Tag: xcode

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CNYO Without The .quota – A Quick Fix And Diagnostic For A Pesky WordPress Hack

From The "Hopelessly Hacked Help" Department

Below is the process I went through to clean up a WordPress site injection into www.cnyo.org – an old astronomy club I directed and a site (now unused) that I still maintain/keep active because there's lots of (a) good information and (b) CNY-based astronomy history to be read. There are many, many files in a WordPress install that can suffer an attack of some kind, many, many ways for a hacker/bot to make such an attack happen, but only a few things everyone seems to recommend doing to try to make the problem go away. In my case, the problem with the website went away after simply renaming two folders, uploading new versions of those folders, and then using the success of that replacement step to find the exact files in the site that were causing me issues. Consider this post a "First Step" if you find yourself similarly inconvenienced.

Some Light Reading (Background)

The CNYO website had, up until quite recently, a bug in the main menu that I initially chalked up to a very old (and free) theme (Vortex) running up against recent updates to WordPress. The romantic perspective on the maintaining of the site mentioned above aside, the site is really only still up because it (a) costs me nothing and (b) is now hosted in a subfolder of this website, and the site only gets a few visits each day (even with the upcoming solar eclipse in Western New York, cnyo.org is crickets). I hadn't much bothered exploring the menu issue further. The specific issue is shown below for the front page of the website, with the "About" menu much larger vertically than all the other menu items and the sub-menu items inside of "About" equally expanded.

A bane of my existence for a while. If you visited the cnyo.org site in the last few years, you know.

Interestingly, this oddity started appearing in Firefox and then, after a year or more, began appearing in Chrome and Safari. Clicking on the About link produced the image at the link below, which was a full-blown insertion of unwanted content and a de-columning of the website (and, even worse, it shows two fewer people subscribed to the site!).

See: Link to a very long and unnecessary-to-render-here screencap of the old contaminated About page.

While making tweaks to the rochesterastronomy.org website and un-doing a menu expansion that shouldn't have been, I decided to check back on the CNYO site to see if I could play the same trick. And I couldn't. But, in exploring how to tailor the css in browser Developer Tools, I noticed a slew of embedded links and class="r67298bc6" calls that I had not previously for Klonopin/Clonazepam.

Enlightenment by way of Developer Tools in Chrome (Firefox, Safari, etc.)

Klonopin is "used to treat panic disorder (including agoraphobia) in adults." I am 100% for adults overcoming anxiety about being outdoors (because I do astronomy) or with groups (because being outside in the middle of nowhere while observing by yourself can get old when the first howls are heard). That said, advertise by injecting something into someone else's WordPress, please.

Files And Tools To Have On Hand

It's a short list, things you probably have on hand or quick access to anyway if you're maintaining your own website (self-hosting or, at least, self-sufficient on your hosting service), and things you should probably always have at-the-ready for when (not if) the situation calls for them.

  1. A local copy (on your computer) of the WordPress version your site is currently using. To be even more exhaustive, have copies of EVERYTHING installed on your site. Themes, plug-ins, custom css, media, etc.
  2. An FTP client of some kind (such as Filezilla)
  3. All the needed credentials to get into your site by (s)ftp
  4. A browser's Developer Tools to do that cursory inspection of whatever looks off (all modern browsers have this option, snoop around the Tools menu)
  5. Access to your site's database (likely phpmyadmin if you're running a WordPress site on a major hosting service)
  6. A tool for comparing the contents of folder A and folder B – this is how you'll find the difference in the content of the before/after files to see which file or files has/have been modified
  7. stackoverflow open. This link, this link, and this link were early first reads on my path (the third link was insightful, but it turns out my problem was in a WordPress core folder itself).

Step 1 – Replace WordPress Files (Carefully!)

A quick check that might save you several hours. This assumes you've done nothing to the contents of wp-admin and wp-includes, which is a pretty good assumption unless you dabble in .php files. All of your themes, plugins, and uploads are in wp-content.

My working FileZilla window, with renamed folders on the right (hosting company) and local folders (with fresh WordPress folders) on the left.
  1. Uncompress your local copy of WordPress to have all of the core files/folders accessible for uploading
  2. Log out of your WordPress site if you're logged in (you probably don't have to do this)
  3. Get into your site account's directory with your (s)ftp client
  4. Rename wp-admin to wp-admin-old and wp-includes to wp-includes-old
  5. Upload the local WordPress copy's wp-admin and wp-includes
  6. When done, hit RELOAD on your problematic site.

For www.cnyo.org, my problem went away completely.

Step 2 – If Needed, Replace More WordPress Files (Very Carefully!)

My next step would have been to VERY CAREFULLY inspect and/or replace the .php files in the main directory (in the image above, index.php and downward, not touching .htaccess or .user.ini until a "Step 2b" when I found past versions to compare these to).

My next-next step would have been to go into wp-content with backup copies of my themes and plugins, but I would have done this VERY, VERY CAREFULLY.

Usual reminder from other sites – make sure you have a copy of wp-config.php somewhere, else you're in for a very long evening if you do something unwanted.

Step 3 – Inspect The Database

I started here, as it seemed the most likely culprit based on lots of searching for similar issues. Consensus among several discussions was that searching for the keywords:

eval, gzinflate, shell_exec, base64_decode

in your database would produce the maximum bang-for-buck. As it happens, only "eval" existed in the CNYO database and, sadly, "eval" is a common combination of four letters on a science-based website (so 100 hits, many of "evaluation").

I was fortunate to do this first-pass, find little that looked problematic, and move on to Step 1 above instead.

Step 4 – Transfers Worked? Now Find The Problem (Locally)

For the academically curious… the wp-admin and wp-includes replacement solved my problem. Doing the next logical step of renaming the new wp-admin to wp-admin-new and renaming the old wp-admin-old to wp-admin (alphabetically, of course), I found the site remained in its original, untouched state – placing the problem file(s) squarely in wp-includes.

To find the official location, one needs a tool that will compare the contents of files and directories. In OSX, this is FileMerge in Xcode (search for the app or Command-Space Bar and type filemerge.app (see this link on stackexchange for a how-to). If you don't have Xcode, similar comparison tools exist on all OSs.

To start this, I moved wp-includes-old to my local machine so as to perform this comparison in filemerge. I renamed it to wp-includes in the pic below.

Once open, select the wp-includes in your clean, unzipped WordPress folder as the Left folder, then select the wp-includes(-old) as the Right folder. And run Compare.

Left folder is the clean WordPress folder, Right is the hacked folder.
FileMerge with the wp-includes folders loaded for comparison, showing only folders containing files with differences (click on Identical to exclude those files).
temdfgp.php, containing a call to a hidden file .quota
.quota, not in the official WordPress release, but very present (and problematic) in the old cnyo.org wp-includes.

Clicking on "Identical" on filemerge's righthand side to exclude all identical files, the list of changed files from old-to-new is small, with the offending .php file identified as temdfpg.php, which calls a .quota file that looks something like below:

php $IBmtKwVMuXQGpgbUH='ur'.'ld'.'ec'.'od'.'e'; … lots of and lots of scribble ... %22%2F%3E%3C%2F%73%62%65%7A%3E'));exit;

Problem identified, problem solved. All in all, I suspect I got lucky in doing a few very simple things to narrow down the location of the problem. I will hope for similar luck next time.

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NAMOT Pre-Release 2.2.0-pre4 In OSX 10.8 (Maybe Older Versions)

A recent visit to the College of Nanoscale Science and Engineering (CNSE) at SUNY Albany inspired a few new DNA ideas that I decided would be greatly simplified by having NAMOT available again for design. Having failed at the base install of the NAMOT 2 version and, unfortunately, not having NAMOT available in Fink for a simple installation, the solution became to build the pre-release from scratch. Ignoring the many errors one encounters while walking through an OSX/Xcode/Fink/X11 bootstrap, the final procedure worked well and without major problem. As usual, the error messages at varied steps are provided below because, I assume, those messages are what you're searching for when you find your way here.

0. Required Installations

You'll need the following installed for this particular build. I believe XCode is the only thing that you'll have to pay for (if you don't already have it. I seem to remember paying $5 through the App Store).

1. XCode

The OSX Developer Suite – developer.apple.com/xcode

2. XQuartz

An OSX (X.Org) X Window System – xquartz.macosforge.org/landing/

3. Fink

An OSX port program for a host of Unix codes and libraries – www.finkproject.org

3a. GSL

The GNU Scientific (C and C++) Libraries – www.gnu.org/software/gsl. This will be installed with Fink.

3b. LessTif

An OSF/Motif clone (made available for OSX through Fink) – lesstif.sourceforge.net. This will be installed with Fink.

4. NAMOT2.2.0-pre4

The -pre4 is currently available (from 2003) from sourceforge.net/projects/namot/files/. I did not try -pre3 and had no luck with the official 2 release.

And, with that…

1. XCode

Blindly follow the install procedure. Several steps below deal with working around the default install locations (specifically, /sw).

2. XQuartz

If you don't have XQuartz installed, you're configure step…

cd Downloads
cd namot-2.2.0-pre4
./configure

will produce the following error…

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
creating libtool
checking for X... no
checking for main in -lX11... no
NAMOT requires Xwindows

Blindly follow the XQuartz install process. After the installations, you'll receive the same error as above. The –x-libraries= and –x-includes= additions to configure below direct the script to the proper libraries and includes.

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

Hopefully, you'll find yourself past the first install problem and onto the second problem.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
creating libtool
checking for X... libraries /usr/X11/lib/, headers /usrX11/include/
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... no
NAMOT requires GNU Scientific Library

3. Fink

The next two codes that need to be installed are the GNU Scientific Libraries and LessTif, both of which are much easier to install using Fink. It is generally useful for many other codes as well, so a good program for any computational chemist to have on hand. The install should be non-problematic despite having to build it from source in 10.6 – 10.8 (as of January 2013). If you build with all the default settings, you'll have no trouble after.

cd Downloads
cd fink-0.34.4
./bootstrap

I chose the default settings throughout.

Fink must be installed and run with superuser (root) privileges. Fink can automatically try to become root when it's run from a user account. Since you're currently running this script as a normal user, the method you choose will also be used immediately for this script. Available methods:

(1)	Use sudo
(2)	Use su
(3)	None, fink must be run as root

Choose a method: [1] 

...

You should now have a working Fink installation in '/sw'. You still need package descriptions if you want to compile packages yourself. You can get them by running either of the commands: 'fink selfupdate-rsync', to update via rsync (generally preferred); or 'fink selfupdate-cvs', to update via CVS (more likely to work through a firewall).

Run '. /sw/bin/init.sh' to set up this terminal session environment to use Fink. To make the software installed by Fink available in all of your future terminal shells, add '. /sw/bin/init.sh' to the init script '.profile' or '.bash_profile' in your home directory. The program /sw/bin/pathsetup.sh can help with this. Enjoy.

Then you run the final step in Fink below:

/sw/bin/pathsetup.sh

Which will produce the following two pop-ups notifying you of shell modifications.

3a. GSL

With the install of Fink, you need to install GSL and LessTif. If you try to install either immediately after installation…

fink install gsl

…you'll receive the following error:

Password:
Scanning package description files..........
Information about 305 packages read in 0 seconds.
no package found for "gsl"
Failed: no package found for specification 'gsl'!

Required after the installation is a fink selfupdate.

fink selfupdate

As usual, follow the default settings…

fink needs you to choose a SelfUpdateMethod.

(1)	cvs
(2)	Stick to point releases
(3)	rsync

Choose an update method [3] 
/usr/bin/find /sw/fink -name CVS -type d -print0 | xargs -0 /bin/rm -rf
fink is setting your default update method to rsync
...
Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-i386
New package: dists/stable/main/binary-darwin-i386/base/base-files_1.9.13-1_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/base/fink-mirrors_0.34.4.1-1_darwin-i386.deb

Which then leads to a successful GSL install.

fink install gsl

Producing the following output…

Information about 12051 packages read in 1 seconds.
The package 'gsl' will be built and installed.
Reading build dependency for gsl-1.15-1...
Reading dependency for gsl-1.15-1...
Reading runtime dependency for gsl-1.15-1...
Reading dependency for gsl-shlibs-1.15-1...
...
Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-i386
New package: dists/stable/main/binary-darwin-i386/sci/gsl-shlibs_1.15-1_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/sci/gsl_1.15-1_darwin-i386.deb

Attempting a fresh build after the GSL step…

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

…then still produces the following error:

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... no
NAMOT requires GNU Scientific Library

As mentioned above, there are a few redirects that need to be made after the XCode / Fink install to put libraries and includes where, in this case, NAMOT expects them. To perform this task, we'll be using symbolic links.

sudo ln -s /sw/include/gsl /usr/include/
sudo ln -s /sw/lib/libgsl* /usr/lib

Now attempting a build…

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include

Gets you past the GSL issue.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... yes
checking for main in -lgsl... yes
checking for XShmCreateImage in -lXext... yes
checking for main in -lXt... yes
checking for main in -lXm... no
NAMOT requires Motif...try LessTif(http://www.lesstif.org)

3b. LessTif

The LessTif symbolic links work the same as the GSL symbolic links. This fink install may take a while.

fink install lesstif

Output below…

Information about 12051 packages read in 1 seconds.
The package 'lesstif' will be built and installed.
Reading build dependency for lesstif-0.95.2-4...
Reading dependency for lesstif-0.95.2-4...
Reading runtime dependency for lesstif-0.95.2-4...
...
Setting up lesstif (0.95.2-4) ...
Clearing dependency_libs of .la files being installed

Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-i386
New package: dists/stable/main/binary-darwin-i386/x11/app-defaults_20010814-12_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/x11/lesstif-bin_0.95.2-4_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/x11/lesstif-shlibs_0.95.2-4_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/x11/lesstif_0.95.2-4_darwin-i386.deb

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

But, unfortunately, the LessTif libraries are not in the expected locations.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... yes
checking for main in -lgsl... yes
checking for XShmCreateImage in -lXext... yes
checking for main in -lXt... yes
checking for main in -lXm... no
NAMOT requires Motif...try LessTif(http://www.lesstif.org)

So we add the symbolic links…

sudo ln -s /sw/lib/libXm.* /usr/lib
sudo ln -s /sw/include/Xm /usr/include

Which, finally, runs configure…

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

…with no errors.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
config.status: creating docs/demos/curve/Makefile
config.status: creating docs/demos/dit/Makefile
config.status: creating docs/demos/Makefile
config.status: creating config.h
config.status: executing depfiles commands

NOTE: The make step with Python 2.6 produces the following error below. I did not diagnose this beyond the failure to build under 10.6. OSX 10.8 comes with Python 2.7, which did not produce this problem (I'm assuming this is the origin of the problem).

make

…will produce the following error at the pngwriter.c step.

/bin/sh ../libtool --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I..    -DLIB_HOME="\"/usr/local/share/namot\"" -DHELP_FILE_DIR="\"/usr/local/share/namot\"" -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -I/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/config -g -O2 -c -o _pynamot_la-pngwriter.lo `test -f 'pngwriter.c' || echo './'`pngwriter.c
gcc -DHAVE_CONFIG_H -I. -I. -I.. -DLIB_HOME=\"/usr/local/share/namot\" -DHELP_FILE_DIR=\"/usr/local/share/namot\" -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -I/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/config -g -O2 -c pngwriter.c -MT _pynamot_la-pngwriter.lo -MD -MP -MF .deps/_pynamot_la-pngwriter.TPlo  -fno-common -DPIC -o _pynamot_la-pngwriter.lo
pngwriter.c: In function 'dump_PNG':
pngwriter.c:28: error: 'png_structp' undeclared (first use in this function)
pngwriter.c:28: error: (Each undeclared identifier is reported only once
pngwriter.c:28: error: for each function it appears in.)
pngwriter.c:28: error: expected ';' before 'png_ptr'
pngwriter.c:29: error: 'png_infop' undeclared (first use in this function)
pngwriter.c:29: error: expected ';' before 'info_ptr'
pngwriter.c:30: error: 'png_byte' undeclared (first use in this function)
pngwriter.c:30: error: 'row_pointers' undeclared (first use in this function)
pngwriter.c:30: error: expected expression before ')' token
pngwriter.c:31: error: 'png_text' undeclared (first use in this function)
pngwriter.c:31: error: expected ';' before 'text_ptr'
pngwriter.c:39: warning: incompatible implicit declaration of built-in function 'memset'
pngwriter.c:39: error: 'text_ptr' undeclared (first use in this function)
pngwriter.c:47: error: 'png_ptr' undeclared (first use in this function)
pngwriter.c:47: error: 'PNG_LIBPNG_VER_STRING' undeclared (first use in this function)
pngwriter.c:48: error: 'png_voidp' undeclared (first use in this function)
pngwriter.c:57: error: 'info_ptr' undeclared (first use in this function)
pngwriter.c:60: error: 'png_infopp' undeclared (first use in this function)
pngwriter.c:82: error: 'PNG_COLOR_TYPE_RGB' undeclared (first use in this function)
pngwriter.c:82: error: 'PNG_INTERLACE_ADAM7' undeclared (first use in this function)
pngwriter.c:83: error: 'PNG_COMPRESSION_TYPE_DEFAULT' undeclared (first use in this function)
pngwriter.c:83: error: 'PNG_FILTER_TYPE_DEFAULT' undeclared (first use in this function)
pngwriter.c:85: error: 'PNG_sRGB_INTENT_ABSOLUTE' undeclared (first use in this function)
pngwriter.c:90: error: 'PNG_TEXT_COMPRESSION_NONE' undeclared (first use in this function)
pngwriter.c:93: error: 'PNG_TEXT_COMPRESSION_zTXt' undeclared (first use in this function)
pngwriter.c:104: error: expected expression before ')' token
make[2]: *** [_pynamot_la-pngwriter.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

The build on 10.8 continues as below, with a few warnings about the symbolic link usage that do not seem to affect the program usability (or continued build).

make

Results below…

make  all-recursive
Making all in src
source='namot_wrap.c' object='_pynamot_la-namot_wrap.lo' libtool=yes \
	depfile='.deps/_pynamot_la-namot_wrap.Plo' tmpdepfile='.deps/_pynamot_la-namot_wrap.TPlo' \
	depmode=gcc3 /bin/sh ../depcomp \
	/bin/sh ../libtool --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I..    -DLIB_HOME="\"/usr/local/share/namot\"" -DHELP_FILE_DIR="\"/usr/local/share/namot\"" -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config -g -O2 -c -o _pynamot_la-namot_wrap.lo `test -f 'namot_wrap.c' || echo './'`namot_wrap.c

...

*** Warning: linker path does not have real file for library -lXm.
*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have
*** because I did check the linker path looking for a file starting
*** with libXm and none of the candidates passed a file format test
*** using a file magic. Last file checked: /sw/lib/libXm.la

*** Warning: linker path does not have real file for library -lgsl.
*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have
*** because I did check the linker path looking for a file starting
*** with libgsl and none of the candidates passed a file format test
*** using a file magic. Last file checked: /sw/lib/libgsl.la

*** Warning: linker path does not have real file for library -lgslcblas.
*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have
*** because I did check the linker path looking for a file starting
*** with libgslcblas and none of the candidates passed a file format test
*** using a file magic. Last file checked: /sw/lib/libgslcblas.la

*** Warning: libtool could not satisfy all declared inter-library
*** dependencies of module _pynamot.  Therefore, libtool will create
*** a static module, that should work as long as the dlopening
*** application is linked with the -dlopen flag.

...

Making all in libs
make[2]: Nothing to be done for `all'.
Making all in docs
Making all in helpfiles
make[3]: Nothing to be done for `all'.
Making all in demos
Making all in 6way
make[4]: Nothing to be done for `all'.
Making all in bending
make[4]: Nothing to be done for `all'.
Making all in cube
make[4]: Nothing to be done for `all'.
Making all in curve
make[4]: Nothing to be done for `all'.
Making all in dit
make[4]: Nothing to be done for `all'.
make[4]: Nothing to be done for `all-am'.
make[3]: Nothing to be done for `all-am'.
Making all in etc
make[2]: Nothing to be done for `all'.

Finally, the install…

make install

Which produces the following:

Making install in src
/bin/sh ../mkinstalldirs /usr/local/lib
 /bin/sh ../libtool --mode=install /usr/bin/install -c  _pynamot.la /usr/local/lib/_pynamot.la
/usr/bin/install -c .libs/_pynamot.lai /usr/local/lib/_pynamot.la
/usr/bin/install -c .libs/_pynamot.a /usr/local/lib/_pynamot.a
ranlib /usr/local/lib/_pynamot.a
chmod 644 /usr/local/lib/_pynamot.a
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
...
/bin/sh ../mkinstalldirs /usr/local/share/namot
 /usr/bin/install -c -m 644 Namot2.512 /usr/local/share/namot/Namot2.512
 /usr/bin/install -c -m 644 Namot2.600 /usr/local/share/namot/Namot2.600
 /usr/bin/install -c -m 644 Namot2.700 /usr/local/share/namot/Namot2.700
 /usr/bin/install -c -m 644 icon1.xv /usr/local/share/namot/icon1.xv
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.

With luck, your launching of NAMOT will open XQuartz and produce a fully operational NAMOT session.

namot

And, for more assistance with producing DNA files for GROMACS, consider the Modifications To The ffG53a6.rtp And ffG53a5.rtp Residue Topology Files Required For Using GROMOS96-NAMOT-GROMACS v1, sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To GROMOS96 Format For GROMACS Topology Generation v1, and sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To ffAMBER Format For GROMACS Topology Generation v1 pages on this blog.