Mount a CD Image on Harddisk

A copy of a CD containing e.g. installation software or a game (so called iso image) can be mounted directly from the harddrive. This might be useful to mimic a CD without inserting the CD into the (very slow and power consuming) CD/DVD-drive.

1. Create a mountpoint e.g. in the /media directory:
sudo mkdir /media/iso

2. Mount the image MyCDimage.iso as a CD:
sudo mount -t iso9660 -o loop MyCDimage.iso /media/iso

3. Display all filesystems to check its mounted:
df -h

In order to play e.g. Windows games with wine the mountpoint /media/iso has to be added as a drive under wine.
winecfg
choose the drive tab and add /media/iso

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Installing RODBC with Ubuntu/Debian amd64

Trying to install RODBC in Ubuntu with
install.packages("RODBC")
failed throwing an error message
ODBC headers sql.h and sqlext.h not found

A glance at the r-help showed that it had to do with something called unixODBC – an ODBC driver manager.

The package was installed, but not the development package and thus not the headers which R complained about.

Again a not-so-obvious-for-the-newbee-Linux-Unix-Shell-goblish thing. The fix is
sudo aptitude install unixodbc-dev

Listing Hardware Specs in the Shell

Just recently found a nice compilation of shell command, listing your computers specs in plain text:

List of hardware:
lspci

Linux Kernel configuration (which version of Linux are you using):
uname -a

Hardisk and memory available and used:
free -m

Very nice: Checking the buffered reading speed of your harddisk or whatever device attached:
sudo hdparm -t /dev/sda
/dev/sda is my harddisk in this example and produced 60Mb/s three times faster than my USB-disk /dev/sdb.

To find the names /dev/WhatName of the devices:
sudo fdisk -l

Checking the cache reading speed, which represents well more reading from RAM then from the specified device:
sudo hdparm -T /dev/sda

Checking the write speed (from Ubuntuforums)
dd count=1k bs=1M if=/dev/zero of=/media/HD2/test.img

.dmrc Beeing Ignored

After installing the Fluxbox desktop in addition to the default Xfce4 in Xubuntu a persistent error message started to show up:

User's $home/.dmrc file is being ignored. This prevents the default session and language from being saved. File should be owned by user and have 644 permission. User's $home directory must be owned by user and not writable by other user's.

It seems to be a bug in Ubuntu. It turned out that the same error message appeared on a Ubuntu Jaunty (Gnome) fresh install and on my Linux Mint 7 (based on Ubuntu Jaunty) fresh install. From time to time it shows up and I have not figured out how to (re-)produce it.

Anyway:
chmod 644 .dmrc
chmod o-w /home/USER

does the job, where USER has to be replaced by you username.

Editing Textfiles via One-line Scripts for Stream EDitor

Editing textfiles often requires repeating the same action in every line or every paragraph or maybe even every word. Examples are: Removing empty lines or inserting them, removing linebreaks or replacing words or expressions. SED, the Stream EDitor is a command line tool, which allows even complex replacements of text, renaming of files and much more with a single line of script.

Eric Pement has compiled an extensive repartoir of these one-line scripts for SED. I have taken a selection of version 5.5 of his compilation.

FILE SPACING:

# double space a file
sed G

# double space a file which already has blank lines in it. Output file
# should contain no more than one blank line between lines of text.
sed ‘/^$/d;G’

# triple space a file
sed ‘G;G’

# undo double-spacing (assumes even-numbered lines are always blank)
sed ‘n;d’

# insert a blank line above every line which matches “regex”
sed ‘/regex/{x;p;x;}’

# insert a blank line below every line which matches “regex”
sed ‘/regex/G’

# insert a blank line above and below every line which matches “regex”
sed ‘/regex/{x;p;x;G;}’

NUMBERING:

# number each line of a file (simple left alignment). Using a tab (see
# note on ‘\t’ at end of file) instead of space will preserve margins.
sed = filename | sed ‘N;s/\n/\t/’

# number each line of a file (number on left, right-aligned)
sed = filename | sed ‘N; s/^/ /; s/ *\(.\{6,\}\)\n/\1 /’

# number each line of file, but only print numbers if line is not blank
sed ‘/./=’ filename | sed ‘/./N; s/\n/ /’

# count lines (emulates “wc -l”)
sed -n ‘$=’

TEXT CONVERSION AND SUBSTITUTION:

# IN UNIX ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format.
sed ‘s/.$//’ # assumes that all lines end with CR/LF
sed ‘s/^M$//’ # in bash/tcsh, press Ctrl-V then Ctrl-M
sed ‘s/\x0D$//’ # works on ssed, gsed 3.02.80 or higher

# IN UNIX ENVIRONMENT: convert Unix newlines (LF) to DOS format.
sed “s/$/`echo -e \\\r`/” # command line under ksh
sed ‘s/$'”/`echo \\\r`/” # command line under bash
sed “s/$/`echo \\\r`/” # command line under zsh
sed ‘s/$/\r/’ # gsed 3.02.80 or higher

# IN DOS ENVIRONMENT: convert Unix newlines (LF) to DOS format.
sed “s/$//” # method 1
sed -n p # method 2

# IN DOS ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format.
# Can only be done with UnxUtils sed, version 4.0.7 or higher. The
# UnxUtils version can be identified by the custom “–text” switch
# which appears when you use the “–help” switch. Otherwise, changing
# DOS newlines to Unix newlines cannot be done with sed in a DOS
# environment. Use “tr” instead.
sed “s/\r//” infile >outfile # UnxUtils sed v4.0.7 or higher
tr -d \r outfile # GNU tr version 1.22 or higher

# delete leading whitespace (spaces, tabs) from front of each line
# aligns all text flush left
sed ‘s/^[ \t]*//’ # see note on ‘\t’ at end of file

# delete trailing whitespace (spaces, tabs) from end of each line
sed ‘s/[ \t]*$//’ # see note on ‘\t’ at end of file

# delete BOTH leading and trailing whitespace from each line
sed ‘s/^[ \t]*//;s/[ \t]*$//’

# insert 5 blank spaces at beginning of each line (make page offset)
sed ‘s/^/ /’

# align all text flush right on a 79-column width
sed -e :a -e ‘s/^.\{1,78\}$/ &/;ta’ # set at 78 plus 1 space

# center all text in the middle of 79-column width. In method 1,
# spaces at the beginning of the line are significant, and trailing
# spaces are appended at the end of the line. In method 2, spaces at
# the beginning of the line are discarded in centering the line, and
# no trailing spaces appear at the end of lines.
sed -e :a -e ‘s/^.\{1,77\}$/ & /;ta’ # method 1
sed -e :a -e ‘s/^.\{1,77\}$/ &/;ta’ -e ‘s/\( *\)\1/\1/’ # method 2

# substitute (find and replace) “foo” with “bar” on each line
sed ‘s/foo/bar/’ # replaces only 1st instance in a line
sed ‘s/foo/bar/4’ # replaces only 4th instance in a line
sed ‘s/foo/bar/g’ # replaces ALL instances in a line
sed ‘s/\(.*\)foo\(.*foo\)/\1bar\2/’ # replace the next-to-last case
sed ‘s/\(.*\)foo/\1bar/’ # replace only the last case

# substitute “foo” with “bar” ONLY for lines which contain “baz”
sed ‘/baz/s/foo/bar/g’

# substitute “foo” with “bar” EXCEPT for lines which contain “baz”
sed ‘/baz/!s/foo/bar/g’

# change “scarlet” or “ruby” or “puce” to “red”
sed ‘s/scarlet/red/g;s/ruby/red/g;s/puce/red/g’ # most seds
gsed ‘s/scarlet\|ruby\|puce/red/g’ # GNU sed only

# reverse order of lines (emulates “tac”)
# bug/feature in HHsed v1.5 causes blank lines to be deleted
sed ‘1!G;h;$!d’ # method 1
sed -n ‘1!G;h;$p’ # method 2

# reverse each character on the line (emulates “rev”)
sed ‘/\n/!G;s/\(.\)\(.*\n\)/&\2\1/;//D;s/.//’

# join pairs of lines side-by-side (like “paste”)
sed ‘$!N;s/\n/ /’

# if a line ends with a backslash, append the next line to it
sed -e :a -e ‘/\\$/N; s/\\\n//; ta’

# if a line begins with an equal sign, append it to the previous line
# and replace the “=” with a single space
sed -e :a -e ‘$!N;s/\n=/ /;ta’ -e ‘P;D’

# add commas to numeric strings, changing “1234567” to “1,234,567”
gsed ‘:a;s/\B[0-9]\{3\}\>/,&/;ta’ # GNU sed
sed -e :a -e ‘s/\(.*[0-9]\)\([0-9]\{3\}\)/\1,\2/;ta’ # other seds

# add commas to numbers with decimal points and minus signs (GNU sed)
gsed -r ‘:a;s/(^|[^0-9.])([0-9]+)([0-9]{3})/\1\2,\3/g;ta’

# add a blank line every 5 lines (after lines 5, 10, 15, 20, etc.)
gsed ‘0~5G’ # GNU sed only
sed ‘n;n;n;n;G;’ # other seds

SELECTIVE PRINTING OF CERTAIN LINES:

# print first 10 lines of file (emulates behavior of “head”)
sed 10q

# print first line of file (emulates “head -1”)
sed q

# print the last 10 lines of a file (emulates “tail”)
sed -e :a -e ‘$q;N;11,$D;ba’

# print the last 2 lines of a file (emulates “tail -2”)
sed ‘$!N;$!D’

# print the last line of a file (emulates “tail -1”)
sed ‘$!d’ # method 1
sed -n ‘$p’ # method 2

# print the next-to-the-last line of a file
sed -e ‘$!{h;d;}’ -e x # for 1-line files, print blank line
sed -e ‘1{$q;}’ -e ‘$!{h;d;}’ -e x # for 1-line files, print the line
sed -e ‘1{$d;}’ -e ‘$!{h;d;}’ -e x # for 1-line files, print nothing

# print only lines which match regular expression (emulates “grep”)
sed -n ‘/regexp/p’ # method 1
sed ‘/regexp/!d’ # method 2

# print only lines which do NOT match regexp (emulates “grep -v”)
sed -n ‘/regexp/!p’ # method 1, corresponds to above
sed ‘/regexp/d’ # method 2, simpler syntax

# print the line immediately before a regexp, but not the line
# containing the regexp
sed -n ‘/regexp/{g;1!p;};h’

# print the line immediately after a regexp, but not the line
# containing the regexp
sed -n ‘/regexp/{n;p;}’

# print 1 line of context before and after regexp, with line number
# indicating where the regexp occurred (similar to “grep -A1 -B1”)
sed -n -e ‘/regexp/{=;x;1!p;g;$!N;p;D;}’ -e h

# grep for AAA and BBB and CCC (in any order)
sed ‘/AAA/!d; /BBB/!d; /CCC/!d’

# grep for AAA and BBB and CCC (in that order)
sed ‘/AAA.*BBB.*CCC/!d’

# grep for AAA or BBB or CCC (emulates “egrep”)
sed -e ‘/AAA/b’ -e ‘/BBB/b’ -e ‘/CCC/b’ -e d # most seds
gsed ‘/AAA\|BBB\|CCC/!d’ # GNU sed only

# print paragraph if it contains AAA (blank lines separate paragraphs)
# HHsed v1.5 must insert a ‘G;’ after ‘x;’ in the next 3 scripts below
sed -e ‘/./{H;$!d;}’ -e ‘x;/AAA/!d;’

# print paragraph if it contains AAA and BBB and CCC (in any order)
sed -e ‘/./{H;$!d;}’ -e ‘x;/AAA/!d;/BBB/!d;/CCC/!d’

# print paragraph if it contains AAA or BBB or CCC
sed -e ‘/./{H;$!d;}’ -e ‘x;/AAA/b’ -e ‘/BBB/b’ -e ‘/CCC/b’ -e d
gsed ‘/./{H;$!d;};x;/AAA\|BBB\|CCC/b;d’ # GNU sed only

# print only lines of 65 characters or longer
sed -n ‘/^.\{65\}/p’

# print only lines of less than 65 characters
sed -n ‘/^.\{65\}/!p’ # method 1, corresponds to above
sed ‘/^.\{65\}/d’ # method 2, simpler syntax

# print section of file from regular expression to end of file
sed -n ‘/regexp/,$p’

# print section of file based on line numbers (lines 8-12, inclusive)
sed -n ‘8,12p’ # method 1
sed ‘8,12!d’ # method 2

# print line number 52
sed -n ’52p’ # method 1
sed ’52!d’ # method 2
sed ’52q;d’ # method 3, efficient on large files

# beginning at line 3, print every 7th line
gsed -n ‘3~7p’ # GNU sed only
sed -n ‘3,${p;n;n;n;n;n;n;}’ # other seds

# print section of file between two regular expressions (inclusive)
sed -n ‘/Iowa/,/Montana/p’ # case sensitive

SELECTIVE DELETION OF CERTAIN LINES:

# print all of file EXCEPT section between 2 regular expressions
sed ‘/Iowa/,/Montana/d’

# delete duplicate, consecutive lines from a file (emulates “uniq”).
# First line in a set of duplicate lines is kept, rest are deleted.
sed ‘$!N; /^\(.*\)\n\1$/!P; D’

# delete duplicate, nonconsecutive lines from a file. Beware not to
# overflow the buffer size of the hold space, or else use GNU sed.
sed -n ‘G; s/\n/&&/; /^\([ -~]*\n\).*\n\1/d; s/\n//; h; P’

# delete all lines except duplicate lines (emulates “uniq -d”).
sed ‘$!N; s/^\(.*\)\n\1$/\1/; t; D’

# delete the first 10 lines of a file
sed ‘1,10d’

# delete the last line of a file
sed ‘$d’

# delete the last 2 lines of a file
sed ‘N;$!P;$!D;$d’

# delete the last 10 lines of a file
sed -e :a -e ‘$d;N;2,10ba’ -e ‘P;D’ # method 1
sed -n -e :a -e ‘1,10!{P;N;D;};N;ba’ # method 2

# delete every 8th line
gsed ‘0~8d’ # GNU sed only
sed ‘n;n;n;n;n;n;n;d;’ # other seds

# delete lines matching pattern
sed ‘/pattern/d’

# delete ALL blank lines from a file (same as “grep ‘.’ “)
sed ‘/^$/d’ # method 1
sed ‘/./!d’ # method 2

# delete all CONSECUTIVE blank lines from file except the first; also
# deletes all blank lines from top and end of file (emulates “cat -s”)
sed ‘/./,/^$/!d’ # method 1, allows 0 blanks at top, 1 at EOF
sed ‘/^$/N;/\n$/D’ # method 2, allows 1 blank at top, 0 at EOF

# delete all CONSECUTIVE blank lines from file except the first 2:
sed ‘/^$/N;/\n$/N;//D’

# delete all leading blank lines at top of file
sed ‘/./,$!d’

# delete all trailing blank lines at end of file
sed -e :a -e ‘/^\n*$/{$d;N;ba’ -e ‘}’ # works on all seds
sed -e :a -e ‘/^\n*$/N;/\n$/ba’ # ditto, except for gsed 3.02.*

# delete the last line of each paragraph
sed -n ‘/^$/{p;h;};/./{x;/./p;}’

SPECIAL APPLICATIONS:

# remove nroff overstrikes (char, backspace) from man pages. The ‘echo’
# command may need an -e switch if you use Unix System V or bash shell.
sed “s/.`echo \\\b`//g” # double quotes required for Unix environment
sed ‘s/.^H//g’ # in bash/tcsh, press Ctrl-V and then Ctrl-H
sed ‘s/.\x08//g’ # hex expression for sed 1.5, GNU sed, ssed

# get Usenet/e-mail message header
sed ‘/^$/q’ # deletes everything after first blank line

# get Usenet/e-mail message body
sed ‘1,/^$/d’ # deletes everything up to first blank line

# get Subject header, but remove initial “Subject: ” portion
sed ‘/^Subject: */!d; s///;q’

# get return address header
sed ‘/^Reply-To:/q; /^From:/h; /./d;g;q’

# parse out the address proper. Pulls out the e-mail address by itself
# from the 1-line return address header (see preceding script)
sed ‘s/ *(.*)//; s/>.*//; s/.*[: /’

# delete leading angle bracket & space from each line (unquote a message)
sed ‘s/^> //’

# remove most HTML tags (accommodates multiple-line tags)
sed -e :a -e ‘s/]*>//g;/zipup.bat
dir /b *.txt | sed “s/^\(.*\)\.TXT/pkzip -mo \1 \1.TXT/” >>zipup.bat

OPTIMIZING FOR SPEED: If execution speed needs to be increased (due to
large input files or slow processors or hard disks), substitution will
be executed more quickly if the “find” expression is specified before
giving the “s/…/…/” instruction. Thus:

sed ‘s/foo/bar/g’ filename # standard replace command
sed ‘/foo/ s/foo/bar/g’ filename # executes more quickly
sed ‘/foo/ s//bar/g’ filename # shorthand sed syntax

On line selection or deletion in which you only need to output lines
from the first part of the file, a “quit” command (q) in the script
will drastically reduce processing time for large files. Thus:

sed -n ‘45,50p’ filename # print line nos. 45-50 of a file
sed -n ’51q;45,50p’ filename # same, but executes much faster

Command line instructions to create a database in MySQL

Still working on a way to port a sloppy Access database to MySQL. In the end it would be lovely to have a shell script doing all steps in a row:

  1. Extract the tables of the database as .csv
  2. Create a new (empty) MySQL database
  3. Create all tables in the new MySQL db
  4. Import the .csvs into those tables

One of the necessary steps is to create a new MySQL database:

$ mysql -u ''adminusername'' -p
mysql> CREATE DATABASE ''databasename'';
mysql> GRANT ALL PRIVILEGES ON ''databasename''.* TO "''username''"@"''hostname''" IDENTIFIED BY "''password''";
mysql> FLUSH PRIVILEGES;
mysql> EXIT

I just collected the code, did not try it out. Just not to forget….

Accessing an Access Database with mdbtools

Basically, what I wanted to do is accessing an MS Access database directly from R. This is probably possible and subject of another post.

Halfway from MS Access to R is mdbtools which can be added to Ubuntu in a terminal with:
sudo aptitude install mdbtools

MDB Tools comes with a set of command line utilties that allow mdb files to be used in shell scripting, extraction to another database, and similar functions. Each program is documented in its man page.

In order to extract the tables of the database into colon separated value (.csv) format create a file, say mdb-explode with the following content:

#! /bin/bash
mkdir $(echo $1|awk -F "." {'print $1'}).csvs
for i in $(mdb-tables $1); do
echo $i
mdb-export $1 $i > $(echo $1|awk -F "." {'print $1'}).csvs/$i.csv
done

Save the the file, open a terminal and make it executable:
chmod +x mdb-explode

If your MS Access database file (.mdb) is in the same directory you would
./mdb-explode YourDatabaseFile.mdb
and all tables of the database end up in a folder called YourDatabaseFile.csvs as .csv files which can be accessed by R via the read.table() function.

The idea is posted on Ubuntuforums by Skrynesaver but the script posted has some typos, which are corrected above. The script posted here worked with Ubuntu 9.04, mdbtools 0.5.99 and an Access 2003 database file.