Closed nicrie closed 5 years ago
Hi. Maybe HYSPLIT didn't run. Has your OS been correctly detected?
get_os <- function() {
if (.Platform$OS.type == "windows") {
"win"
} else if (Sys.info()["sysname"] == "Darwin") {
"mac"
} else if (.Platform$OS.type == "unix") {
"unix"
} else {
stop("Unknown OS")
}
}
get_os()
If the result is unix
, then check if the file hyts_std
is in the right place and if it's executable
file.access(system.file("linux-amd64/hyts_std",package = "SplitR"),1)==0
Moreover, check whether a 64-bit architecture is present
.Machine$sizeof.pointer == 8
Thank you very much for your help! Though I still couldn't find the error. I checked your ideas but everything seems to work correctly:
get_os <- function() { if (.Platform$OS.type == "windows") { "win" } else if (Sys.info()["sysname"] == "Darwin") { "mac" } else if (.Platform$OS.type == "unix") { "unix" } else { stop("Unknown OS") } } get_os()
throws "unix".
If the result is
unix
, then check if the filehyts_std
is in the right place and if it's executablefile.access(system.file("linux-amd64/hyts_std",package = "SplitR"),1)==0
"TRUE" Moreover, check whether a 64-bit architecture is present
.Machine$sizeof.pointer == 8
"TRUE"
It's even more confusing as I just put on a fresh installation of Ubuntu (and therefore Anaconda/RStudio).
Since the error message states that there is a problem with moving files in/out a directory which does not exist: Could it be due to overlong file/directory names? I don't know if SplitR
is internally calling HYSPLIT GUI which complained about too long directory names on my machine (seems to be a known bug as others reported it too).
ls -l /home/nrieger/HYSPLIT/ArabianSea/*
MESSAGE
less /home/nrieger/HYSPLIT/ArabianSea/MESSAGE
* check from the shell if the Hysplit output files are there
ls -l /home/nrieger/HYSPLIT/ArabianSea/*
Output
-rw-r--r-- 1 nrieger nrieger 269 nov. 23 01:12 /home/nrieger/HYSPLIT/ArabianSea/ASCDATA.CFG -rw-r--r-- 1 nrieger nrieger 389 nov. 23 01:24 /home/nrieger/HYSPLIT/ArabianSea/CONTROL -rw-r--r-- 1 nrieger nrieger 598888640 nov. 23 01:15 /home/nrieger/HYSPLIT/ArabianSea/gdas1.mar12.w1 -rw-r--r-- 1 nrieger nrieger 598888640 nov. 23 01:18 /home/nrieger/HYSPLIT/ArabianSea/gdas1.mar12.w2 -rw-r--r-- 1 nrieger nrieger 598888640 nov. 23 01:20 /home/nrieger/HYSPLIT/ArabianSea/gdas1.mar12.w3 -rw-r--r-- 1 nrieger nrieger 598888640 nov. 23 01:23 /home/nrieger/HYSPLIT/ArabianSea/gdas1.mar12.w4 -rw-r--r-- 1 nrieger nrieger 256666560 nov. 23 01:24 /home/nrieger/HYSPLIT/ArabianSea/gdas1.mar12.w5 -rw-r--r-- 1 nrieger nrieger 100 nov. 23 01:24 /home/nrieger/HYSPLIT/ArabianSea/met_file_list -rw-r--r-- 1 nrieger nrieger 661 nov. 23 01:12 /home/nrieger/HYSPLIT/ArabianSea/SETUP.CFG
/home/nrieger/HYSPLIT/ArabianSea/datasets: total 352936 -rw-r--r-- 1 nrieger nrieger 54 nov. 22 22:27 met_file_list -rw-r--r-- 1 nrieger nrieger 123110672 nov. 22 22:26 RP199912.gbl -rw-r--r-- 1 nrieger nrieger 123110672 nov. 22 22:26 RP200001.gbl -rw-r--r-- 1 nrieger nrieger 115168048 nov. 22 22:27 RP200002.gbl
/home/nrieger/HYSPLIT/ArabianSea/storage: total 0
/home/nrieger/HYSPLIT/ArabianSea/traj-2018-11-23-01-12-39: total 0
/home/nrieger/HYSPLIT/ArabianSea/working: total 0
The additional datasets `RP******.gbl` were downloaded in another test run I did earlier.
> * check the file `MESSAGE`
>
>
> ```
> less /home/nrieger/HYSPLIT/ArabianSea/MESSAGE
> ```
The `MESSAGE` file, however, does not exist!?
uhm, no output (traj--*
), no log (MESSAGE
) from Hysplit...
try to execute it and please paste the standard output/error
binary_path <- system.file("linux-amd64/hyts_std",package = "SplitR")
setwd("/home/nrieger/HYSPLIT/ArabianSea/")
system(binary_path)
Output
/home/nrieger/anaconda3/envs/rstudio/lib/R/library/SplitR/linux-amd64/hyts_std: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
Warning message:
In system(binary_path) : error in running command
Indeed, only libgfortran.so.4 was available in my libraries. Just installed additionally .so.3
alongside via
sudo apt-get install libgfortran3
Now it works like a charm - thanks a lot @jobonaf :+1:
Running the example given in the description
throws the following error (after having successfully downloaded the data sets which were saved in the working directory):
Can me someone give me a hint what I am missing? This seems to be a local problem on my machine though. I am using Linux 18.04 with RStudio (with R version 3.5.1) in Anaconda.