There was a space, I fixed that and it started compiling.
However it got to the same point and stopped with the following output:
# Copy all source executables and configuration files to their location
cp -f
/usr/local/src/TPP-4.6.2/src/../build/Ubuntu-x86_64/ASAPRatioPeptideParser
It looks to me like the problem is arising in from this piece of code in
the Makefile:
install-linux-xml:
# Create Directories
mkdir -p ${TPP_ROOT}
mkdir -p ${BIN_DIR}
mkdir -p ${CGI_DIR}
mkdir -p ${SCHEMA_DIR}
mkdir -p ${HTML_DIR}js
This was the last bit of successsfully executed code
# Copy
Liam,
Try looking in the OBJ_ARCH directory and making sure things are built.
Besides that I can't be much more help at the moment as I'm heading out of
town. Hopefully someone else will have some good suggestions.
-Joe
On Thu, Apr 18, 2013 at 12:16 AM, Liam Bell bell.l...@gmail.com wrote:
Where would the OBJ_ARCH directory be or how can I find it?
On 18 April 2013 16:34, Joseph Slagel joseph.sla...@systemsbiology.orgwrote:
Liam,
Try looking in the OBJ_ARCH directory and making sure things are built.
Besides that I can't be much more help at the moment as I'm heading out of
Its typically one directory up, and then under the directory build, so
../build/. You can also add a simple test to the end of the Makefile to
see what its value is:
showarch:
echo $(OBJ_ARCH)
then run make showarch. Oh and its a tab character not spaces in front
of the word echo.
Is sudo make make install possibly equivalent to sudo make followed
by make install? If so, that explains the permissions issue with make
install. It's easy to test. Just do any of the following and see if the
copy permissions issue goes away
sudo make; sudo make install
or
sudo make
I went another route,
sudo -i
and then;
make make install
Ran without any issues...
IT's setup and I've followed the instructions from
herehttp://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3
for
setting up apache but now that does not seem to be
Just note that you link to setup instructions for TPP 4.5.2 but I'm
assuming you're installing the latest 4.6.2. version. If so, look at the
end of the README file for the mod_rewrite settings that you'll need to add
to your apache config (and anything else that might've changed).
On Thu, Apr
Yip, I was aware of the newer version being installed and adjusted
directory names, file names and paths accordingly...
On 18 April 2013 22:41, Jimmy Eng jke...@gmail.com wrote:
Just note that you link to setup instructions for TPP 4.5.2 but I'm
assuming you're installing the latest 4.6.2.
Hi guys,
Could you clarify for me if I need to add in SRC_ROOT=`pwd`/ install into
the makefile.incl or whether I need to execute the make make install
differently from the terminal?
Thanks,
Liam
On Tuesday, 24 April 2012 12:27:59 UTC+2, Chris wrote:
For anyone else with the same problem
Liam,
Typically make followed by make install should work. (This is pretty much
the same as running make make install). But we've seen now that for
some newer installations that it doesn't propertly locate the current
working directory. It could be a shell thing, or a Ubuntu version specific
Hi Joe,
So I took the second option of adjusting the the Makefile in the target
directory and adding in it's absolute path.
The line ended up looking like this:
SRC_ROOT= $(PWD)/usr/local/src/TPP-4.6.2/src/
From the same directory in the path above, I executed in a shell sudo make
make
Glad it worked. Just for the record you shouldn't have the $(PWD) in there
if you are setting it explicitly. That's the root of the problem -- its
blank so the actual path just turns into /usr/local/src/TPP-4.6.2/src/. If
it were to suddenly have a value again then your Makefile would break.
I spoke to soon,
It's made and compiled plenty but I got this error after a while:
echo JAVA_HOME not defined, skipping Java targets
JAVA_HOME not defined, skipping Java targets
make -C ../COVERAGE/
make[1]: Entering directory `/usr/local/src/TPP-4.6.2/COVERAGE'
mkdir -p Ubuntu-x86_64
g++
Having adjusted my makefile again so that the $(PWD) is removed and tried
building again I manage to get over the issue I highlighted below however
now I am left with:
JAVA_HOME not defined, skipping Java targets
make -C ../COVERAGE/
make[1]: Entering directory
It just means you don't have Java installed. In my hands on Ubuntu 11.x or
12.04 server the Java needs to be Sun Java not OpenJDK which is the default
for Ubuntu. I do not know why Sun Java is detected and not OpenJDK. Maybe
something isn't configured properly on my system. As far as I can
Sounds like you may not nave run the command as root.
Brian
Brian Hampton
Protein Analysis Lab
Center for Vascular and Inflammatory Diseases
University of Maryland School of Medicine
800 West Baltimore Street Rm 307
Baltimore MD 21201
V: 410-706-8207
F: 410-706-8234
On Wed, Apr 17, 2013 at
I already have Sun Java installed on this machine as I come across the same
issue for using IPA - in that it doesn't recognise OpenJDK for some reason.
However I am more concerned that the whole process quite at the point where
it needed to # Copy all source executables and configuration files to
Did you remove the ($PWD) from the top of your make file when you
explicitly defined the install directory? If not it looks like what Joe
warned about may have happened.
Just curious, if you type pwd at the command prompt does it return your
working directory? If so its odd that the the $PWD
So I went back to scratch and removed what I had installed/compiled.
I extracted the files again and then made the Makefile.config.incl file as
well as adjusted the Makefile so that SRC_ROOT =
/usr/local/src/TPP-4.6.2/src/ and then executed:
$ cd /usr/local/src/TPP-4.6.2/src/
$ sudo make make
Liam,
There won't happen to be a space after the /usr/local/src/TPP-4.6.2/src/
would there me?
-Joe
On Wed, Apr 17, 2013 at 3:22 PM, Liam Bell bell.l...@gmail.com wrote:
So I went back to scratch and removed what I had installed/compiled.
I extracted the files again and then made the
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