makefile in ubuntu giving bash syntax error near unexpected token `( - linux

Question

I am trying to compile a program on ubuntu 12.04 64bit using make.While compiling i get an error
/bin/bash: -c: line 0: syntax error near unexpected token `(
This is after I changed the symlink of /bin/sh to /bin/bash instead of dash. (I did it because i had the same kind of error before and looking around the internet I found that the script may call bash functions which are not available in sh/dash.)
I also tried putting SHELL = /bin/bash at the top of my makefile but still no use...
Any help would be much appreciated.
edit
SHELL = /bin/bash
CC = gcc
CFLAGS= -std=gnu99 -L/ATLAS/lib/ubuntu12.04 -lflint -lgsl -lcblas -latlas -lm -lmpfr -lmpir -lrt -Wall -fopenmp
default: GPVSignature
GPVSignature: GPVSignature.o Keygeneration.o chol_parallel.o Sampling2.o sha1.o sha2.o timing.o
$(CC) $(CFLAGS) -o GPVSignature GPVSignature.o Keygeneration.o chol_parallel.o Sampling2.o sha1.o sha2.o timing.o
clean:
rm -f GPVSignature *.o
SSH_AGENT_PID=2065
GPG_AGENT_INFO=/tmp/keyring-alBJt6/gpg:0:1
TERM=xterm
SHELL=/bin/bash
XDG_SESSION_COOKIE=ff0e3de12be325b4ae6276d100000009-1353535027.801191-1696704263
WINDOWID=56623110
GNOME_KEYRING_CONTROL=/tmp/keyring-alBJt6
NO_PROXY=localhost,127.0.0.0/8
USER=salman
http_proxy=http:(---)
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40; 33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
SSH_AUTH_SOCK=/tmp/keyring-alBJt6/ssh
SESSION_MANAGER=local/ubuntu:#/tmp/.ICE-unix/2026,unix/ubuntu:/tmp/.ICE-unix/2026
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg
PATH=/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin: /bin:/usr/games
DESKTOP_SESSION=ubuntu
PWD=/home/salman/
GNOME_KEYRING_PID=2015
LANG=en_US.UTF-8
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
UBUNTU_MENUPROXY=libappmenu.so
COMPIZ_CONFIG_PROFILE=ubuntu
GDMSESSION=ubuntu
HOME=/home/salman
SHLVL=1
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
no_proxy=localhost,127.0.0.0/8
LOGNAME=salman
BUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-RUfHXImIYm,guid=c49ca476a7f4b008964105c90000004e
LESSOPEN=| /usr/bin/lesspipe %s
DISPLAY=:0
XDG_CURRENT_DESKTOP=Unity
LESSCLOSE=/usr/bin/lesspipe %s %s
COLORTERM=gnome-terminal
XAUTHORITY=/home/salman/.Xauthority
_=/usr/bin/env
OLDPWD=/home/salman/Desktop

Answer 1

How about this?:
SHELL:=/bin/bash
CC:=gcc
CFLAGS:=-std=gnu99 -L/ATLAS/lib/ubuntu12.04 -lflint -lgsl -lcblas -latlas -lm -lmpfr -lmpir -lrt -Wall -fopenmp
default: GPVSignature
GPVSignature: GPVSignature.c Keygeneration.c chol_parallel.c Sampling2.c sha1.c sha2.c timing.c
clean:
rm -f GPVSignature *.o
The indentation under the clean: line (before the rm) is a TAB character! This is important. My guess is that you don't have the indentation correct on the recipe lines (under GPVSignature: and under clean:). Also, you don't need to give an explicit recipe, because GNU make comes with a number of recipes of its own.
Note: I am assuming the file extensions are .c here, because it is customary and you use gcc, not g++. If that's not the case you need to introduce a pattern rule to tell GNU make how to create .o files from whatever extension you are using for your source files.
Even assuming your original recipe, I'd suggest the following more succinct line:
$(CC) $(CFLAGS) -o $# $^
... also indented by a single tab character (unless you tell GNU make to use a different character, which you obviously don't).
Two more things.
Is the Makefile/GNUmakefile a simple ASCII text file or a UTF-8 file with BOM? Execute file Makefile and post the output, please.
Check the following screenshots. This (second screenshot) is how it should look correctly indented with tabs in Vim (assuming you have the syntax file installed) ... specifically note the colors of the recipe for GPVSignature. The first screenshot is wrong, the second is
Other than that I am out of ideas. And there would have to be something you aren't mentioning.