nimble installation

[Lei Cao]

Dear all,

     There are some issues when I reinstall my nimble packages in one  of my computer. My other computer could install the nimle, when I use the same installation method. Here is the information, I don’t have the C:/Rtools/usr/mingw_64, the other computers which can succefully install nimble show that C:/Rtools/mingw_64 compile…

 

R_PACKAGE_DIR: C:/Users/caole/Documents/R/win-library/3.5/nimble

R_HOME = C:/PROGRA~1/R/R-35~1.2, R_ARCH=/x64

Creating inst/CppCode/libnimble_x64.a

C:/Rtools/usr/mingw_64/bin/g++  -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -DR_NO_REMAP -I"../include"         -O2 -Wall  -mtune=generic -c RcppUtils.cpp -o RcppUtils.o

sh: C:/Rtools/usr/mingw_64/bin/g++: No such file or directory

make: *** [C:/PROGRA~1/R/R-35~1.2/etc/x64/Makeconf:215: RcppUtils.o] Error 127

The R package directory has not been created yet

** libs

Warning: this package has a non-empty 'configure.win' file,

so building only the main architecture

C:/Rtools/usr/mingw_64/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -DR_NO_REMAP -I../inst/include         -O2 -Wall  -mtune=generic -c RcppUtils.cpp -o RcppUtils.o

sh: C:/Rtools/usr/mingw_64/bin/g++: No such file or directory

make: *** [C:/PROGRA~1/R/R-35~1.2/etc/x64/Makeconf:215: RcppUtils.o] Error 127

ERROR: compilation failed for package 'nimble'

* removing 'C:/Users/caole/Documents/R/win-library/3.5/nimble'

In R CMD INSTALL

Warning in install.packages :

  installation of package ‘C:/Users/caole/AppData/Local/Temp/Rtmp6JhplM/downloaded_packages/nimble_0.6.13.tar.gz’ had non-zero exit status.

  Thank's already,

   Best regards,

   Lei

 

 

 

 

从 Windows 版邮件发送

 

[Perry de Valpine]

It looks like your versions of R and nimble aren't up to date.  I would start by using current versions.  You'll need to install Rtools on Windows and set the path.

See the link about Rtools from here: https://r-nimble.org/download

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[Lei Cao]

Dear ALL;

I exactly follow the link about Rtools from here: https://r-nimble.org/download. I type PATH="${RTOOLS40_HOME}\usr\bin;${PATH}", restart R, and type  Sys.which("make") , the R shows ## "C:\\rtools40\\usr\\bin\\make.exe". But when I use the code in the nimble manual to check whether nimbles works. I’ve checked the code in my other computer and it works well. This the example code in the manual.

 

pumpCode <- nimbleCode({ 
  for (i in 1:N){ 
    theta[i] ~ dgamma(alpha,beta) 
    lambda[i] <- theta[i]*t[i] 
    x[i] ~ dpois(lambda[i])
  } 
  alpha ~ dexp(1.0) 
  beta ~ dgamma(0.1,1.0)
})
pumpConsts <- list(N = 10, t = c(94.3, 15.7, 62.9, 126, 5.24, 31.4, 1.05, 1.05, 2.1, 10.5))
pumpData <- list(x = c(5, 1, 5, 14, 3, 19, 1, 1, 4, 22))
pumpInits <- list(alpha = 1, beta = 1, theta = rep(0.1, pumpConsts$N))

pump <- nimbleModel(code = pumpCode, name = "pump", constants = pumpConsts, data = pumpData, inits = pumpInits)
mcmc.out <- nimbleMCMC(code = pumpCode, constants = pumpConsts,
                      data = pumpData, inits = pumpInits,
                       nchains = 2, niter = 10000,
                       summary = TRUE, WAIC = TRUE,
                       monitors = c(&apos;alpha&apos;,&apos;beta&apos;,&apos;theta&apos;))

The R shows that

Defining model

Building model

Setting data and initial values

Running calculate on model

  [Note] Any error reports that follow may simply reflect missing values in model variables.

Checking model sizes and dimensions

Checking model calculations

Compiling

  [Note] This may take a minute.

  [Note] Use 'showCompilerOutput = TRUE' to see C++ compilation details.

 

Failed to create the shared library. Run 'printErrors()' to see the compilation errors.

I also used the code which works in my other computer in the R 3.5.3 , unfortanately, it doen’t work neither. Path0=Sys.getenv('PATH')

Pathrtools = paste("C:\\Rtools\\bin;C:\\Rtools\\mingw_64\\bin")  Sys.setenv(PATH = Pathrtools).

  

      I reall appreciate that some methods to fix this problem.

 

               Best wishes,

               Lei

 

 

 

 

 

从 Windows 版邮件发送

 

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发件人: Perry de Valpine <pdeva...@berkeley.edu>
发送时间: Wednesday, December 1, 2021 12:49:20 AM
收件人: Lei Cao <caole...@outlook.com>
抄送: nimble-users <nimble...@googlegroups.com>
主题: Re: nimble installation

 

[Lei Cao]

Dear All;

I fixed nimble installation, especiall thank Perry de Valpine, your link is very useful.

 

Thanks.

Lei

 

从 Windows 版邮件发送

 

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发件人: nimble...@googlegroups.com <nimble...@googlegroups.com> 代表 Lei Cao <caole...@outlook.com>
发送时间: Sunday, December 5, 2021 9:27:05 AM
收件人: Perry de Valpine <pdeva...@berkeley.edu>
抄送: nimble-users <nimble...@googlegroups.com>
主题: 回复: nimble installation

 

To view this discussion on the web visit https://groups.google.com/d/msgid/nimble-users/TYCP286MB1316345E4A05722CC260222DC36C9%40TYCP286MB1316.JPNP286.PROD.OUTLOOK.COM.