I want to redirect all console text to a file. Here is what I tried:
> sink("test.log", type=c("output", "message"))
> a <- "a"
> a
> How come I do not see this in log
Error: unexpected symbol in "How come"
Here is what I got in test.log:
[1] "a"
Here is what I want in test.log:
> a <- "a"
> a
[1] "a"
> How come I do not see this in log
Error: unexpected symbol in "How come"
What am I doing wrong? Thanks!
You have to sink "output" and "message" separately (the sink function only looks at the first element of type)
Now if you want the input to be logged too, then put it in a script:
script.R
1:5 + 1:3 # prints and gives a warning
stop("foo") # an error
And at the prompt:
con <- file("test.log")
sink(con, append=TRUE)
sink(con, append=TRUE, type="message")
# This will echo all input and not truncate 150+ character lines...
source("script.R", echo=TRUE, max.deparse.length=10000)
# Restore output to console
sink()
sink(type="message")
# And look at the log...
cat(readLines("test.log"), sep="\n")
If you have access to a command line, you might prefer running your script from the command line with R CMD BATCH.
== begin contents of script.R ==
a <- "a"
a
How come I do not see this in log
== end contents of script.R ==
At the command prompt ("$" in many un*x variants, "C:>" in windows), run
$ R CMD BATCH script.R &
The trailing "&" is optional and runs the command in the background.
The default name of the log file has "out" appended to the extension, i.e., script.Rout
== begin contents of script.Rout ==
R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: i686-pc-linux-gnu (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
> a <- "a"
> a
[1] "a"
> How come I do not see this in log
Error: unexpected symbol in "How come"
Execution halted
== end contents of script.Rout ==
If you are able to use the bash shell, you can consider simply running the R code from within a bash script and piping the stdout and stderr streams to a file. Here is an example using a heredoc:
File: test.sh
#!/bin/bash
# this is a bash script
echo "Hello World, this is bash"
test1=$(echo "This is a test")
echo "Here is some R code:"
Rscript --slave --no-save --no-restore - "$test1" <<EOF
## R code
cat("\nHello World, this is R\n")
args <- commandArgs(TRUE)
bash_message<-args[1]
cat("\nThis is a message from bash:\n")
cat("\n",paste0(bash_message),"\n")
EOF
# end of script
Then when you run the script with both stderr and stdout piped to a log file:
$ chmod +x test.sh
$ ./test.sh
$ ./test.sh &>test.log
$ cat test.log
Hello World, this is bash
Here is some R code:
Hello World, this is R
This is a message from bash:
This is a test
Other things to look at for this would be to try simply pipping the stdout and stderr right from the R heredoc into a log file; I haven't tried this yet but it will probably work too.
You can't. At most you can save output with sink and input with savehistory separately. Or use external tool like script, screen or tmux.
Run R in emacs with ESS (Emacs Speaks Statistics) r-mode. I have one window open with my script and R code. Another has R running. Code is sent from the syntax window and evaluated. Commands, output, errors, and warnings all appear in the running R window session. At the end of some work period, I save all the output to a file. My own naming system is *.R for scripts and *.Rout for save output files.
Here's a screenshot with an example.
You can print to file and at the same time see progress having (or not) screen, while running a R script.
When not using screen, use R CMD BATCH yourscript.R & and step 4.
When using screen, in a terminal, start screen
screen
run your R script
R CMD BATCH yourscript.R
Go to another screen pressing CtrlA, then c
look at your output with (real-time):
tail -f yourscript.Rout
Switch among screens with CtrlA then n
To save text from the console: run the analysis and then choose (Windows) "File>Save to File".
Set your Rgui preferences for a large number of lines, then timestamp and save as file at suitable intervals.
If you want to get error messages saved in a file
zz <- file("Errors.txt", open="wt")
sink(zz, type="message")
the output will be:
Error in print(errr) : object 'errr' not found
Execution halted
This output will be saved in a file named Errors.txt
In case, you want printed values of console to a file you can use 'split' argument:
zz <- file("console.txt", open="wt")
sink(zz, split=TRUE)
print("cool")
print(errr)
output will be:
[1] "cool"
in console.txt file. So all your console output will be printed in a file named console.txt
This may not work for your needs, but one solution might be to run your code from within an Rmarkdown file. You could write both the code and console output to HTML/PDF/Word.
Related
I'm trying to find a way to write some content to a file using Jenkins Groovy Script-Console.
The use-case: Our CI manages some state-machine using a volume shared between all the nodes (which is in turn mapped to EFS). However - following the discovery of a bug in our CI groovy shared libs I found that some state files gone corrupt, and needed to write to them the corrected values, together with fixing the bug.
I could do that using ssh connection, however, as we're in process of abstracting out the workers we're trying to back off from that and manage ourselves only from the script-console and/or ci jobs.
I tried all these forms, all of which failed:
"echo 'the text' > /mnt/efs-ci-state/path/to/the-state-file.txt".execute().text
"""
cat <<<EOF > /mnt/efs-ci-state/path/to/the-state-file.txt
the text
EOF
""".execute().text
"bash -c 'echo the text > /mnt/efs-ci-state/path/to/the-state-file.txt'".execute().text
"echo 'the text' | tee /mnt/efs-ci-state/path/to/the-state-file.txt"
Can anybody show me the way to do that?
I'd also appreciate an explanation why the forms above won't work and/or a hint on how to execute commands that include piping and/or stdio directing from that script console.
Thanks :)
["bash", "echo the text > /mnt/efs-ci-state/path/to/the-state-file.txt"].execute().text
or use plain groovy:
new File('/mnt/efs-ci-state/path/to/the-state-file.txt').text = "echo the text"
why not working:
options 1, 2, 4 : echo and piping is a feature of shell/bash - it will not work without bash
option 3 you have c echo and c is not a valid command
use array to execute complex commands and to separate bash from main part
i suggest you to use this kind of code if you want to capture and validate stderr
["bash", 'echo my text > /222/12345.txt'].execute().with{proc->
def out=new StringBuilder(), err=new StringBuilder()
proc.waitForProcessOutput(out, err)
assert !err.toString().trim()
return out.toString()
}
So I am trying to write my first shell script that can automatically run some C codes for me. I read some materials online and here is my short shell script:
#!/bin/sh
# script for grading assignment 3
echo -n "Enter the student's index >"
read index
echo "You entered: $index"
#### Functions
function question_one
{
gcc -pthread -o $index.1 $index.1.c
taskset -c 1 ./$index.1 5 5
}
#### Main
$(question_one)
As you can see, the shell script is quite simple and what it does is also quite easy to understand. First compile a C source file named like 1.1.c, 2.1.c or 3.1.c and then run the output file with just one single CPU.
When I run this script, looks like it can successfully compile the file but unable to run the output file correctly. The error message is "assignment_three_grading: line 18: Thread: command not found". However, if I type in the commands manually by myself, everything is fine.
$(question_one)
Change this to simply:
question_one
To invoke a function you just name it as if it were a regular command. Using $(...) captures its output and tries to execute that output as another command name: definitely not what you want here.
I'm using lldb inside Xcode, and one of my variables contains a huge chunk of JSON data. Using po myVar isn't much helpful to analyse this data, as it will output in the tiny Xcode debug console.
Is there a way to redirect lldb output to a file ?
I saw here that such a feature seems to be available on gdb as :
(gdb) set logging on
(gdb) set logging file /tmp/mem.txt
(gdb) x/512bx 0xbffff3c0
(gdb) set logging off
and is "translated" in lldb as :
(lldb) memory read --outfile /tmp/mem.txt --count 512 0xbffff3c0
(lldb) me r -o/tmp/mem.txt -c512 0xbffff3c0
(lldb) x/512bx -o/tmp/mem.txt 0xbffff3c0
However, the memory read command will not help in my case, and apparently, --outfile is not available for the print command.
You can use a Python script to do so (and much more), as explained here:
LLDB Python scripting in Xcode
Create a file named po.py in a directory of your choice (for example "~/.lldb"):
import lldb
def print_to_file(debugger, command, result, dict):
#Change the output file to a path/name of your choice
f=open("/Users/user/temp.txt","w")
debugger.SetOutputFileHandle(f,True);
#Change command to the command you want the output of
command = "po self"
debugger.HandleCommand(command)
def __lldb_init_module (debugger, dict):
debugger.HandleCommand('command script add -f po.print_to_file print_to_file ')
Then in lldb write:
command script import ~/.lldb/po.py
print_to_file
I found session save <filename> to be a much better, easier option than those listed here. It's not quite the same as you can't use it (to my knowledge selectively) but for generating logs, it's quite handy.
Here is a slight modification incorporating some of the comments from above:
def toFile(debugger, command, result, dict):
f=open("/Users/user/temp.txt","w")
debugger.SetOutputFileHandle(f,True);
debugger.HandleCommand(command)
f.close()
debugger.SetOutputFileHandle(sys.stdout, True)
This allows the command to be supplied as an argument, and reverts the output file handle to stdout after the command is run.
Assuming that you have a variable named jsonData (which has a Data type) you can save it to a file with this command:
expr jsonData.write(to: URL(fileURLWithPath: "/tmp/datadump.bin"))
Alternatively instead of above command you could dump memory used by this variable to a file as in the example below:
(lldb) po jsonData
▿ Optional<Data>
▿ some : 32547 bytes
- count : 32547
▿ pointer : 0x00007fe8b69bb410
- pointerValue : 140637472797712
(lldb) memory read --force --binary --outfile /tmp/datadump.bin --count 32547 0x00007fe8b69bb410
32547 bytes written to '/tmp/datadump.bin'
I have a batch file which calls a java program.
The output is redirected to a log file in the same directory.
However the log file is replaced everytime the batch file is run...
I would like to keep the old outputs in the log file and always append the new output to the log file.
Instead of using ">" to redirect like this:
java Foo > log
use ">>" to append normal "stdout" output to a new or existing file:
java Foo >> log
However, if you also want to capture "stderr" errors (such as why the Java program couldn't be started), you should also use the "2>&1" tag which redirects "stderr" (the "2") to "stdout" (the "1"). For example:
java Foo >> log 2>&1
This is not an answer to your original question: "Appending output of a Batch file To log file?"
For reference, it's an answer to your followup question: "What lines should i add to my batch file which will make it execute after every 30mins?"
(But I would take Jon Skeet's advice: "You probably shouldn't do that in your batch file - instead, use Task Scheduler.")
Timeout:
timeout command 1
timeout command 2
Example (1 second):
TIMEOUT /T 1000 /NOBREAK
Sleep:
sleep command (if sleep.exe is installed)
Example (1 second):
sleep -m 1000
Alternative methods:
Sleeping in a batch file
batch script, put to sleep until certain time
Here's an answer to your 2nd followup question: "Along with the Timestamp?"
Create a date and time stamp in your batch files
Example:
echo *** Date: %DATE:/=-% and Time:%TIME::=-% *** >> output.log
Use log4j in your java program instead. Then you can output to multiple media, create rolling logs, etc. and include timestamps, class names and line numbers.
It's also possible to use java Foo | tee -a some.log. it just prints to stdout as well. Like:
user at Computer in ~
$ echo "hi" | tee -a foo.txt
hi
user at Computer in ~
$ echo "hello" | tee -a foo.txt
hello
user at Computer in ~
$ cat foo.txt
hi
hello
I just got knocked down after our server has been updated from Debian 4 to 5.
We switched to UTF-8 environment and now we have problems getting the text printed correctly on the browser, because all files are in non-utf8 encodings like iso-8859-1, ascii, etc.
I tried many different scripts.
The first one I tried is "iconv". That one doesn't work, it changes the content, but the file's encoding is still non-utf8.
Same problem with enca, encamv, convmv and some other tools I installed via apt-get.
Then I found a python code, which uses chardet Universal Detector module, to detect encoding of a file (which works fine), but using the unicode class or the codec class to save it as utf-8 doesn't work, without any errors.
The only way I found to get the file and its content converted to UTF-8, is vi.
These are the steps I do for one file:
vi filename.php
:set bomb
:set fileencoding=utf-8
:wq
That's it. That one works perfect. But how can I get this running via a script?
I would like to write a script (Linux shell) which traverses a directory taking all php files, then converting them using vi with the commands above.
As I need to start the vi app, I do not know how to do something like this:
"vi --run-command=':set bomb, :set fileencoding=utf-8' filename.php"
Hope someone can help me.
This is the simplest way I know of to do this easily from the command line:
vim +"argdo se bomb | se fileencoding=utf-8 | w" $(find . -type f -name *.php)
Or better yet if the number of files is expected to be pretty large:
find . -type f -name *.php | xargs vim +"argdo se bomb | se fileencoding=utf-8 | w"
You could put your commands in a file, let's call it script.vim:
set bomb
set fileencoding=utf-8
wq
Then you invoke Vim with the -S (source) option to execute the script on the file you wish to fix. To do this on a bunch of files you could do
find . -type f -name "*.php" -exec vim -S script.vim {} \;
You could also put the Vim commands on the command line using the + option, but I think it may be more readable like this.
Note: I have not tested this.
You may actually want set nobomb (BOM = byte order mark), especially in the [not windows] world.
e.g., I had a script that didn't work as there was a byte order mark at the start. It isn't usually displayed in editors (even with set list in vi), or on the console, so its difficult to spot.
The file looked like this
#!/usr/bin/perl
...
But trying to run it, I get
./filename
./filename: line 1: #!/usr/bin/perl: No such file or directory
Not displayed, but at the start of the file, is the 3 byte BOM. So, as far as linux is concerned, the file doesn't start with #!
The solution is
vi filename
:set nobomb
:set fileencoding=utf-8
:wq
This removes the BOM at the start of the file, making it correct utf8.
NB Windows uses the BOM to identify a text file as being utf8, rather than ANSI. Linux (and the official spec) doesn't.
The accepted answer will keep the last file open in Vim. This problem can be easily resolved using the -c option of Vim,
vim +"argdo set bomb | set fileencoding=utf-8 | w" -c ":q" file1.txt file2.txt
If you need only process one file, the following will also work,
vim -c ':set bomb' -c ':set fileencoding=utf-8' -c ':wq' file1.txt