sybilLog-class: Class '"sybilLog"'

In sybil: Efficient Constrained Based Modelling

Description

Handles log files, messages warnings and errors.

Objects from the Class

Objects can be created by calls of the function sybilLog:

logObj <- sybilLog(filename).

Slots

fh:

Object of class file which is a connection to a file to print to.

fname:

Object of class "character" being the name of the file to print to. If set to NA, no logfile is used. Default: NA.

fpath:

Object of class "character" giving the path to the file mentioned in fname. Default: ".".

fenc:

Object of class "character" encoding of the log file. Default: "".

loglevel:

Object of class "integer" controlling the amount of details to log: If set to 0, nothing will be written to the logfile. If set to > 0, all warnings are logged; if set do > 1, also messages are logged. If loglevel is > 2, the used function call will be printed. Default: 0.

verblevel:

Object of class "integer" controlling the amount of details to log: If set to 0, nothing will be written to the standard output connection. If set to > 0, all warnings are logged; if set do > 1, also messages are logged. Default: 0.

lastStep:

Object of class "list" which is a stack, containing character strings describing performed steps. See also sybilStack.

lstname:

Object of class "list" giving the name of the stack in lastStep.

didFoot:

Object of class "logical" which is FALSE, if the footer of the log file is not yet printed, otherwise TRUE. This is useful if the function which is logged, stops unexpected.

Methods

didFoot

signature(object = "sybilLog"): gets the didFoot slot.

didFoot<-

signature(object = "sybilLog"): sets the didFoot slot.

fenc

signature(object = "sybilLog"): gets the fenc slot.

fenc<-

signature(object = "sybilLog"): sets the fenc slot.

fh

signature(object = "sybilLog"): gets the fh slot.

fh<-

signature(object = "sybilLog"): sets the fh slot.

fname

signature(object = "sybilLog"): gets the fname slot.

fname<-

signature(object = "sybilLog"): sets the fname slot.

fpath

signature(object = "sybilLog"): gets the fpath slot.

fpath<-

signature(object = "sybilLog"): sets the fpath slot.

loglevel

signature(object = "sybilLog"): gets the loglevel slot.

loglevel<-

signature(object = "sybilLog"): sets the loglevel slot.

lstname

signature(object = "sybilLog"): gets the lstname slot.

verblevel

signature(object = "sybilLog"): gets the verblevel slot.

verblevel<-

signature(object = "sybilLog"): sets the verblevel slot.

logCall

signature(object = "sybilLog") (nog): writes all arguments and values of the function call to be logged to the log file. Nothing is printed to the standard output; verblevel has no meaning here; verblevel must be > 2.

nog	number of generations to go back

logClose<-

signature(object = "sybilLog"): close the connection in slot fh and set it to NA. If slot didFoot is not TRUE, it prints a log comment to the connection in fh mentioning, that the logging ended unexpected.

logComment

signature(object = "sybilLog") (cmt, commentChar): add a comment to the log file if loglevel is > 2 and to stdout if verblevel is > 2.

cmt	the comment text
cmtChar	a string to prefix cmt, default: #

logError

signature(object = "sybilLog") (msg, num): add an error message to the log file. Returns an object of class sybilError.

msg	the error message
num	an error number

logFH

signature(object = "sybilLog"): Returns TRUE, if slot fh is of class file, otherwise FALSE.

logFoot<-

signature(object = "sybilLog"): Print a head for your log file.

logHead

signature(object = "sybilLog"): Print a foot for your log file.

logMessage

signature(object = "sybilLog"): add a message to the log file if loglevel is > 1.

...	strings pasted to the log file

logOptimization

signature(object = "sybilLog"): (ok, stat, obj, del, i): add a row containing results of an optimization to the log file if loglevel is > 2 and to stdout if verblevel is > 2.

opt no.	(integer) a consecutive number
ret	(integer) return value of the used solver
stat	(integer) solution status after optimization
obj value	(numeric) value of the objective function after optimization
dir	if not given, it is a global value of the algorithm (here empty), otherwise the current setting of the direction of optimization
obj c	if not given, it is a globel value of the model (here empty), otherwise the current setting of the objective coefficients of the variables given in column ‘flux no.’
flux no.	fluxes (variables) which are considered in the current optimization

logOptimizationTH

signature(object = "sybilLog"): add a row containing a table header for results of an optimization to the log file if loglevel is > 2 and to stdout if verblevel is > 2. This should be used prior logOptimization.

logStep<-

signature(object = "sybilLog"): (value): add a status message to the log file if loglevel is > 1, like “performing step x”.

value	strings giving the status

If is.na(value) evaluates to TRUE, the current process is assumed to have finished as expected. If verblevel is > 1, “OK” will be printed on the command line end if loglevel is > 1, “# done step x” will be printed to the log file.

logWarning

signature(object = "sybilLog"): (...): add a warning to the log file if loglevel is > 0.

...	strings pastes to the log file

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

Examples

  showClass("sybilLog")

sybil documentation built on May 31, 2021, 5:08 p.m.