Problem with gadget.iterative in Mac

[be2lla]

Hi,

I am new to Gadget and RGadget and am working on it on a MAC (OS X El Capitan v. 10.11.6). I have managed to install gadget and run it from the terminal no problems. I have also installed RGadget - my sessionInfo is reported below.

I am getting errors when running gadget.iterative: gadget.iterative(rew.sI=TRUE, grouping=list( sind=c('acoustic.like','bias.a0.like')), params.file='params.base', wgts='WGTS')

The error I get is: Error in system(run.string, intern = TRUE, ignore.stderr = ignore.stderr) : error in running command Joining by: comp

and when running debug(gadget.iterative) it reports an error at: callGadget(s = 1, main = paste(wgts, "main.init", sep = "/"), o = paste(wgts, "lik.init", sep = "/"), i = params.file, gadget.exe = gadget.exe) Browse[2]> Error in system(run.string, intern = TRUE, ignore.stderr = ignore.stderr) : error in running command

Any help would be fantastic! Thank you, Betulla

sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.6 (El Capitan)

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] gridExtra_2.2.1 Rgadget_0.5 purrr_0.2.2.2 stringr_1.0.0 lubridate_1.6.0 data.table_1.9.6 [7] dplyr_0.5.0 reshape2_1.4.1 plyr_1.8.4 ggplot2_2.1.0

loaded via a namespace (and not attached): [1] Rcpp_0.12.6 assertthat_0.1 chron_2.3-47 R6_2.1.2 gtable_0.2.0 DBI_0.4-1
[7] magrittr_1.5 scales_0.4.0 stringi_1.1.1 tools_3.3.1 munsell_0.4.3 colorspace_1.2-6 [13] tibble_1.1

[bthe]

Looks to me that either the gadget executable is not installed in the path or some likelihood component has returned a likelihood value of exactly zero (which is usually a sign of something wrong that should be looked at prior to running gadget.iterative). It if is the former there is a quick fix and proper fix. The quick fix to your problem is to set the path to gadget explicitly in R:

.Options$gadget.path <- '/absolute/path/to/gadget'

And you can test whether this works by:

callGadget(s=1,ignore.stderr=FALSE,log='test.log')

This should print what gadget is doing and a detailed debug log can be read from the test.log file.

The proper way to do this: when compiling gadget you do:

make 
sudo make install

which should install gadget to correct directory ( /usr/local/bin/on my mac). However R may in some cases read the environment parameters incorrectly, so you can set the PATH variable explicitly in the .Renviron file in you home directory (create it if needed).

[be2lla]

Thank you Bjarki,

for your prompt reply. I am still not managing, but will keep persevering and will get back to you should I fail.

Betulla

On 1 Aug 2017, at 18:37, Bjarki Þór Elvarsson notifications@github.com wrote:

Looks to me that either the gadget executable is not installed in the path or some likelihood component has returned a likelihood value of exactly zero (which is usually a sign of something wrong that should be looked at prior to running gadget.iterative). It if is the former there is a quick fix and proper fix. The quick fix to your problem is to set the path to gadget explicitly in R:

.Options$gadget.path <- '/absolute/path/to/gadget' And you can test whether this works by:

callGadget(s=1,ignore.stderr=FALSE,log='test.log') This should print what gadget is doing and a detailed debug log can be read from the test.log file.

The proper way to do this: when compiling gadget you do:

make sudo make install which should install gadget to correct directory ( /usr/local/bin/on my mac). However R may in some cases read the environment parameters incorrectly, so you can set the PATH variable explicitly in the .Renviron file in you home directory (create it if needed).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Hafro/rgadget/issues/73#issuecomment-319426028, or mute the thread https://github.com/notifications/unsubscribe-auth/AJmvht1eFBAf4TTPpoXGoSE1XjHo0q1rks5sT1QygaJpZM4Op3Z5.