linse

Data for dot-bracket notation (a.k.a. Vienna notation)

> type Viennachar = Char 
> type RNAchar = Char 

Data for tree structure

> data Tree a = N a (Forest a) deriving (Show,Eq,Ord)
> type Forest a = [Tree a]

linse

The CLISP specialty is used when producing a png from the dot file in Chapter 7.

brew install graphviz

which dot -> /usr/local/bin/dot

(defun dot->png (fname thunk)

(with-open-file (standard-output

linse

mvn -X test -Dandroid.sdk.path="path/to/my/sdk"

Apache Maven 3.0.3 (r1075438; 2011-02-28 12:31:09-0500)
Maven home: /usr/share/maven
Java version: 1.6.0_29, vendor: Apple Inc.
Java home: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Default locale: en_US, platform encoding: MacRoman
OS name: "mac os x", version: "10.7.2", arch: "x86_64", family: "mac"
[INFO] Error stacktraces are turned on.
[DEBUG] Reading global settings from /usr/share/maven/conf/settings.xml

linse

The Unix time command

man time is a good start - on Linux you get the GNU time version.

Note: some shells (e.g.,bash(1)) have a built-in time command that provides less functionality than the command described here. To access the real command, you may need to specify its pathname (something like /usr/bin/time).

GNU time

A call of /usr/bin/time gives a lot of information:

/usr/bin/time ls > /dev/null

linse

The ``syntax error near unexpected token`` means a m4 macro (for me: PKG_CHECK_MODULES) could not be expanded.
 
This can be a problem of autotoos / aclocal on OSX using homebrew. The tool aclocal is very oldschool and uses m4 macros. These .m4 macros for aclocal are expected to be in ``/usr/share/aclocal``, but homebrew puts them in ``/usr/local/share/aclocal`` without telling aclocal so.

Solution is adding a line ``/usr/local/share/aclocal`` in a ``/usr/share/aclocal/dirlist`` file.

linse

instance Num a => Num [a] where               -- (1)

   (f:fs) + (g:gs) = f+g : fs+gs               -- (2)
   fs + [] = fs                                -- (3a)
   [] + gs = gs                                -- (3b)

   (f:fs) * (g:gs) = f*g : [f]*gs + fs*(g:gs)  -- (4)
   _ * _ = []                                  -- (5)

   abs           = undefined   -- I can't think of a sensible definition

linse

# http://www.sailmaker.co.uk/blog/2013/05/05/migrating-from-svn-to-git-preserving-branches-and-tags-3/

# svn 2 git transformation, with prefix to avoid ambiguity and no metadata to avoid ugly commit messages
git svn -A ../MC-Fold/authors-transform.txt clone --prefix=svn/ --no-metadata -s http://svn.bioinfo.iric.ca/MC-Fold/
cd MC-Fold/

# transform svn branches into local git branches
git branch -r
for branch in `git branch -r | grep -v "svn/tags/" | sed 's/svn\///'`; do 
  git branch $branch refs/remotes/svn/$branch; 

linse

-- this is very simple and also ambiguous, e.g. the open structure will be constructed multiple times

s :: Integer -> [String]
s 2 = [".."]
s 1 = ["."]
s n = (map inbrackets $ s (n-2)) ++ (map adddot $ s (n-1) ) ++ (concatMap branches (splits n))
      where
         inbrackets a = "("++a++")"
         adddot a = '.':a
         branches (a,b) = [a'++b' | a' <- s a, b' <- s b ]

linse

Keybase proof

I hereby claim:

• I am linse on github.
• I am linse (https://keybase.io/linse) on keybase.
• I have a public key whose fingerprint is 5148 4174 C54D A514 3342 77BA 2334 6873 8FF9 BABA

To claim this, I am signing this object:

linse

SUBDIRS = src doc whatever

.PHONY: all clean

all clean:
  for dir in $(SUBDIRS); do \
    $(MAKE) -C $$dir -f Makefile $@; \
  done