Documentation for Eidos function system, which is a method of
Eidos.
Note that the R function is a stub, it does not do anything in R (except bring
up this documentation). It will only do
anything useful when used inside a slim_block function further
nested in a slim_script
function call, where it will be translated into valid SLiM code as part of a
full SLiM script.
eidos_system(command, args, input, stderr, wait)An object of type string or string or string or logical or logical. Must be of length 1 (a singleton). See details for description.
An object of type string or string or string or logical or logical.
The default value is "". See details for description.
An object of type string or string or string or logical or logical.
The default value is "". See details for description.
An object of type string or string or string or logical or
logical. Must be of length 1 (a singleton). The default value is F. See
details for description.
An object of type string or string or string or logical or logical.
Must be of length 1 (a singleton). The default value is T. See details
for description.
An object of type string.
Documentation for this function can be found in the official SLiM manual: page NA.
Runs a Un*x command in a /bin/sh shell with optional arguments and input, and returns the result as a vector of output lines. The args parameter may contain a vector of arguments to command; they will be passed directly to the shell without any quoting, so applying the appropriate quoting as needed by /bin/sh is the caller's responsibility. The arguments are appended to command, separated by spaces, and the result is passed to the shell as a single command string, so arguments may simply be given as part of command instead, if preferred. By default no input is supplied to command; if input is non-empty, however, it will be written to a temporary file (one line per string element) and the standard input of command will be redirected to that temporary file (using standard /bin/sh redirection with <, appended to the command string passed to the shell). By default, output sent to standard error will not be captured (and thus may end up in the output of the SLiM process, or may be lost); if stderr is T, however, the standard error stream will be redirected into standard out (using standard /bin/sh redirection with 2>&1, appended to the command string passed to the shell). Arbitrary command strings involving multiple commands, pipes, redirection, etc., may be used with system(), but may be incompatible with the way that args, input, and stderr are handled by this function, so in this case supplying the whole command string in command may be the simplest course. You may redirect standard error into standard output yourself in command with 2>&1. Supplying input to a complex command line can often be facilitated by the use of parentheses to create a subshell; for example, system("(wc -l | sed 's/ //g')", input=c('foo', 'bar', 'baz')); will supply the input lines to wc courtesy of the subshell started for the () operator. If this strategy doesn't work for the command line you want to execute, you can always write a temporary file yourself using writeFile() or writeTempFile() and redirect that file to standard input in command with <. If wait is T (the default), system() will wait for the command to finish, and return the output generated as a string vector, as described above. If wait is F, system() will instead append " &" to the end of the command line to request that it be run in the background, and it will not collect and 84 return the output from the command; instead it will return string(0) immediately. If the output from the command is needed, it could be redirected to a file, and that file could be checked periodically in Eidos for some indication that the command had completed; if output is not redirected to a file, it may appear in SLiM's output stream. If the final command line executed by system() ends in " &", the behavior of system() should be just as if wait=T had been supplied, but it is recommended to use wait=T instead to ensure that the command line is correctly assembled.
This is documentation for a function in the SLiM software, and has been reproduced from the official manual, which can be found here: http://benhaller.com/slim/SLiM_Manual.pdf. This documentation is Copyright © 2016-2020 Philipp Messer. All rights reserved. More information about SLiM can be found on the official website: https://messerlab.org/slim/
Other Eidos:
Eidos,
eidos_abs(),
eidos_acos(),
eidos_all(),
eidos_any(),
eidos_apply(),
eidos_array(),
eidos_asFloat(),
eidos_asInteger(),
eidos_asLogical(),
eidos_asString(),
eidos_asin(),
eidos_assert(),
eidos_atan2(),
eidos_atan(),
eidos_beep(),
eidos_catn(),
eidos_cat(),
eidos_cbind(),
eidos_ceil(),
eidos_citation(),
eidos_clock(),
eidos_cmColors(),
eidos_color2rgb(),
eidos_colors(),
eidos_cor(),
eidos_cos(),
eidos_cov(),
eidos_createDirectory(),
eidos_cumProduct(),
eidos_cumSum(),
eidos_c(),
eidos_date(),
eidos_dbeta(),
eidos_debugIndent(),
eidos_defineConstant(),
eidos_defineGlobal(),
eidos_deleteFile(),
eidos_dexp(),
eidos_dgamma(),
eidos_diag(),
eidos_dim(),
eidos_dmvnorm(),
eidos_dnorm(),
eidos_drop(),
eidos_elementType(),
eidos_exists(),
eidos_exp(),
eidos_fileExists(),
eidos_filesAtPath(),
eidos_findInterval(),
eidos_float(),
eidos_floor(),
eidos_flushFile(),
eidos_format(),
eidos_functionSignature(),
eidos_functionSource(),
eidos_getSeed(),
eidos_getwd(),
eidos_heatColors(),
eidos_hsv2rgb(),
eidos_identical(),
eidos_ifelse(),
eidos_integerDiv(),
eidos_integerMod(),
eidos_integer(),
eidos_isFinite(),
eidos_isFloat(),
eidos_isInfinite(),
eidos_isInteger(),
eidos_isLogical(),
eidos_isNAN(),
eidos_isNULL(),
eidos_isObject(),
eidos_isString(),
eidos_length(),
eidos_license(),
eidos_log10(),
eidos_log2(),
eidos_logical(),
eidos_log(),
eidos_lowerTri(),
eidos_ls(),
eidos_match(),
eidos_matrixMult(),
eidos_matrix(),
eidos_max(),
eidos_mean(),
eidos_min(),
eidos_nchar(),
eidos_ncol(),
eidos_nrow(),
eidos_object(),
eidos_order(),
eidos_paste0(),
eidos_paste(),
eidos_pmax(),
eidos_pmin(),
eidos_pnorm(),
eidos_print(),
eidos_product(),
eidos_qnorm(),
eidos_quantile(),
eidos_rainbow(),
eidos_range(),
eidos_rank(),
eidos_rbeta(),
eidos_rbind(),
eidos_rbinom(),
eidos_rcauchy(),
eidos_rdunif(),
eidos_readCSV(),
eidos_readFile(),
eidos_repEach(),
eidos_rep(),
eidos_rev(),
eidos_rexp(),
eidos_rf(),
eidos_rgamma(),
eidos_rgb2color(),
eidos_rgb2hsv(),
eidos_rgeom(),
eidos_rlnorm(),
eidos_rmvnorm(),
eidos_rm(),
eidos_rnbinom(),
eidos_rnorm(),
eidos_round(),
eidos_rpois(),
eidos_runif(),
eidos_rweibull(),
eidos_sample(),
eidos_sapply(),
eidos_sd(),
eidos_seqAlong(),
eidos_seqLen(),
eidos_seq(),
eidos_setDifference(),
eidos_setIntersection(),
eidos_setSeed(),
eidos_setSymmetricDifference(),
eidos_setUnion(),
eidos_setwd(),
eidos_sin(),
eidos_size(),
eidos_sortBy(),
eidos_sort(),
eidos_source(),
eidos_sqrt(),
eidos_stop(),
eidos_strcontains(),
eidos_strfind(),
eidos_string(),
eidos_strprefix(),
eidos_strsplit(),
eidos_strsuffix(),
eidos_str(),
eidos_substr(),
eidos_sumExact(),
eidos_sum(),
eidos_suppressWarnings(),
eidos_sysinfo(),
eidos_tabulate(),
eidos_tan(),
eidos_tempdir(),
eidos_terrainColors(),
eidos_time(),
eidos_trunc(),
eidos_ttest(),
eidos_type(),
eidos_t(),
eidos_unique(),
eidos_upperTri(),
eidos_usage(),
eidos_var(),
eidos_version(),
eidos_whichMax(),
eidos_whichMin(),
eidos_which(),
eidos_writeFile(),
eidos_writeTempFile()