Introduction
- -## [1] TRUEThis vignette describes how you can use the
ParallelLogger package to perform logging. Logging is the
activity of recording events that occur during an analysis in a log. The
@@ -196,7 +193,7 @@
Creating a console loggerThe code below demonstrates how one would create a logger that writes
all events at level INFO or greater to the console using a
layout with time stamp:
-
+
logger <- createLogger(name = "SIMPLE",
threshold = "INFO",
appenders = list(createConsoleAppender(layout = layoutTimestamp)))
@@ -212,7 +209,7 @@ Creating a console logger
-
+
clearLoggers()
logger <- createLogger(name = "SIMPLE",
@@ -228,10 +225,10 @@ Shorthand
+
is equivalent to
-
+
registerLogger(createLogger(name = "DEFAULT_CONSOLE_LOGGER",
threshold = "INFO",
appenders = list(createConsoleAppender(layout = layoutSimple))))
@@ -244,7 +241,7 @@ Creating a file loggerTRACE (so including all events), and using the layout for
parallel processing.
-
+
logFileName <- "log.txt"
logger <- createLogger(name = "PARALLEL",
@@ -260,23 +257,23 @@ Creating a file loggerlogInfo("Hello world")
## 2021-02-23 09:04:06 Hello world
We can read the log file:
-
+
writeLines(readChar(logFileName, file.info(logFileName)$size))
## 2021-02-23 09:04:06 [Main thread] TRACE evaluate timing_fn Executed this line
## 2021-02-23 09:04:06 [Main thread] DEBUG evaluate timing_fn There are 2 loggers
## 2021-02-23 09:04:06 [Main thread] INFO evaluate timing_fn Hello world
And clean it up when we’re done:
-
+
unlink(logFileName)
Shorthand
A shorthand for creating the file logger detailed here is offered by
the addDefaultFileLogger function. The code
-
+
addDefaultFileLogger(logFileName)
is equivalent to
-
+
registerLogger(createLogger(name = "DEFAULT_FILE_LOGGER",
threshold = "TRACE",
appenders = list(createFileAppender(layout = layoutParallel,
@@ -307,10 +304,10 @@ Shorthand
+
which is equivalent to
-
+
fileName <- file.path(getwd(), "errorReportR.txt")
registerLogger(createLogger(name = "DEFAULT_ERRORREPORT_LOGGER",
@@ -328,7 +325,7 @@ Creating an e-mail logger
-
+
mailSettings <- list(from = "someone@gmail.com",
to = c("someone_else@gmail.com"),
smtp = list(host.name = "smtp.gmail.com",
@@ -354,10 +351,10 @@ Shorthand
+
addDefaultEmailLogger(mailSettings)
is equivalent to
-
+
registerLogger(createLogger(name = "DEFAULT_EMAIL_LOGGER",
threshold = "FATAL",
appenders = list(createEmailAppender(layout = layoutEmail,
@@ -369,7 +366,7 @@ Messages, warnings and fatal errors<
All R warnings and errors are automatically logged, and therefore do
not require explicit logging. For example:
-
+
clearLoggers()
addDefaultFileLogger(logFileName)
@@ -397,7 +394,7 @@ Logging when parallel processinglayoutParallel
records thread identifiers, making it
possible to later untangle the various threads. Below is a simple
example:
-
+
clearLoggers() # Clean up the loggers from the previous example
addDefaultFileLogger(logFileName)
@@ -443,7 +440,7 @@ Creating loggers in functions
+
subSubTask <- function() {
addDefaultFileLogger("subSubTaskLog.txt")
# do something
@@ -461,7 +458,7 @@ Creating loggers in functionssubTask()
}
it would be better to have only one logger:
-
+
subSubTask <- function() {
# do something
}
@@ -480,7 +477,7 @@ Creating loggers in functions
+
mainTask <- function() {
addDefaultFileLogger("log.txt")
on.exit(unregisterLogger("DEFAULT_FILE_LOGGER"))
@@ -493,11 +490,11 @@ Shiny log viewerA Shiny app for viewing a log file created using the
layoutParallel is included in the package. To explore the
log created in the prior example, run
-
+
launchLogViewer(logFileName)
to launch the viewer shown in Figure 1.
-
-
Shiny log viewer app
+
+Shiny log viewer app
@@ -519,7 +516,7 @@ Shiny log viewer
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/Parallel.html b/docs/articles/Parallel.html
index d4a05bb..29b36f9 100644
--- a/docs/articles/Parallel.html
+++ b/docs/articles/Parallel.html
@@ -6,7 +6,7 @@
Parallel execution using ParallelLogger • ParallelLogger
-
+
@@ -33,7 +33,7 @@
@@ -88,7 +88,7 @@ Parallel execution using ParallelLogger
Martijn J.
Schuemie
- 2023-08-22
+ 2024-08-23
Source: vignettes/Parallel.Rmd
Parallel.Rmd
@@ -158,15 +158,7 @@ Executing in parallel
x <- 1:3
clusterApply(cluster, x, fun, constant = 2)
-##
- |
- | | 0%
- |
- |======================= | 33%
- |
- |=============================================== | 67%
- |
- |======================================================================| 100%
+## | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100%
## [[1]]
## [1] 2
##
@@ -272,7 +264,7 @@ Support for Andromeda objects
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 4b686b0..7791ad7 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,5 +1,5 @@
-Articles • ParallelLogger Articles • ParallelLogger
@@ -17,7 +17,7 @@
@@ -80,7 +80,7 @@ All vignettes
diff --git a/docs/authors.html b/docs/authors.html
index e24050e..1649d65 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,5 +1,5 @@
-Authors and Citation • ParallelLogger Authors and Citation • ParallelLogger
@@ -17,7 +17,7 @@
@@ -60,7 +60,7 @@
- Schuemie M, Suchard M (2023).
+
Schuemie M, Suchard M (2024).
ParallelLogger: Support for Parallel Computation, Logging, and Function Automation.
-https://ohdsi.github.io/ParallelLogger/, https://github.com/OHDSI/ParallelLogger.
+R package version 3.3.1, https://github.com/OHDSI/ParallelLogger, https://ohdsi.github.io/ParallelLogger/.
@Manual{,
title = {ParallelLogger: Support for Parallel Computation, Logging, and Function Automation},
author = {Martijn Schuemie and Marc Suchard},
- year = {2023},
- note = {https://ohdsi.github.io/ParallelLogger/, https://github.com/OHDSI/ParallelLogger},
+ year = {2024},
+ note = {R package version 3.3.1, https://github.com/OHDSI/ParallelLogger},
+ url = {https://ohdsi.github.io/ParallelLogger/},
}
@@ -107,7 +108,7 @@ Citation
diff --git a/docs/index.html b/docs/index.html
index 0bef234..1f20afd 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,15 +6,13 @@
Support for Parallel Computation, Logging, and Function Automation • ParallelLogger
-
+
-
+
Changelog • ParallelLogger Changelog • ParallelLogger
@@ -17,7 +17,7 @@
@@ -64,7 +64,12 @@ Changelog
+
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 4b41b5d..ff8220f 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,8 +1,8 @@
-pandoc: 2.19.2
-pkgdown: 2.0.7
+pandoc: 3.1.11
+pkgdown: 2.0.9
pkgdown_sha: ~
articles:
Logging: Logging.html
Parallel: Parallel.html
-last_built: 2023-08-22T10:33Z
+last_built: 2024-08-23T06:25Z
diff --git a/docs/reference/ParallelLogger-package.html b/docs/reference/ParallelLogger-package.html
index 671e836..9673388 100644
--- a/docs/reference/ParallelLogger-package.html
+++ b/docs/reference/ParallelLogger-package.html
@@ -1,5 +1,5 @@
-ParallelLogger: Support for Parallel Computation, Logging, and Function Automation — ParallelLogger-package • ParallelLogger ParallelLogger: Support for Parallel Computation, Logging, and Function Automation — ParallelLogger-package • ParallelLogger
@@ -17,7 +17,7 @@
@@ -95,7 +95,7 @@ Author
diff --git a/docs/reference/addDefaultConsoleLogger.html b/docs/reference/addDefaultConsoleLogger.html
index 33054e8..a010fa8 100644
--- a/docs/reference/addDefaultConsoleLogger.html
+++ b/docs/reference/addDefaultConsoleLogger.html
@@ -1,5 +1,5 @@
-Add the default console logger — addDefaultConsoleLogger • ParallelLogger Add the default console logger — addDefaultConsoleLogger • ParallelLogger
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/addDefaultEmailLogger.html b/docs/reference/addDefaultEmailLogger.html
index ac5454c..3d5e275 100644
--- a/docs/reference/addDefaultEmailLogger.html
+++ b/docs/reference/addDefaultEmailLogger.html
@@ -1,5 +1,5 @@
-Add the default e-mail logger — addDefaultEmailLogger • ParallelLogger Add the default e-mail logger — addDefaultEmailLogger • ParallelLogger
@@ -17,7 +17,7 @@
@@ -135,7 +135,7 @@ Examples
# Setting test to TRUE in this example so we don't really send an e-mail:
addDefaultEmailLogger(mailSettings, "My R session", test = TRUE)
-#> Error: 'sendmailR' must be installed for this functionality.
+#> Error: ‘sendmailR’ must be installed for this functionality.
logFatal("Something bad")
unregisterLogger("DEFAULT_EMAIL_LOGGER")
@@ -155,7 +155,7 @@ Examples
diff --git a/docs/reference/addDefaultErrorReportLogger.html b/docs/reference/addDefaultErrorReportLogger.html
index fde45f5..3712c77 100644
--- a/docs/reference/addDefaultErrorReportLogger.html
+++ b/docs/reference/addDefaultErrorReportLogger.html
@@ -1,5 +1,5 @@
-Add the default error report logger — addDefaultErrorReportLogger • ParallelLogger Add the default error report logger — addDefaultErrorReportLogger • ParallelLogger
@@ -17,7 +17,7 @@
@@ -104,7 +104,7 @@ Details
diff --git a/docs/reference/addDefaultFileLogger.html b/docs/reference/addDefaultFileLogger.html
index c6722ee..aebb09f 100644
--- a/docs/reference/addDefaultFileLogger.html
+++ b/docs/reference/addDefaultFileLogger.html
@@ -1,5 +1,5 @@
-Add the default file logger — addDefaultFileLogger • ParallelLogger Add the default file logger — addDefaultFileLogger • ParallelLogger
@@ -17,7 +17,7 @@
+logger <- createLogger(name = "SIMPLE", threshold = "INFO", appenders = list(createConsoleAppender(layout = layoutTimestamp))) @@ -212,7 +209,7 @@Creating a console logger -
@@ -104,7 +104,7 @@+diff --git a/docs/reference/addDefaultErrorReportLogger.html b/docs/reference/addDefaultErrorReportLogger.html index fde45f5..3712c77 100644 --- a/docs/reference/addDefaultErrorReportLogger.html +++ b/docs/reference/addDefaultErrorReportLogger.html @@ -1,5 +1,5 @@ -clearLoggers() logger <- createLogger(name = "SIMPLE", @@ -228,10 +225,10 @@Shorthand
+is equivalent to
-+@@ -244,7 +241,7 @@registerLogger(createLogger(name = "DEFAULT_CONSOLE_LOGGER", threshold = "INFO", appenders = list(createConsoleAppender(layout = layoutSimple))))Creating a file loggerTRACE (so including all events), and using the layout for parallel processing. -
@@ -135,7 +135,7 @@+logFileName <- "log.txt" logger <- createLogger(name = "PARALLEL", @@ -260,23 +257,23 @@Creating a file loggerlogInfo("Hello world")
## 2021-02-23 09:04:06 Hello worldWe can read the log file:
-diff --git a/docs/reference/addDefaultEmailLogger.html b/docs/reference/addDefaultEmailLogger.html index ac5454c..3d5e275 100644 --- a/docs/reference/addDefaultEmailLogger.html +++ b/docs/reference/addDefaultEmailLogger.html @@ -1,5 +1,5 @@ -+writeLines(readChar(logFileName, file.info(logFileName)$size))## 2021-02-23 09:04:06 [Main thread] TRACE evaluate timing_fn Executed this line ## 2021-02-23 09:04:06 [Main thread] DEBUG evaluate timing_fn There are 2 loggers ## 2021-02-23 09:04:06 [Main thread] INFO evaluate timing_fn Hello worldAnd clean it up when we’re done:
-+unlink(logFileName)@@ -108,7 +108,7 @@Shorthand
A shorthand for creating the file logger detailed here is offered by the
-addDefaultFileLoggerfunction. The codediff --git a/docs/reference/addDefaultConsoleLogger.html b/docs/reference/addDefaultConsoleLogger.html index 33054e8..a010fa8 100644 --- a/docs/reference/addDefaultConsoleLogger.html +++ b/docs/reference/addDefaultConsoleLogger.html @@ -1,5 +1,5 @@ -+addDefaultFileLogger(logFileName)is equivalent to
-+@@ -95,7 +95,7 @@registerLogger(createLogger(name = "DEFAULT_FILE_LOGGER", threshold = "TRACE", appenders = list(createFileAppender(layout = layoutParallel, @@ -307,10 +304,10 @@Shorthand
+which is equivalent to
-diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4b41b5d..ff8220f 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,8 +1,8 @@ -pandoc: 2.19.2 -pkgdown: 2.0.7 +pandoc: 3.1.11 +pkgdown: 2.0.9 pkgdown_sha: ~ articles: Logging: Logging.html Parallel: Parallel.html -last_built: 2023-08-22T10:33Z +last_built: 2024-08-23T06:25Z diff --git a/docs/reference/ParallelLogger-package.html b/docs/reference/ParallelLogger-package.html index 671e836..9673388 100644 --- a/docs/reference/ParallelLogger-package.html +++ b/docs/reference/ParallelLogger-package.html @@ -1,5 +1,5 @@ -++fileName <- file.path(getwd(), "errorReportR.txt") registerLogger(createLogger(name = "DEFAULT_ERRORREPORT_LOGGER", @@ -328,7 +325,7 @@Creating an e-mail logger -
@@ -64,7 +64,12 @@+diff --git a/docs/index.html b/docs/index.html index 0bef234..1f20afd 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,15 +6,13 @@mailSettings <- list(from = "someone@gmail.com", to = c("someone_else@gmail.com"), smtp = list(host.name = "smtp.gmail.com", @@ -354,10 +351,10 @@Shorthand
+addDefaultEmailLogger(mailSettings)is equivalent to
-+@@ -60,7 +60,7 @@registerLogger(createLogger(name = "DEFAULT_EMAIL_LOGGER", threshold = "FATAL", appenders = list(createEmailAppender(layout = layoutEmail, @@ -369,7 +366,7 @@Messages, warnings and fatal errors<
All R warnings and errors are automatically logged, and therefore do not require explicit logging. For example:
-diff --git a/docs/authors.html b/docs/authors.html index e24050e..1649d65 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,5 +1,5 @@ -+clearLoggers() addDefaultFileLogger(logFileName) @@ -397,7 +394,7 @@records thread identifiers, making it possible to later untangle the various threads. Below is a simple example: -Logging when parallel processinglayoutParallel
@@ -80,7 +80,7 @@+diff --git a/docs/articles/index.html b/docs/articles/index.html index 4b686b0..7791ad7 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,5 +1,5 @@ -clearLoggers() # Clean up the loggers from the previous example addDefaultFileLogger(logFileName) @@ -443,7 +440,7 @@Creating loggers in functions
+subSubTask <- function() { addDefaultFileLogger("subSubTaskLog.txt") # do something @@ -461,7 +458,7 @@Creating loggers in functionssubTask() }
it would be better to have only one logger:
--+@@ -88,7 +88,7 @@subSubTask <- function() { # do something } @@ -480,7 +477,7 @@Creating loggers in functions
+diff --git a/docs/articles/Parallel.html b/docs/articles/Parallel.html index d4a05bb..29b36f9 100644 --- a/docs/articles/Parallel.html +++ b/docs/articles/Parallel.html @@ -6,7 +6,7 @@mainTask <- function() { addDefaultFileLogger("log.txt") on.exit(unregisterLogger("DEFAULT_FILE_LOGGER")) @@ -493,11 +490,11 @@Shiny log viewerA Shiny app for viewing a log file created using the
layoutParallelis included in the package. To explore the log created in the prior example, run -@@ -519,7 +516,7 @@+launchLogViewer(logFileName)to launch the viewer shown in Figure 1.
--Shiny log viewer app
++Shiny log viewer appShiny log viewer -
Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
Parallel execution using ParallelLogger • ParallelLogger - + @@ -33,7 +33,7 @@Parallel execution using ParallelLogger
Martijn J. Schuemie
-2023-08-22
+2024-08-23
Source:vignettes/Parallel.Rmd@@ -158,15 +158,7 @@Parallel.RmdExecuting in parallel
x <- 1:3 clusterApply(cluster, x, fun, constant = 2)+## - | - | | 0% - | - |======================= | 33% - | - |=============================================== | 67% - | - |======================================================================| 100%## | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100%## [[1]] ## [1] 2 ## @@ -272,7 +264,7 @@Support for Andromeda objects -
Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
Articles • ParallelLogger Articles • ParallelLogger @@ -17,7 +17,7 @@All vignettes
Authors and Citation • ParallelLogger Authors and Citation • ParallelLogger @@ -17,7 +17,7 @@-@@ -107,7 +108,7 @@Schuemie M, Suchard M (2023). +
Schuemie M, Suchard M (2024). ParallelLogger: Support for Parallel Computation, Logging, and Function Automation. -https://ohdsi.github.io/ParallelLogger/, https://github.com/OHDSI/ParallelLogger. +R package version 3.3.1, https://github.com/OHDSI/ParallelLogger, https://ohdsi.github.io/ParallelLogger/.
@Manual{, title = {ParallelLogger: Support for Parallel Computation, Logging, and Function Automation}, author = {Martijn Schuemie and Marc Suchard}, - year = {2023}, - note = {https://ohdsi.github.io/ParallelLogger/, https://github.com/OHDSI/ParallelLogger}, + year = {2024}, + note = {R package version 3.3.1, https://github.com/OHDSI/ParallelLogger}, + url = {https://ohdsi.github.io/ParallelLogger/}, }Citation
Support for Parallel Computation, Logging, and Function Automation • ParallelLogger - + - +Changelog • ParallelLogger Changelog • ParallelLogger @@ -17,7 +17,7 @@Changelog
ParallelLogger: Support for Parallel Computation, Logging, and Function Automation — ParallelLogger-package • ParallelLogger ParallelLogger: Support for Parallel Computation, Logging, and Function Automation — ParallelLogger-package • ParallelLogger @@ -17,7 +17,7 @@Author
Add the default console logger — addDefaultConsoleLogger • ParallelLogger Add the default console logger — addDefaultConsoleLogger • ParallelLogger @@ -17,7 +17,7 @@Examples
Add the default e-mail logger — addDefaultEmailLogger • ParallelLogger Add the default e-mail logger — addDefaultEmailLogger • ParallelLogger @@ -17,7 +17,7 @@Examples
# Setting test to TRUE in this example so we don't really send an e-mail: addDefaultEmailLogger(mailSettings, "My R session", test = TRUE) -#> Error: 'sendmailR' must be installed for this functionality. +#> Error: ‘sendmailR’ must be installed for this functionality. logFatal("Something bad") unregisterLogger("DEFAULT_EMAIL_LOGGER") @@ -155,7 +155,7 @@Examples
Add the default error report logger — addDefaultErrorReportLogger • ParallelLogger Add the default error report logger — addDefaultErrorReportLogger • ParallelLogger @@ -17,7 +17,7 @@Details