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@ -163,9 +163,18 @@ the script in a directory that can be read from ~$PATH~
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*** Option c: run from graphical interface
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** Run R scripts
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Write the script and save it. Then go to the directory where the script
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was saved and run this code from terminal
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#+begin_src bash
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Rscript script.R
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#+end_src
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* Manuals
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Use the command ~man~ or ~info~ followed by the name of the function or program
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To explore the manuals use the command ~man~ or ~info~ followed by the name of the function or program
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#+begin_src bash
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man
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@ -175,11 +184,15 @@ man
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| What manual page do you want? |
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| For example, try 'man man'. |
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Search for information about the manual interface within ~man~
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: man man
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Description of the system hierarchy
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: man hier
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Showing only the first four lines
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Showing only the first four lines of "info" interface
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#+begin_src bash
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info | head -4
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@ -191,8 +204,18 @@ info | head -4
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| This | is | the | Info | main | menu | (aka | directory | node). | | | |
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| A | few | useful | Info | commands: | | | | | | | |
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Search for ~info~ page about Bash shell features
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: info bash
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The manuals can also be accessed from emacs using "M-x" (using the "meta" key or CTRL + x)
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: M-x info
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: M-x man
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: M-x woman
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* Show command history
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: history
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@ -216,7 +239,7 @@ Apertium can be used in the command line
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: echo Hola | apertium spa-eng
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: echo Hello | apertium eng-spa
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"|" pipe lets the input to be passed to apertium
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The pipe operator "~|~" is used to pass the input to apertium
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* Files and directories
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@ -230,6 +253,92 @@ Create a file redirecting the shell output using "~>~" operator
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: echo I will put this text wthin a file > file2.txt
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** Redirect input, output and standard error
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Everything in GNU systems is a file. The keyboard and the terminal are also a file.
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The keyboard is used for input and the terminal is used by commands as output.
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The files can be found in directory "fd", which stands for file descriptor)
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#+begin_src bash
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cd /dev/fd/
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ls -l
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#+end_src
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#+RESULTS:
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| total | 0 | | | | | | | | | |
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| lr-x------ | 1 | user | user | 64 | dec | 15 | 10:31 | 0 | -> | /tmp/babel-yl1RTd/ob-input-izpXuk |
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| l-wx------ | 1 | user | user | 64 | dec | 15 | 10:31 | 1 | -> | pipe:[42063] |
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| lr-x------ | 1 | user | user | 64 | dec | 15 | 10:31 | 17 | -> | /dev/pts/0 |
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| l-wx------ | 1 | user | user | 64 | dec | 15 | 10:31 | 2 | -> | /tmp/emacsA1M18o |
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* standard input stream is bound to /dev/fd/0
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* standard output (stout) stream is bound to /dev/fd/1
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* standard errror (stderr) stream is bound to /dev/fd/2
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During interaction a terminal gets written to stdin (dev/fd/0), which
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a command read. The command then do an action and writes the output
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(stout or stderr) where it will read by the terminal and is displayed
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to the user.
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To redirect use the operator `>` as follows:
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* `command > file_to_redirect`
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The operator `>` redirects stout, i.e., is the same that 1>. This code
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creates a new file with the list of files present in the actual directory:
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#+begin_src bash
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ls -l > file_redirect.txt
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cat file_redirect.txt
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#+end_src
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#+RESULTS:
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| total | 32 | | | | | | | |
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| -rw-r--r-- | 1 | user | user | 15782 | dec | 15 | 10:49 | bash_tutorial.org |
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| -rw-r--r-- | 1 | user | user | 0 | dec | 15 | 10:49 | file_redirect.txt |
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| -rw-r--r-- | 1 | user | user | 11895 | dec | 9 | 17:44 | markdown.md |
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| -rw-r--r-- | 1 | user | user | 121 | dec | 9 | 17:17 | README.org |
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Use "2>&1" to redirect stderr with the stout. Using an arbitrary word and redirect it
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to the file should print a warning message that is redirected to the file:
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#+begin_src bash
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ls -l > file_redirect.txt
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paco >> file_redirect.txt 2>&1
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cat file_redirect.txt
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#+end_src
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#+RESULTS:
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| total | 32 | | | | | | | |
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| -rw-r--r-- | 1 | user | user | 15995 | dec | 15 | 12:39 | bash_tutorial.org |
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| -rw-r--r-- | 1 | user | user | 0 | dec | 15 | 13:41 | file_redirect.txt |
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| -rw-r--r-- | 1 | user | user | 11895 | dec | 9 | 17:44 | markdown.md |
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| -rw-r--r-- | 1 | user | user | 121 | dec | 9 | 17:17 | README.org |
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| bash: | line | 2: | paco: | command | not | found | | |
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Use the "<" operator to pass commands to the file:
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#+begin_src bash
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ls -l > file_redirect.txt
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paco >> file_redirect.txt 2>&1
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sort < file_redirect.txt
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cat file_redirect.txt
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#+end_src
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#+RESULTS:
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| bash: | line | 2: | paco: | command | not | found | | |
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| -rw-r--r-- | 1 | user | user | 0 | dec | 15 | 13:44 | file_redirect.txt |
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| -rw-r--r-- | 1 | user | user | 121 | dec | 9 | 17:17 | README.org |
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| -rw-r--r-- | 1 | user | user | 16501 | dec | 15 | 13:41 | bash_tutorial.org |
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| total | 24 | | | | | | | |
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| total | 24 | | | | | | | |
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| -rw-r--r-- | 1 | user | user | 16501 | dec | 15 | 13:41 | bash_tutorial.org |
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| -rw-r--r-- | 1 | user | user | 0 | dec | 15 | 13:44 | file_redirect.txt |
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| -rw-r--r-- | 1 | user | user | 121 | dec | 9 | 17:17 | README.org |
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| bash: | line | 2: | paco: | command | not | found | | |
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** List files
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Use ~ls~ in the directory you want to explore
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@ -277,11 +386,17 @@ Create directory
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: mkdir new_dir
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Removes directory
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Remove (unlink) a directory
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Some arguments:
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* -r: recursively unlink
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* -v: verbose
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* -f: force
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: rm -r new_dir
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Removes a file
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Remove a file
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: rm file.txt
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@ -368,7 +483,7 @@ In the example a file "foo" is converted from ~odt~ to ~org~
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Convert odt file "tcl_online3.odt" to pdf
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: $ libreoffice --headless --convert-to pdf tcl_online3.odt
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: libreoffice --headless --convert-to pdf tcl_online3.odt
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** Using 'sed' to substitute text
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@ -516,11 +631,11 @@ Showing the first two entries
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Back up of "home"
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- c = create file
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- v = verbose
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- f = write to a file/device
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- z = compress the file (gzip) "tar.bz"
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- j = compress the file (bzip2)
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* c = create file
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* v = verbose
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* f = write to a file/device
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* z = compress the file (gzip) "tar.bz"
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* j = compress the file (bzip2)
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: tar -czvf /tmp/home.tar.gz /home
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@ -537,7 +652,68 @@ Showing the first two entries
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** Searching
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Print lines that match patterns
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*** Search for files
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'find' can be used with multiple arguments such as:
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* -name: search for name
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* -iname: search for case-insensitive name
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* -type: type of file
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* f = file
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* d = directory
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Search within all the directory and subdirectories by name
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#+begin_src bash
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find ./ -name "gitea*"
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#+end_src
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#+RESULTS:
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./imagens/gitea-sm.png
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Search for all the files ending in '.png'
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#+begin_src bash
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find ./ -name "*.png"
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#+end_src
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#+RESULTS:
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./imagens/gitea-sm.png
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./files/plot.png
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Search for empty files in 'home'
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#+begin_src bash
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find /home -type f -empty
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#+end_src
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'find' can also be used with grep to match patterns:
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#+begin_src bash
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cd ~/Documentos/dat/intro_r/answers
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find . | grep -E '.js|.png'
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#+end_src
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#+RESULTS:
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| ./plot.png |
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| ./vizjs.js |
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| ./Rplot.png |
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| ./bipartiteD3Script.js |
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| ./demo1.js |
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To find file with different name patters, 'find' can also be used as follows:
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#+begin_src bash
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find . -type f \( -name "*.org" -o -name "*.md" \)
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#+end_src
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#+RESULTS:
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| ./README.org |
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| ./bash_tutorial.org |
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*** Matching patterns
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Print lines within files that match patterns
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: grep
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@ -550,6 +726,31 @@ grep 'root' /etc/passwd
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#+RESULTS:
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: root:x:0:0::/root:/bin/bash
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Additional arguments can be used with ~grep~:
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* r: recursive search (within directories)
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* n: print line number
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* i: case-insensitive search
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* '*' Wildcards to search in all the directories
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Search within files in the actual directory with wildcards
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#+begin_src bash
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grep -rni IFELSE *
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#+end_src
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#+RESULTS:
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|answers/repl_values.R:137: mutate(Status = ifelse(Status == "almost peak" &|
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|answers/categ_colum.R:40:df$lead_likely <- ifelse(grepl("UNCOVERED CURB | SERVICE", df$remarks), "non-lead", "unknown")|
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|docs/vectorization.org:354:(counting number of repeated value), and =ifelse= (vectorized if...else|
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'grep' can be used also to search for files in directories as shown in the anterior
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example using grep with extended regular expressions ("-E") and 'find'
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: find . | grep -E '.js|.png'
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In this example, 'find' will be passed to 'grep' and any pattern matching
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will be printed
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** Download files
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This code download the file and the argument ~-O~ is to rename the file
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@ -557,6 +758,7 @@ This code download the file and the argument ~-O~ is to rename the file
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#+begin_example
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wget https://filetodownload.org -O new_file
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#+end_example
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* Devices
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- mount /what /where
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