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slucey / RpathDev

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Can't install on Mac #4

Open Goiageshiketa opened 7 years ago

Goiageshiketa commented 7 years ago

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’

Does anyone help this? Thank you.

Goiageshiketa commented 7 years ago

It solved. I changed CXX in Makevars. Thanks

slucey commented 7 years ago

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 notifications@github.com wrote:

It solved. I changed CXX in Makevars. Thanks

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-- 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 commented 7 years ago

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'

Goiageshiketa commented 7 years ago

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 commented 6 years ago

@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 commented 6 years ago

https://github.com/slucey/RpathDev/issues/4#issuecomment-342329459 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 commented 6 years ago

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 commented 6 years ago

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

slucey commented 6 years ago

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 notifications@github.com 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 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)

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Goiageshiketa commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

Leonardo,

How about CXX=clang ?

leomarameo7 commented 6 years ago

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

Goiageshiketa commented 6 years ago

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

leomarameo7 commented 6 years ago

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/Rtmpn9X9MA/devtools18bf57c069fe/slucey-RpathDev-2df2714/Rpath' \ --no-resave-data --no-manual

Goiageshiketa commented 6 years ago

Can you find c++-4.2 in /usr/include/ ? You can move to /usr/include by typing shit + command + g on finder. If it is located ther, try

cxx = /usr/include/c++-4.2

leomarameo7 commented 6 years ago

I find the folder "C++" in /usr/include/ . In this folder there's another folder called 4.2.1. But it seems that there's no such file in this folder. When I try CC=clang CXX=/usr/include/c++-4.2

It returns

Goiageshiketa commented 6 years ago

Hi, Leonard After updating R or Rstudio, or macOS installation was failed on my Mac. Now I'm trying to resolve this problem. Let you know if it is figured out.

Goiageshiketa commented 6 years ago

Ok, recently I have installed Rpath on clean mac following method.

  1. install gcc from brew. g++ then installed in /usr/local/bin/g++ in default.
  2. Make "Makevars" file in ~/.R/
  3. Write in Makevars CC = gcc CXX = /usr/local/bin/g++
  4. devtools::install_github('slucey/RpathDev/Rpath', ref = 'Public', build_vignettes = TRUE)

This worked for me. Hope this help someone.

leomarameo7 commented 6 years ago

Ok, recently I have installed Rpath on clean mac following method.

  1. install gcc from brew. g++ then installed in /usr/local/bin/g++ in default.
  2. Make "Makevars" file in ~/.R/
  3. Write in Makevars CC = gcc CXX = /usr/local/bin/g++
  4. devtools::install_github('slucey/RpathDev/Rpath', ref = 'Public', build_vignettes = TRUE)

This worked for me. Hope this help someone.

Hi Goiageshiketa idon't understand the first step. Now, when I install Rpath, the message is as follow:

Goiageshiketa commented 6 years ago

Hi, Leo

brew is a library and software management software installed form https://brew.sh. Type /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" on terminal. Then brew will be installed. After that you can install gcc using "brew install gcc". This is the step 1.

Cheers