unknown error code when fitting SSM

[Spines151]

Addition to post # 25 Error when running fit_ssm - closed

I get a cryptic error message trying to run fit_SSM

fit <-fit_ssm(argos, vmax = 5, model ="crw", time.step = 6)
fitting crw...
Error in .Call("getParameterOrder", data, parameters, new.env(), NULL, : Incorrect number of arguments (4), expecting 3 for 'getParameterOrder'

Some googling later, I found people reporting issues with the matrix and TBM versions, so I followed the advice (post #25) to install tbm from the source, but the error remained.
Rv 4.1.1
foieGras (0.7.6)
matrix (1.4.0)
tbm (0.3.5)

Any advice?
Thanks

[jlguilherme]

Hi, today I started experiencing the exact same issue after updating all packages in R (trying to solve a different issue).

I just removed the latest TMB version 1.8.0 (not tbm - I believe you have that wrong) and installed 1.722 and it is working now.

I hope that helps!

[jamesgrecian]

Thanks for highlighting the issue @Spines151.

I've noticed it today while trying to run some example code. It looks like there's been a change in the latest version of TMB that's resulting in some incompatibility issues. I've seen a similar issue come up on the glmmTMB forum: glmmTMB/glmmTMB#791

A patch for now would be to role back the version of TMB you are using:
devtools::install_version("TMB", version = "1.7.20", repos = "http://cran.r-project.org")

HTH,
James

[ianjonsen]

If you have installed the binary foieGras 0.7-6 from CRAN (ie. on Windows or Mac) then you are getting C++ code compiled against TMB 1.7.20. If you have TMB versions 1.8.0 or up installed then you'll get this error. You can:

1. install the CRAN version from source using install.packages("foieGras", type = "source")

2. install from GitHub using remotes::install_github("ianjonsen/foieGras@staging")

Either option will build the package from source & compile the C++ code against whatever version of TMB you have installed. This will stop the error.

[BelindaCannell]

Hi Ian
I have been having the same issue :
Error in .Call("getParameterOrder", data, parameters, new.env(), NULL, : Incorrect number of arguments (4), expecting 3 for 'getParameterOrder'.

I uninstalled the foiegras package and tried to reinstall from Github (i.e. install from GitHub using remotes::install_github("ianjonsen/foieGras@staging"). There were many packages that also need to be upgraded, so I chose to upgrade all of them. However, the package cli was unable to be upgraded and foiegras was unable to be installed. I then tried install.packages("foieGras", type = "source"). This had installed foieGras_1.0.0.9500.tar.gz’ into a temp file. So I then tried to install from github again.

Unfortunately the package failed to install. Here are the last few lines from the installation:

C:/R/Library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__vector(2) double'} [-Wignored-attributes]
(cd TMB; //uniwa.uwa.edu.au/userhome/staff8/00041818/My Documents/R/R-4.0.5/bin/i386/Rscript --no-save --no-restore compile.R)
sh: //uniwa.uwa.edu.au/userhome/staff8/00041818/My: No such file or directory
make: *** [Makevars.win:9: tmblib] Error 127
ERROR: compilation failed for package 'foieGras'

• removing 'C:/R/Library/foieGras'

Warning messages:
1: In i.p(...) : installation of package ‘cli’ had non-zero exit status
2: In i.p(...) :
installation of package ‘C:/Users/00041818/AppData/Local/Temp/Rtmp0KyQvN/file282c62935898/foieGras_1.0.0.9500.tar.gz’ had non-zero exit status

Can you please advise what I need to do in order to be able to install foiegras.

Kind regards
Belinda

[ianjonsen]

Hi Belinda,

The cli package isn't a direct requirement for foieGras but must be for one of foieGras's dependencies. You probably don't need the latest cli version so I would try reinstalling from the CRAN package versions, rather than GitHub, using this sequence:

1. uninstall foieGras with: remove.packages("foieGras")
2. close R/RStudio and then reopen
3. install cli with install.packages("cli") - if you get a message asking if you want to install from source, choose "no"
4. install foieGras with: install.packages("foieGras", type = "source")`

This should install the CRAN versions of cli and foieGras 0.7-6. The GitHub version is currently experimental and mostly untested.