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Error in model fit: C++14 standard requested but CXX14 is not defined #569

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RichardIanBarnes opened this issue Oct 15, 2018 · 26 comments
Open

Error in model fit: C++14 standard requested but CXX14 is not defined #569

RichardIanBarnes opened this issue Oct 15, 2018 · 26 comments

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@RichardIanBarnes
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@RichardIanBarnes RichardIanBarnes commented Oct 15, 2018

Summary:

Error message relating to C++compiler when running a linear model fit.

Description:

I am new to Stan and RStan and trying out the tutorial by Max Farrell and Isla Myers-Smith on:
https://ourcodingclub.github.io/2018/04/17/stan-intro.html

The step by step process is shown below under 'Reproducible Steps'.

When I run the stanc() it compiles fine. But when I fit the linear model I receive the following error message:
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! Error in .shlib_internal(commandArgs(TRUE)) :
C++14 standard requested but CXX14 is not defined
Calls: -> .shlib_internal
Execution halted
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command 'C:/PROGRA1/R/R-351.1/bin/x64/R CMD SHLIB file55c71d73e8e.cpp 2> file55c71d73e8e.cpp.err.txt' had status 1

I've searched everywhere for possible solutions. I reviewed the following issue posted by yanys7
#565

As suggested by bgoodri I created a ~/.R/Makevars file and inserted the following:
CXX14 = g++

However the problem still persists.

I don't know if this is a bug or if I'm doing something wrong.
Thanks in advance for any help you can provide.

Reproducible Steps:

This follows almost exactly the steps shown in the tutorial.

Sys.setenv(USE_CXX14 = 1)
library(rstan)
library(gdata)
library(bayesplot)
rstan_options(auto_write = TRUE)
options(mc.cores = parallel::detectCores())
seaice <- read.csv("seaice.csv", stringsAsFactors = F)
colnames(seaice)<-c("year", "extent_north", "extent_south")
x <- I(seaice$year - 1978)
y <- seaice$extent_north
N <- length(seaice$year)
stan_data <- list(N = N, x = x, y = y)
write("// Stan model for simple linear regression
data {
      int <lower = 1> N;
      vector[N] x; 
      vector[N] y;
      }
      
      parameters {
      real alpha; 
      real beta; 
      real<lower = 0> sigma;
      }
      
      model {
      y ~ normal(alpha + x * beta, sigma);
      }
      generated quantities {
      }, 
"stan_model1.stan")
stanc("stan_model1.stan")
stan_model1 <- "stan_model1.stan"
fit <- stan(file = stan_model1, data = stan_data, warmup = 500, iter = 1000, chains = 4, thin = 1)

Current Output:

The output from stanc("stan_model1.stan") is below:
$status
[1] TRUE

$model_cppname
[1] "model55c23451a60_stan_model1"

$cppcode
[1] "// Code generated by Stan version 2.17.0\n\n#include <stan/model/model_header.hpp>\n\nnamespace model55c23451a60_stan_model1_namespace {\n\nusing std::istream;\nusing std::string;\nusing std::stringstream;\nusing std::vector;\nusing stan::io::dump;\nusing stan::math::lgamma;\nusing stan::model::prob_grad;\nusing namespace stan::math;\n\ntypedef Eigen::Matrix<double,Eigen::Dynamic,1> vector_d;\ntypedef Eigen::Matrix<double,1,Eigen::Dynamic> row_vector_d;\ntypedef Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic> matrix_d;\n\nstatic int current_statement_begin__;\n\nstan::io::program_reader prog_reader__() {\n stan::io::program_reader reader;\n reader.add_event(0, 0, "start", "model55c23451a60_stan_model1");\n reader.add_event(19, 19, "end", "model55c23451a60_stan_model1");\n return reader;\n}\n\nclass model55c23451a60_stan_model1 : public prob_grad {\nprivate:\n int N;\n vector_d x;\n vector_d y;\npublic:\n model55c23451a60_stan_model1(stan::io::va...

$model_name
[1] "stan_model1"

$model_code
[1] "// Stan model for simple linear regression\ndata {\n int <lower = 1> N; // Sample size\n vector[N] x; //Predictor\n vector[N] y; // Outcome\n}\n\nparameters {\n real alpha; //Intercept\n real beta; // Slope\n real<lower = 0> sigma; //Error SD\n}\n\nmodel {\n y ~ normal(alpha + x * beta, sigma);\n}\n\ngenerated quantities {\n} // The posterior predictive distribution"
attr(,"model_name2")
[1] "stan_model1"

Expected Output:

If applicable, the output you expected from RStan.

RStan Version:

RStan version 2.17.3

R Version:

R Version 3.5.1

Operating System:

Windows 8 64bit
@bgoodri
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@bgoodri bgoodri commented Oct 15, 2018

@RichardIanBarnes
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@RichardIanBarnes RichardIanBarnes commented Oct 15, 2018

Hi

Thank you very much for replying so soon!
The ~/.R/Makevars is attached - I wasn't sure what file extension it should be - I found a similar one in one of the package folders that had a .win extension.

The Sys.getenv("R_MAKEVARS_USER") returns an empty string so it looks like, as you said, it isn't able to find it.

Makevars.txt
I must admit I need to do a bit of reading up to understand this aspect but if you could help with any pointers as to what I should be doing that would be great - thanks again.

@bgoodri
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@bgoodri bgoodri commented Oct 17, 2018

Try it after changing ~/.R/Makevars to

CXX14 = g++ -std=c++1y

You may also want to add -Wno-unused-variable -Wno-unused-function to the CXX14FLAGS line.

@RichardIanBarnes
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@RichardIanBarnes RichardIanBarnes commented Oct 18, 2018

Hi

I added those lines to the ~/.R/Makevars and it seems to have resolved this particular issue. Thank you very much for your help.

In fact - much to my shame - I just realised that there was a section on RStan installation for Windows which sets out the contents of the Makevars file! I hadn't followed these steps when I originally installed RStan (I just went straight to install.packages("rstan")) so that would explain how I ended up with this problem. Thank you for your patience and sorry I hadn't fully set out the steps that led to this error.

Having resolved this though I encountered another error with StanHeaders which I thought I had seen in one of the open issues but can't find it at the moment. I will try to find it again and then post on there.

@bgoodri bgoodri closed this as completed Oct 18, 2018
@statwonk statwonk mentioned this issue Dec 18, 2018
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@pescobar
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@pescobar pescobar commented Jan 17, 2019 •
edited

I was also getting this error:

ld: chains.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
chains.o: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
make: *** [rstan.so] Error 1
ERROR: compilation failed for package ‘rstan’

and I had to modify my ~/.R/Makevars like this:

CXX14 = g++ -std=c++1y -Wno-unused-variable -Wno-unused-function -fPIC

@colemonnahan
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@colemonnahan colemonnahan commented Mar 15, 2019

I'm having this issue, not locally but when I do a TravisCI build on my package that depends on rstan. Is there a recommended way to setup an rstan dependency to avoid this? Below is the output I get:

* installing *source* package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** libs
Error in .shlib_internal(args) : 
  C++14 standard requested but CXX14 is not defined
* removing ‘/home/travis/R/Library/rstan’
Error in i.p(...) : 
  (converted from warning) installation of package ‘rstan’ had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
The command "Rscript -e 'deps <- devtools::dev_package_deps(dependencies = NA);devtools::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 during .
Your build has been stopped.

@colemonnahan
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@colemonnahan colemonnahan commented Mar 15, 2019

Nevermind, after much digging I needed to add this to my travis config file:

# from https://discourse.mc-stan.org/t/building-rstanarm-like-packagee-on-travis-with-c-14/6054/10?
before_install:
  - mkdir -p ~/.R
  - echo "CXX14FLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function  -Wno-macro-redefined" >> ~/.R/Makevars
  - echo "CXX14=g++ -std=c++1y -fPIC" >> ~/.R/Makevars

This was necessary even though I'm not packaging a compiled Stan model.

@nickschurch nickschurch mentioned this issue May 9, 2019
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@willtudorevans
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@willtudorevans willtudorevans commented Jun 11, 2019

I'm afraid I'm getting the same error message and can't resolve the issue.

Sys.getenv("R_MAKEVARS_USER") returns blank but the only makevars I can find is in RccpEigen/skeleton, where there are two of them. I've tried inserting:

CXX14 = g++ -std=c++1y

in both of them, but no luck. I'm afraid I don't have a computer science background so I may not be looking in the right place, or doing the right thing. Any additional guidance would be much appreciated.

@RichardIanBarnes
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@RichardIanBarnes RichardIanBarnes commented Jun 11, 2019

Hi there - I need to rack my memory on this. Let me have a look later on and I'll try to figure out what I did to resolve it and get back to you.

@bob-carpenter
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@bob-carpenter bob-carpenter commented Jun 12, 2019

Sorry the doc's so confusing. We're certainly open to suggestions in improving it if you have any. It's really hard with all the platform-specific config that's shared across R applications.

You want the top-level Makevars for R. On my mac, that's in ~/.R/Makevars. You'll need to create it if it doesn't already exist. Mine looks like this:

CXX=g++ -arch x86_64  -ftemplate-depth-256 -stdlib=libstdc++
CXXFLAGS= -O3 -mtune=native $(LTO) -w #set_by_rstan (and Bob)
R_XTRA_CPPFLAGS =  -I$(R_INCLUDE_DIR)      #set_by_rstan
CXX=clang++
CC=clang

I set the -O3 -mtune-native config myself, but that's not the critical part.

@willtudorevans
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@willtudorevans willtudorevans commented Jun 18, 2019 •
edited

Sorry unfortunately I'm still not having any luck with this.

I'm on Windows, I understand that the ~ means home directory, so home directory for R? I've tried putting the Makevars file in both:

C:\Program Files\R and
C:\Users\User\Documents\R

but I still get the same error message when trying to run a stan model:

Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created! Error in .shlib_internal(commandArgs(TRUE)) : C++14 standard requested but CXX14 is not defined Calls: <Anonymous> -> .shlib_internal Execution halted In addition: Warning message: In system(cmd, intern = !verbose) : running command 'C:/PROGRA~1/R/R-36~1.0/bin/x64/R CMD SHLIB file227c6da617cf.cpp 2> file227c6da617cf.cpp.err.txt' had status 1 Error in sink(type = "output") : invalid connection

Stan was working ok on my computer until I upgraded RStudio and R to version 3.6.0.

I've also tried searching for a makevars file on a computer where stan is working, to try and copy that structure for my computer, but I can't locate the file.

@bob-carpenter
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@bob-carpenter bob-carpenter commented Jun 18, 2019

You have to create a new Makevars.win from scratch (like everything else, the name's different on Windows). Have you tried running the script from section "Configuration of the C++ Toolchain":

The script will show you where it needs to go and I think will just create it all for you if you run it.

I'm re-opening this issue, as nobody's going to react to comments on a closed issue.

@bob-carpenter bob-carpenter reopened this Jun 18, 2019
@bgoodri
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@bgoodri bgoodri commented Jun 18, 2019

@willtudorevans
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@willtudorevans willtudorevans commented Jun 19, 2019

Just do install.packages(" https://win-builder.r-project.org/1vUk5Gxm9QqM/rstan_2.19.1.zip", repos = NULL)
…

Unfortunately I receive the following error message:

Error in install.packages : zip file ‘ https://win-builder.r-project.org/1vUk5Gxm9QqM/rstan_2.19.1.zip’ not found

@willtudorevans
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@willtudorevans willtudorevans commented Jun 19, 2019 •
edited

The main problem now seems to be R not being able to 'find' Rtools. Every time I run:

pkgbuild::has_build_tools(debug = TRUE)

it determines FALSE and asks me if I want to install 'additional tools'. It then recommends I uninstall the existing Rtools first (version 3.5) before installing Rtools. This process repeats itself now matter how many times i uninstall and reintsall Rtools. This seems to be a new problem only after I tried reinstalling Rtools to see if that solved the original problem. Originally this returned TRUE:

pkgbuild::has_build_tools(debug = TRUE)

Not sure what to try next!I should probably refer to the Rtools debug manual.

@willtudorevans
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@willtudorevans willtudorevans commented Jun 19, 2019

OK I seem to solve the Rtools issue by setting:

options(buildtools.check = NULL)

as detailed here rstudio/rstudio#3563. I'm still having the Makevars issue even after running the 'Configuration of the C++ Toolchain' script.. I can see the Makevars.win document in the ~/.R/ folder, and no matter if I populate it with the script's default settings or Bob's I get the same error message:

Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created! Error in .shlib_internal(commandArgs(TRUE)) : C++14 standard requested but CXX14 is not defined Calls: <Anonymous> -> .shlib_internal Execution halted In addition: Warning message: In system(cmd, intern = !verbose) : running command 'C:/PROGRA~1/R/R-36~1.0/bin/x64/R CMD SHLIB file22fc4479512d.cpp 2> file22fc4479512d.cpp.err.txt' had status 1 Error in sink(type = "output") : invalid connection

I'm not sure what next to try. I'm tempted to try a complete reinstallation of R, Rstudio, Rtools and Rstan to see if that helps.

@qdread
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@qdread qdread commented Jun 19, 2019

Just do install.packages(" https://win-builder.r-project.org/1vUk5Gxm9QqM/rstan_2.19.1.zip", repos = NULL)
…

Unfortunately I receive the following error message:

Error in install.packages : zip file ‘ https://win-builder.r-project.org/1vUk5Gxm9QqM/rstan_2.19.1.zip’ not found

There is a space at the beginning of the string (typo) in bgoodri's comment so just remove that.

@willtudorevans
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@willtudorevans willtudorevans commented Jun 19, 2019

There is a space at the beginning of the string (typo) in bgoodri's comment so just remove that.

I feel stupid for having missed this. Thanks so much qdread, Bob and Ben everything now seems to be working.

@SebAtWork SebAtWork mentioned this issue Jul 11, 2019
Closed
mrustl added a commit to KWB-R/kwb.flusshygiene.app that referenced this issue Jul 17, 2019
@mrustl
travis: fix "rstan" c++ compiler problem
289c120 
"Error in .shlib_internal(args) :
  C++14 standard requested but CXX14 is not defined
* removing ‘/home/travis/R/Library/rstan’"

by using solution: stan-dev/rstan#569 (comment)
mrustl added a commit to KWB-R/pkgmeta that referenced this issue Jul 17, 2019
@mrustl
travis: fix "rstan" c++ compiler problem
47209e7 
"Error in .shlib_internal(args) : 
  C++14 standard requested but CXX14 is not defined
* removing ‘/home/travis/R/Library/rstan’"

by using solution: stan-dev/rstan#569 (comment)
@leungi leungi mentioned this issue Aug 29, 2019
Closed
@DiegoDVillacreses
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@DiegoDVillacreses DiegoDVillacreses commented Sep 25, 2019

I understand that this issue was closed based on:
install.packages("https://win-builder.r-project.org/1vUk5Gxm9QqM/rstan_2.19.1.zip", repos = NULL)
But that link isn't available anymore:
https://win-builder.r-project.org/1vUk5Gxm9QqM

@bgoodri
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@bgoodri bgoodri commented Sep 25, 2019

@ngupta23
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@ngupta23 ngupta23 commented Sep 25, 2019

I am facing the same issue on Linux. Do you have a solution for Linux machines?

@bgoodri
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@bgoodri bgoodri commented Sep 25, 2019

@DiegoDVillacreses
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@DiegoDVillacreses DiegoDVillacreses commented Sep 25, 2019

Thank you very much for your quick and accurate response @bgoodri . Actually my problem is when I try:
install.packages("OpenMx")
I get:

Installing package into ‘~/R/win-library/3.6’
(as ‘lib’ is unspecified)

  There is a binary version available but the source version is later:
       binary  source needs_compilation
OpenMx 2.13.2 2.14.11              TRUE

installing the source package ‘OpenMx’

trying URL 'https://cran.rstudio.com/src/contrib/OpenMx_2.14.11.tar.gz'
Content type 'application/x-gzip' length 3386317 bytes (3.2 MB)
downloaded 3.2 MB

* installing *source* package 'OpenMx' ...
** package 'OpenMx' successfully unpacked and MD5 sums checked
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
Error in .shlib_internal(args) : 
  C++14 standard requested but CXX14 is not defined
* removing 'C:/Users/dvill/Documents/R/win-library/3.6/OpenMx'
Warning in install.packages :
  installation of package ‘OpenMx’ had non-zero exit status

Specifications:

  1. OS: Windows 10 home-64 bits-x64-based processor
  2. R: x86_64-w64-mingw32; arch x86_64; os mingw32; system x86_64, mingw32
  3. Rtools: 3.5.0.4

I am only having troubles with this package. For example, curl was installed using compilation perfectly.

I have tried everything and this issue is the best documented, it's possible to solve this here or should I open another issue?

Also, @ngupta23 I have in this same machine Ubuntu, and I have no problem whatsoever with any package there (I have the same packages in both OS). I believe you should:

sudo apt update
sudo apt upgrade

@bgoodri
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@bgoodri bgoodri commented Sep 25, 2019

@atfields atfields mentioned this issue Jun 2, 2020
Closed
@IndrajeetPatil IndrajeetPatil mentioned this issue Jan 8, 2021
Closed
@thistleknot
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@thistleknot thistleknot commented Jan 9, 2021 •
edited

`cat ~/.R/Makevars

CXX14 = g++
CXX14FLAGS = -O3
CXX14FLAGS += -fPIC
#LIBS += -lm
`

@NikKrieger
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@NikKrieger NikKrieger commented Aug 30, 2021

`cat ~/.R/Makevars

CXX14 = g++
CXX14FLAGS = -O3
CXX14FLAGS += -fPIC
#LIBS += -lm
`

This allowed me to install the xgboost R package

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