much Goiageshiketa. But Rpath still doesn't work.

I'm using OSX High Sierra, 10.13.6. R version 3.5.1 (2018-07-02)
I installed XCODE and Command Line Tools.
I changed CXX in Makevars.

R studio returns:
devtools::install_github('slucey/RpathDev/Rpath', ref = 'Public', build_vignettes = T)
Downloading GitHub repo slucey/RpathDev@Public
from URL https://api.github.com/repos/slucey/RpathDev/zipball/Public
Installing Rpath
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore
--quiet CMD build
'/private/var/folders/p4/f6_qlcws5bn0t43ytfhf18x00000gn/T/RtmpYHxUo4/devtoolsa6379341c26/slucey-RpathDev-2df2714/Rpath'
--no-resave-data --no-manual

• checking for file ‘/private/var/folders/p4/f6_qlcws5bn0t43ytfhf18x00000gn/T/RtmpYHxUo4/devtoolsa6379341c26/slucey-RpathDev-2df2714/Rpath/DESCRIPTION’ ... OK
• preparing ‘Rpath’:
• checking DESCRIPTION meta-information ... OK
• cleaning src
• installing the package to build vignettes
  -----------------------------------
• installing source package ‘Rpath’ ...
  ** libs
  /opt/local/bin/c++-mp-4.6 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
  /bin/sh: /opt/local/bin/c++-mp-4.6: No such file or directory
  make: *** [RcppExports.o] Error 127
  ERROR: compilation failed for package ‘Rpath’
• removing ‘/private/var/folders/p4/f6_qlcws5bn0t43ytfhf18x00000gn/T/Rtmp2tItb5/Rinsta9e11aee778/Rpath’
  -----------------------------------
  ERROR: package installation failed
  Installation failed: Command failed (1)

[slucey]

Leo, It looks like you are still missing something in your Path for compiling the C++ code that in the underlying engine of the ecosim part of Rpath. If you have an IT person in your institution they may be able to help you troubleshoot it. I don't think this error is on our end. Sean Sean M. Lucey Fisheries Biologist Ecosystem Dynamics and Assessment Branch U. S. Dept. of Commerce/NOAA/NMFS Northeast Fisheries Science Center 166 Water Street, Woods Hole, MA 02543 508-495-2011 (voice) 508-495-2232 (fax)

…

On Wed, Sep 5, 2018 at 1:31 PM, leomarameo7 ***@***.***> wrote: Thank you very much Goiageshiketa. But Rpath still doesn't work. I'm using OSX High Sierra, 10.13.6. R version 3.5.1 (2018-07-02) I installed XCODE and Command Line Tools. I changed CXX in Makevars. *R studio returns:* devtools::install_github('slucey/RpathDev/Rpath', ref = 'Public', build_vignettes = T) Downloading GitHub repo ***@***.*** from URL https://api.github.com/repos/slucey/RpathDev/zipball/Public Installing Rpath '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD build '/private/var/folders/p4/f6_qlcws5bn0t43ytfhf18x00000gn/T/RtmpYHxUo4/ devtoolsa6379341c26/slucey-RpathDev-2df2714/Rpath' --no-resave-data --no-manual - checking for file ‘/private/var/folders/p4/f6_ qlcws5bn0t43ytfhf18x00000gn/T/RtmpYHxUo4/devtoolsa6379341c26/slucey- RpathDev-2df2714/Rpath/DESCRIPTION’ ... OK - preparing ‘Rpath’: - checking DESCRIPTION meta-information ... OK - cleaning src - installing the package to build vignettes ----------------------------------- - installing *source* package ‘Rpath’ ... ** libs /opt/local/bin/c++-mp-4.6 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/ Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o /bin/sh: /opt/local/bin/c++-mp-4.6: No such file or directory make: *** [RcppExports.o] Error 127 ERROR: compilation failed for package ‘Rpath’ - removing ‘/private/var/folders/p4/f6_qlcws5bn0t43ytfhf18x00000gn/T/ Rtmp2tItb5/Rinsta9e11aee778/Rpath’ ----------------------------------- ERROR: package installation failed Installation failed: Command failed (1) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#4 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFUeDhMY1-Nr4GtMMaAcBiS65PvH6ryRks5uYApegaJpZM4P0_7k> .

[Goiageshiketa]

Hi Leo,

What kind of c and c++ compiler are you using?

"/opt/local/bin/c++-mp-4.6: No such file or directory"

Maybe you are not using c++ compiler named mp-4.6, this is my case in my environment.
So you need to find the cc and c++ compiler names and directory where they are installed.

To find the version of compilers, open terminal and type "gcc -c". It returns version of c compilers.
Let me know the results

Gaia

[leomarameo7]

Goiageshiketa, I type the command "gcc--version" because "gcc -c" returns
gcc -cclang: error: no input files

MacBook-Air-di-Leonardo:~ leonardocapitani$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 9.1.0 (clang-902.0.39.2)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

[Goiageshiketa]

Leonardo,

How about
CXX=clang
?

[leomarameo7]

I try with
CC=clang
CXX= clang
As Sean says, It seems that It is still missing something for the Ecosim part.

devtools::install_github('slucey/RpathDev/Rpath', ref = 'Public', build_vignettes = T)
Downloading GitHub repo slucey/RpathDev@Public
from URL https://api.github.com/repos/slucey/RpathDev/zipball/Public
Installing Rpath
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore
--quiet CMD build
'/private/var/folders/p4/f6_qlcws5bn0t43ytfhf18x00000gn/T/Rtmp7GBIrP/devtools13f92353db73/slucey-RpathDev-2df2714/Rpath'
--no-resave-data --no-manual

• checking for file ‘/private/var/folders/p4/f6_qlcws5bn0t43ytfhf18x00000gn/T/Rtmp7GBIrP/devtools13f92353db73/slucey-RpathDev-2df2714/Rpath/DESCRIPTION’ ... OK
• preparing ‘Rpath’:
• checking DESCRIPTION meta-information ... OK
• cleaning src
• installing the package to build vignettes
  -----------------------------------
• installing source package ‘Rpath’ ...
  ** libs
  clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
  clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ecosim.cpp -o ecosim.o
  In file included from ecosim.cpp:2:
  ./ecosim.h:33:4: error: no matching function for call to 'transform'
  std::transform(base.begin(), base.end(),
  ^~~~~~~~~~~~~~
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/algorithm:2038:1: note: candidate template ignored: couldn't infer template argument '_BinaryOperation'
  transform(_InputIterator1 __first1, _InputIterator1 __last1, _InputIterator2 __first2,
  ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/algorithm:2028:1: note: candidate function template not viable: requires 4 arguments, but 5 were provided
  transform(_InputIterator __first, _InputIterator __last, _OutputIterator __result, _UnaryOperation __op)
  ^
  1 error generated.
  make: *** [ecosim.o] Error 1
  ERROR: compilation failed for package ‘Rpath’
• removing ‘/private/var/folders/p4/f6_qlcws5bn0t43ytfhf18x00000gn/T/RtmpygPebk/Rinst14367ff2712/Rpath’
  -----------------------------------
  ERROR: package installation failed
  Installation failed: Command failed (1)

[Goiageshiketa]

How about try
cxx = /usr/include/c++
?