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SugiharaLab / rEDM

Applications of Empirical Dynamic Modeling from Time Series
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Compilation failed for package ‘rEDM’ #41

Closed giancarlo-bonotto closed 3 years ago

giancarlo-bonotto commented 4 years ago

I am trying to install rEDM 1.2.2 because the later version does not have the EmbedDimension. I trying to install using the archive repository https://cran.r-project.org/src/contrib/Archive/rEDM/, devtools::install_github("SugiharaLab/rEDM") and install.packages("rEDM") but it gives the same error message, which follows below:

install.packages("~/GW_SW_Correlation_Analysis/rEDM_1.2.2.tar.gz", repos = NULL, type = "source") Installing package into ‘/home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6’ (as ‘lib’ is unspecified)

  • installing source package ‘rEDM’ ... package ‘rEDM’ successfully unpacked and MD5 sums checked using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/3.6.3/lib/R/include" -DNDEBUG -I ./cppEDM/src/ -I"/opt/R/3.6.3/lib/R/library/Rcpp/include" -I"/home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include" -I/usr/local/include -fpic -g -O2 -c CCM.cpp -o CCM.o In file included from /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread.h:11:0, from RcppEDMCommon.h:8, from CCM.cpp:2: /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/Thread.hpp: In lambda function: /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/Thread.hpp:42:19: error: parameter packs not expanded with ‘...’: f(args...); ^ /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/Thread.hpp:42:19: note: ‘args’ /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/Thread.hpp:42:23: error: expansion pattern ‘args’ contains no argument packs f(args...); ^ In file included from /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread.h:13:0, from RcppEDMCommon.h:8, from CCM.cpp:2: /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp: In member function ‘void RcppThread::ThreadPool::push(F&&, Args&& ...)’: /home/gbonotto/R/x8664-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp:127:31: error: expected ‘,’ before ‘...’ token jobs.emplace([f, args...] { f(args...); }); ^ /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp:127:31: error: expected identifier before ‘...’ token /home/gbonotto/R/x8664-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp:127:34: error: parameter packs not expanded with ‘...’: jobs.emplace([f, args...] { f(args...); }); ^ /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp:127:34: note: ‘args’ /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp: In lambda function: /home/gbonotto/R/x8664-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp:127:44: error: expansion pattern ‘args’ contains no argument packs jobs.emplace([f, args...] { f(args...); }); ^ /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp: In member function ‘std::future<decltype (f(args ...))> RcppThread::ThreadPool::pushReturn(F&&, Args&& ...)’: /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp:144:54: error: expected ‘,’ before ‘...’ token auto job = std::make_shared([&f, args...] { ^ /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp:144:54: error: expected identifier before ‘...’ token /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp:144:57: error: parameter packs not expanded with ‘...’: auto job = std::make_shared([&f, args...] { ^ /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp:144:57: note: ‘args’ /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp: In lambda function: /home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/RcppThread/include/RcppThread/ThreadPool.hpp:145:22: error: expansion pattern ‘args’ contains no argument packs return f(args...); ^ make: *** [CCM.o] Error 1 ERROR: compilation failed for package ‘rEDM’
  • removing ‘/home/gbonotto/R/x86_64-pc-linux-gnu-library/3.6/rEDM’ Warning in install.packages : installation of package ‘/home/gbonotto/GW_SW_Correlation_Analysis/rEDM_1.2.2.tar.gz’ had non-zero exit status
Data-Anal-Ojisan commented 4 years ago

I also faced this problem. I suspected the version of Rtools causes the problem because the error happened when compiling the source of rEDM. So, I updated Rtools and R to the latest version. However, the the problem did not be solved. This is just a short note to inform you. my current environment: R version 4.0.2, Rtools version rtools40 my previous environment: R version3.6.2, Rtools version rtools35

nonlinearnature commented 4 years ago

Data-Anal-Ojisan, are you able to install the latest version rEDM 1.5? The functionality of EmbedDimension is easily replicated in 1.5 if this is the case.

Data-Anal-Ojisan commented 4 years ago

I couldn't install the latest version. So instead, I installed older version(0.6.9) of rEDM from CRAN(https://cran.r-project.org/src/contrib/Archive/rEDM/), as follows. And it worked.

install.packages('rEDM_0.6.9.tar.gz', repos=NULL, type='source')

I guess that the compilation error has occurred since January of this year according to another issue reports of this repository.

nonlinearnature commented 4 years ago

Can you give an overview of your system architecture? Is the installation error you are receiving identical to the original error above from May 24th by giancarlo-bonotto? If can you please supply the equivalent output.

nonlinearnature commented 4 years ago

Also please note that version 1.5 is now available on CRAN.

https://CRAN.R-project.org/package=rEDM

Data-Anal-Ojisan commented 4 years ago

My system architecture is as follows. os: Windows10 Home CPU: Intel corei7-6700 RAM: 64GB

More specifically, I can install rEDM1.5 with the following command.

install.packages('rEDM')

However, when I try to load the rEDM library after the installation, the process of R hangs up. So I also tried to install the latest version of rEDM1.5 from source, but the result of installation process was as follows and the installation failed. Installation error was little bit different from May 24th by giancarlo-bonotto. 

> install.packages('rEDM_1.5.0.tar.gz', repos=NULL, type='source')
* installing *source* package 'rEDM' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CCM.cpp -o CCM.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ComputeError.cpp -o ComputeError.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DataFrame.cpp -o DataFrame.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Embed.cpp -o Embed.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c EmbedDim.cpp -o EmbedDim.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Multiview.cpp -o Multiview.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PredictInterval.cpp -o PredictInterval.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PredictNL.cpp -o PredictNL.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppEDMCommon.cpp -o RcppEDMCommon.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c SMap.cpp -o SMap.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I./cppEDM/src -I../ -I'C:/Program Files/R/R-4.0.0/library/Rcpp/include' -I'C:/Program Files/R/R-4.0.0/library/RcppThread/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Simplex.cpp -o Simplex.o
make[1]: Entering directory '/Users/rhira/AppData/Local/Temp/Rtmpg9I1iv/R.INSTALL648c7c444a4b/rEDM/src/cppEDM/src'
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c API.cc
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c CCM.cc
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c Common.cc
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c DateTime.cc
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c EDM.cc
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c EDM_Formatting.cc
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c EDM_Neighbors.cc
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c Eval.cc
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c Multiview.cc
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c Parameter.cc
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c Simplex.cc
C:/rtools40/mingw64/bin/gcc  -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../  -c SMap.cc
ar -rcs libEDM.a API.o CCM.o Common.o DateTime.o EDM.o EDM_Formatting.o EDM_Neighbors.o Eval.o Multiview.o Parameter.o Simplex.o SMap.o
make[1]: ar: Command not found
make[1]: *** [makefile.mingw:29: libEDM.a] Error 127
make[1]: Leaving directory '/Users/AppData/Local/Temp/Rtmpg9I1iv/R.INSTALL648c7c444a4b/rEDM/src/cppEDM/src'
make: *** [Makevars.win:16: cppEDM/src/libEDM.a] Error 2
ERROR: compilation failed for package 'rEDM'
* removing 'C:/Program Files/R/R-4.0.0/library/rEDM'
* restoring previous 'C:/Program Files/R/R-4.0.0/library/rEDM'
Warning in install.packages :
  installation of package ‘rEDM_1.5.0.tar.gz’ had non-zero exit status

This is the why I installed older version of rEDM as I commented below.

JPGibert commented 4 years ago

Hello, I'm having issues installing the v1.5 as well.

install.packages('rEDM') runs but throws an error in the end and rEDM does not properly install. I have installed v1.2.3 instead. I have the same issue if I try to build from source using the command line. Any help would be welcome.

Below is the error encountered:

There is a binary version available but the source version is later: binary source needs_compilation rEDM 1.2.3 1.5.0 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes installing the source package ‘rEDM’

trying URL 'https://mirrors.nics.utk.edu/cran/src/contrib/rEDM_1.5.0.tar.gz' Content type 'application/x-gzip' length 1797589 bytes (1.7 MB)

downloaded 1.7 MB

The downloaded source packages are in ‘/private/var/folders/bp/61k_8c5j5p32zkh4b0sz811h0000gn/T/RtmpJf7UNk/downloaded_packages’ Warning message: In install.packages("rEDM") : installation of package ‘rEDM’ had non-zero exit status

SoftwareLiteracy commented 4 years ago

Regarding the windows issues, these seem congruent with the build failure reported by CRAN for r-oldrel-windows-ix86+x86_64, the "old" release of R based on GCC 4.6. https://www.r-project.org/nosvn/R.check/r-oldrel-windows-ix86+x86_64/rEDM-00install.html make[2]: ar: Command not found

The current R release r-release-windows-ix86+x86_64 is based on GCC 8.3. It seems the R build script in the old release is not recognising the enviroment variable for the linker (ar).

If you are on an old release of R, is it possible to upgrade to a current release?

SoftwareLiteracy commented 4 years ago

Regarding macOS, both old release and current release pass CRAN build checks. You should be able to install 1.5 from CRAN.

The error reported by clang for 1.2.3 build ld: library not found for -lgfortran seems to be that R cannot find the gfortran libraries, which is odd, since R includes it's own version of these.

JPGibert commented 4 years ago

Updating R solved the Fortran library issues for me.

Cheers and thanks