A minor revision of Scisoft is available for downloading. Many people are experiencing many problems with the Apple Package Installer and I am distributing this release as a simple tar.gz file.

This version of Scisoft is distributed as a simple tar file that can be un-tarred in /. Scisoft expect to be located in /Applications/scisoft/

I can confirm the CONTENTS file distributed with the install is identical to the file for Scisoft 2009.9.1 so this release may just be a way to avoid some issues with the Apple Package Installer program.

This change to a tarball format is good, but it changes how to install the software. However, there is at least one major glitch in this distribution

• WCSTools is missing from the installation! There are symbolic links to the package, but the /Application/scisoft/i386/Packages/wcstools-3.7.3/ directory is empty! If you are upgrading from a previous version of Scisoft OSX, there is an easy way to recover from this problem. I am outlining my suggested installation routine below.
• As I noted for Scisoft 2009.9.1, “on Snow Leopard, Gordon Richards discovered that if you attempt ‘import pylab’ in python, you get a bus error. I can confirm the same error occurs on my Snow Leopard machine using either this SciSoft OSX release or the previous one. Furthermore, I can confirm the error DOES NOT occur in Leopard. I am not a heavy Python user, so I will leave it to Gordon, Nor, and others to investigate this issue. Gordon notes that this blog posting contains instructions for getting pylab installed under a vanilla Snow Leopard install, in case you need them.”

My suggested routine for upgrading to this version of Scisoft OSX from a previous version is the following:

1. Backup the previous version of Scisoft by renaming the /Application/scisoft/ directory to /Application/scisoft_old/.
2. Download the current gzipped tarball of Scisoft OSX. The current version of Scisoft OSX is available for download from the Scisoft OSX website, but I have made the package available on my Scisoft OSX mirror as well, in case it is faster for people.
3. Using the command line in an administrative account, you can untar the tarball using the command:

   sudo tar -C / -xzvf Scisoft_OSX_macintel_2009.10.1.tar.gz

   You will be asked for your account password to allow ’sudo’ to run the tar command as root.
4. The files are untarred with their ownership intact from when Nor created the tarball, so be sure to change the ownership to match your root account using
   

   sudo chown -R root:admin /Applications/scisoft/

5. Finally, if you want to copy over the WCStools package from the previous Scisoft OSX installation, you can use the command:

   sudo cp -r -p /Applications/scisoft_old/i386/Packages/wcstools-3.7.3/ /Applications/scisoft/i386/Packages/wcstools-3.7.3/

   That should get your back the WCStools.

I have alerted Nor to the missing wcstools directory as well as some other minor issues with this release. Hopefully, if Nor has some time, he will make

This version should fix a few outstanding bugs in version 2009.6.1. People running on case sensitive file system will hopefully stopped having problems. This version otherwise upgrades a few minor packages as described in the NEWS and CONTENTS files.

This version requires OSX Intel 10.5.x or higher. It also works fine with OSX 10.6.0 and OSX 10.6.1.

From reviewing the CONTENTS file distributed with the install, the major changes from the previous version as as he indicated, quite minor. They include:

• The following Python packages were updated:
• • matplotlib 0.99 (upgraded from version 0.98.5.2)
  • pyraf 1.8 (upgraded to the current release version from version 1.7.1)
  • pygsl 0.9.4 (upgraded from version 0.9.3)
  • mxDateTime 3.1.2 was added to the distribution. Adds certain useful date manipulation functions to the python installation.
  • pysao 2.1.8 was added to the distribution. This appears to add direct XPA communication capability between python scripts and SAOImage DS9.

• The gsl library was update from version 1.11 to 1.13.
• [From NEWS file] Changed ds9 [command line] unix version a [symbolic] link from an alias. I noticed the SAOImage DS9 website currently says “Note: the next release of DS9, version 5.7, will be available October 15th.”
• [From NEWS file] Fixed references to “packages” to “Packages” in Setup scripts

The glitches I have noticed in this distribution

• As with previous versions, the installer for Scisoft OSX (due to bugs, apparently in Apple’s installer.app) changes the ownership of /Applications after the install. I would run Disk Utility and Fix the Permissions on your root volume after installing Scisoft OSX.
• [Added Sept. 23] Gordon Richards and I have have been investigating some serious annoyances with the python installation on Snow Leopard in this version of SciSoft OSX.
  1. First of all, the installer apparently doesn’t install /Applications/scisoft/i386/Packages/Python-2.5.4/Python.framework/Versions/2.5/Resources/Python.app/ when running on Snow Leopard. This directory contains the python executable. Therefore, in the new SciSoft OSX on Snow Leopard, you can’t run python from the clean install. If you manually copy this directory from the previous SciSoft OSX installation to this one, then I find you can run python again (or in my case, pyraf). I can confirm this directory is apparently installed under Leopard.
  2. On Snow Leopard, Gordon Richards discovered that if you attempt ‘import pylab’ in python, you get a bus error. I can confirm the same error occurs on my Snow Leopard machine using either this SciSoft OSX release or the previous one. Furthermore, I can confirm the error DOES NOT occur in Leopard. I am not a heavy Python user, so I will leave it to Gordon, Nor, and others to investigate this issue. Gordon notes that this blog posting contains instructions for getting pylab installed under a vanilla Snow Leopard install, in case you need them.

The current version of Scisoft OSX is available for download from the Scisoft OSX website, but I have made the package available on my Scisoft OSX mirror as well, in case it is faster for people.

Scisoft OSX Intel 2009.6.1 Released

This version updates the STSDAS/TABLES packages and a few other packages.
It also fixes the issues pointed out by J. Cabanela

The new version of Scisoft OSX 2009.6.1 differs from Scisoft OSX 2009.5.2 in the following ways:

• Stiff was updated from version 1.10 to version 1.12
• HEASARC fv.app was updated from version 5.1 to version 5.2.1 and properly installed.
• HEASARC hera.app was updated from version 5.1 to version 5.2.1 and properly installed.
• HEASARC StudentHera.app was updated from version 5.1 to version 5.2.1 and properly installed.
• SAOImage DS9 was updated to version 5.6.3 from version 5.3b.
• Interestingly, the STSDAS and TABLES IRAF packages are still version 3.10, so I am not sure what updates Nor refers to above for STSDAS/TABLES.

The only glitch I noticed is that permissions problems persist. Specifically, when the installer installs Scisoft OSX, it appears that a bug in Apple’s Installer program triggers a change in ownership of the /Applications directory to that of the second user on the system. I strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using:

sudo chown username:admin /Applications

(where “username” is the primary administrator’s username, in most cases, your username) to perform the repair. I know Nor spent a bit of time trying to resolve this without success last summer, so its a glitch that will probably persist.

I also have a minor gripe. This is not a bug, so much a feature I prefer. I like having the X11 command-line version of ds9 available, so I manually installed the current ds9 command line binary into /Applications/scisoft/i386/bin/.

The current version of Scisoft OSX is available for download from the Scisoft OSX website (or will be shortly) and I have made the package available on my Scisoft OSX mirror as well.

• Eclipse 5.0.0 has been added to the distribution. Eclipse is an Integrated Development Environment (IDE) for programming. I don’t find it to be terribly useful, and in fact find it fairly awful in its implementation for IDL, but I am sure there are many people who disagree (enough to foster development of five major versions of it).
• Gnuplot has been updated to version 4.2.5 from 4.2.3
• Eye 1.4.1 has been added to the distribution. Eye is a program designed to allow you to use an artificial neural network to construct SExtractor filters for “adaptive filtering, feature detection and cosmetic corrections.”
• Swarp was updated to 2.17.6 from 2.17.1
• WeightWatcher was updated to 1.8.10 from 1.8.7
• The Python distribution was updated to version 2.5.4 from 2.5.2 and the following python packages were updated:
  • ipython updated to 0.9.1 from 0.8.4
  • Numpy updated to 1.3 from 1.1.1
  • pyfits updated to 2.1.1 from 1.1 (or this could be a typo in the old CONTENTS)
  • matplotlib updated to 0.98.5.2 from 0.98.3
  • pyraf updated to 1.7.1 from 1.6
  • stsci_python updated to 2.8 from 2.6
  • AstroAsciiData updated to 1.1 from 1.0
  • scipy updated to 0.7.0 from 0.6.0
• The STSDAS and TABLES IRAF packages were updated to version 3.10 from 3.08
• fftw library version 3.2.1 added. This will be useful to me since we have been using fftw in the computational physics class I have been teaching this semester.
• I noticed the Aquaterm.app application (used for graphics display by PGPLOT and Gnuplot) is now pre-installed in /Applications/scisoft/i386/Applications/.

Some minor glitches I have noticed in this distribution

1. Permission Problems Persist: When the installer installs Scisoft OSX, it appears that a bug in Apple’s Installer program triggers a change in ownership of the /Applications directory to that of the second user on the system. I strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using: sudo chown username:admin /Applications (where “username” is the primary administrator’s username, in most cases, your username) to perform the repair. I know Nor spent a bit of time trying to resolve this without success last summer, so its a glitch that will probably persist.
2. Older SAOImage DS9 included: I noticed that the SAOImage DS9 distributed with this version of Scisoft OSX is version 5.3b, whereas the current version is 5.6.1, so I manually installed the current ds9 command line binary into /Applications/scisoft/i386/bin/ and the current Aqua application into /Applications/scisoft/i386/Applications/ and everything is working fine there.
3. HEASARC fv.app not installed: The fv.app application in the /Applications/scisoft/i386/Applications/ is actually a second copy of studenthera.app, misnamed. Not sure how that happened, but I manually installed the current version of HEASARC fv.app there without an issue.

All in all, a bunch of small updates, but it gets the package mostly up-to-date again. The current version of Scisoft OSX is available for download from the Scisoft OSX website, but I have made the package available on my Scisoft OSX mirror as well, in case it is faster for people.

• Aqua 10.4 Tiger (Universal)
• Aqua 10.5 Leopard (Universal)
• X11 10.4 Tiger (Universal)
• X11 10.5 Leopard (Universal)
• X11 10.5 Leopard (Universal) with Firewall

To quote the release notes on the SAOImage DS9 website, the changes in the newly released version 5.3 are

Regions: Regions now support a centroid function. The centroid function can be manually invoked or regions can automatically snap to a centroid when moved or edited. Regions now have a DASH line property.

Colorbar: Now supports a vertical colorbar layout option, via the View Menu. Users can configure the font type and size of the colorbar, via the View Menu.

GUI: Now supports a vertical button bar, when in vertical layout mode.

Aqua MacOSX 10.5 firewall: The MacOSX Aqua 10.5 Leopard port of DS9 can be used with the MacOSX 10.5 firewall enabled.

X11 MacOSX 10.5: There are now two versions available for X11 MacOSX 10.5 Leopard. The non-firewall version is recommended for all unless you wish to enable the 10.5 firewall. [Juan's Note: While not stating this, they mean specifically the application-specific version of the MacOS firewall. See my notes on this problem here.] In that case, please use the firewall enabled version. Please note: this version consist of 2 files, ds9 and ds9.zip. It is very important that ds9.zip be placed in the same directory as the ds9 binary at all times.

Contours: Contours now have a DASH line option.

I have previously posted notes for integrating upgrades of DS9 into the Scisoft OS X installation and they still work just fine except that newer releases of Scisoft OS X place the binaries in /Applications/scisoft/i386/bin/ instead of /scisoft/i386/bin/ and if you are installing the X11 binary that is compatible with the firewall, you have to install both the ds9 and ds9.zip file in the bin/ directory of Scisoft OSX.

should resolve a few outstanding problems created when changing the location of scisoft from /scisoft to /Applications/scisoft/. Packages such as MIDAS and Gnuplot should now work properly.

This version removes some remaining dependencies on the HPC OSX compilers, which I had on my machine but which most users do not have (and do not want to have).

I compared the /Application/scisoft/i386/Packages directory from this release of Scisoft OSX to the last one and there are no new packages installed. The few issues I noted with the Scisoft OSX 2008.8.1 release all appear to still be valid. Notably:

1. Permission Problems Persist: When the installer installs /Applications/scisoft, it appears that a bug in Apple’s Installer program triggers a change in ownership of the /Applications directory to that of the second user on the system. I strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using:
   

   sudo chown username:admin /Applications
   

   
   (where “username” is the primary administrative users username, in most cases, your username) to perform the repair.
2. ds9 command line executable missing: This release has the same glitch I noticed in version 2008.8.1 in that /Applications/scisoft/i386/bin doesn’t appear to have a ds9 binary installed. You can fix this by installing the X11 version of ds9 there or by linking to the Aqua version of ds9 that was installed using the command line
   

   ln -s "/Applications/scisoft/i386/Applications/SAOImage DS9.app/Contents/MacOS/ds9" /Applications/scisoft/i386/bin/ds9

I have placed a copy of this release in my Scisoft OSX Mirror in case the main Scisoft OSX repository gets bogged down.

There are a few changes in this version and all packages have been updated to the latest available versions. Starting with this version, Scisoft is installed in /Applications/scisoft (it previously was installed in /scisoft). Make sure that you remove any old /scisoft installation and properly update your startup files to source the Setup.csh or Setup.bash from their new locations.

In the README file you are told

Once the collection is successfully installed csh and tcsh users should invoke the command:

source /Applications/scisoft/all/bin/Setup.csh

to gain access to all the software and configure their environment correctly.

Users of the “bash” shell should instead use:

. /Applications/scisoft/all/bin/Setup.bash

Personally, to avoid problems in tcsh with a script breaking or with modifying my PATH multiple times by repeated execution of the Setup.csh script, I use the following line in my .tcshrc to first check for the existence of the Setup.csh script and SCISOFT environmental variables before executing it.

if (! $?SCISOFT) then
test -r /Applications/scisoft/all/bin/Setup.csh && source /Applications/scisoft/all/bin/Setup.csh
endif

Permission Problems Persist
This version addresses all the issues I noticed with Scisoft OSX 2008.5.1 except for one annoying one, the reassignment of ownership of the enclosing directory on installation. If you installed the old version of Scisoft OSX, it would reassign ownership of the root (/) directory to the second user on the system (in my case, since their is none, it showed the user as “502″). I beta-tested various versions of Scisoft OSX but Nor was not able to stamp out this particular problem. I believe Nor has come to the conclusion after extensive testing that this is a problem with Apple’s software for constructing installer packages. By moving the Scisoft OSX installation to /Applications/scisoft, it is the /Applications directory that gets its ownership changed instead of the root directory, which is less damaging. However, I would strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using:

sudo chown username:admin /Applications

(where “username” is the primary administrative users username, in most cases, your username) to perform the repair.

A Quick-Fix for any Legacy Scisoft-related scripts
If you had a few scripts that relied on Scisoft OSX being located in /scisoft and you don’t want to edit them all is you can make /scisoft point to /Applications/scisoft. This can be accomplished by first moving the old version of Scisoft OSX before installing 2008.8.1 via the command line:

sudo mv /scisoft /scisoft_old

and then once you have installed the new Scisoft OSX in 2008.8.1, create a symbolic link from the old location to the new by typing (again from the command line)

sudo ln -s /Applications/scisoft /scisoft

This will allow any scripts that refer to items in /scisoft to continue to work for the most part.

What’s New?
An investigation of the /Application/scisoft/i386/Packages directory as well as the NEWS file reveals the following changes to this version of SciSoft OSX over the 2008.5.1 version.

• DS9 updated from 5.1 to 5.3beta
  
• FV updated from 5.1 to 5.2.1
• ATLAS updated to version 3.8.2
• MIDAS updated to 08FEBpl1.1
• cdsclient was updated to version 2.87
• OpenMotif updated to 2.1.32_compat
• cfitsio library updaed from 3.090 to 3.090 (the current version is 3.100)
• pango library updated from version 1.20.2 to 1.21.3
• pixman library updated from 0.10.0 to 0.11.2
  
• expat library updated from 2.0.0 to 2.0.1
  
• fontconfig library updated from 2.3.2 to 2.6.0
• freetype library updated from 2.2.1 to 2.3.6
• gettext library updated from 0.14.5 to 0.17
• gtk+ updated from 2.12.9 to 2.12.10
• libpng library updated from 1.2.10 to 1.2.29
• netCDF library version 3.6.2 added
• pkg-config updated from 0.20 to 0.23
• TclTk package updated from 8.4.13 to 8.4.19
• wcstools library updated from 3.6.4 to 3.7.3 (current version is 3.7.5)
• IRAF package rvsao updated t version 2.5.7 to 2.6.4
• Python was updated to 2.5.2 and the following Python libraries were updated:
  
• • ScientificPython updated to 2.6.1

Minor Glitches
The only other minor glitch I noticed was that /Applications/scisoft/i386/bin doesn’t appear to have a ds9 binary installed. You can fix this by installing the X11 version of ds9 there or by linking to the Aqua version of ds9 that was installed using the command line

ln -s "/Applications/scisoft/i386/Applications/SAOImage DS9.app/Contents/MacOS/ds9" /Applications/scisoft/i386/bin/ds9

The latest update to Scisoft OSX is now available. This includes an update to Pyraf (v. 1.6), GSL, pygsl, Gunplot, and a few backend libraries.

I went ahead and decided to install it today to investigate the improvements. As is usually my procedure, I first moved the directory containing my functional SciSoft OSX install temporarily out of the way via the command line:

sudo mv /scisoft /scisoft_old

Having done that I double-clicked on the installer package and let it do its thing, installing everything in the /scisoft directory. I poked around a bit an realized almost immediately that /scisoft/i386/Applications directory was empty! This one is kind of a show stopper as it means DS9 and FV are unavailable. I copied the files back from the previous installation without too much of a hitch. I did check, the installer package file with Pacifist and it does appear to contain those files in it, so I am not sure why they didn’t appear to install. I hope this is an isolated incident and not a recurring issue with the installer.

Other minor glitches I noticed:

• I discovered that /scisoft/i386/Packages, /scisoft/NEWS and /scisoft/i386/share are set to have owner 502:502 instead of root:admin. This glitch is easily fixed by issuing the following command from the Terminal
  

  sudo chown -R root:admin /scisoft/

• I also noticed that in addition to the x11iraf-1.5DEV installation, the entire x11iraf-1.3.2 installation is still sitting in the /scisoft/i386/Packages directory. All the x11iraf binaries in /scisoft/i386/bin/ are linked to x11iraf-1.5DEV instead of the older 1.3.2 binaries. I suspect this is an oversight.

An investigation of the /scisoft/i386/Packages directory as well as the NEWS file reveals the following changes to this version of SciSoft OSX over the 2008.3.1 version.

• GSL updated from 1.9 to 1.11
• DS9 updated from 4.13 to 5.1 (The current version of SAOImage DS9 is actually version 5.2, you can read about how to update the SciSoft version of DS9 in this post)
• GNUPlot updated from 4.0.0 to 4.2.3
• Swarp updated from version 2.15.7 to 2.17.1
• WeightWatcher updated from version 1.7 to 1.8.7
• pyraf updated from version 1.3 to version 1.6
• The following Python libraries were updated:
• • pygtk updated from 2.8.6 to 2.12.1
  • matplotlib updated from 0.90 to 0.91.2
• atk library updated from 1.10.3 to 1.22.0
• cairo library updated from 1.1.6 to 1.6.4
• cfitsio library updaed from 3.040 to 3.080
• glib library updated from 2.8.6 to 2.16.3
• glib-1.2.10 library added as well (possibly for a particular package needing older version of library)
• gtk+ library updated from 2.8.19 to 2.12.9
• gtk+-1.2.10 library added as well (possibly for a particular package needing older version of library)
• pango library updated from version 1.10.4 to 1.20.2
• pixman 0.10.0 library added
• libtiff library upgraded from 3.7.4 to 3.8.2

Hats off to the SciSoft OSX folks for keeping this package up to date. I have placed a copy in my SciSoft OSX mirror in case there are any access issues.

The folks in Cambridge have kept busy. They have released SAOImage DS9 version 5.2. The versions for MacOS X include the following:

• Aqua 10.4 Tiger (Universal)
• Aqua 10.5 Leopard (Universal)
• X11 10.4 Tiger (Universal)
• X11 10.5 Leopard (Universal)

The rather extensive changes are detailed in the release notes here, but the notable ones to me include:

• ANALYSIS: for MacOSX tiger, wrap cmds with shell and PATH.
• GUI: change default directory for standard dialog to $HOME.
• ANALYSIS: add /sw/bin to default path for MacOSX. While unstated in the release notes, this is clearly an attempt to support Fink, which places its installation in the /sw directory.
• GUI: ds9 will now start in the users home directory for MacOSX Aqua users when invoked from a double click and the default dialog box is Motif or Windows.
• MACOSX: fixed a problem with printing non standard colors.
• MACOSX: restore postscript printing.
• REGIONS: apply WCS to fits regions if present.
• GUI: add support for user configured button bar.
• CATALOGS: add support for simbad.
• IMEXAMINE: added support for key stroke events.
• Although unstated in their release notes, they are now apparently providing universal binaries instead of PPC and Intel binaries for MacOS X.

I have previously posted notes for integrating upgrades of DS9 into the Scisoft OS X installation and they still work just fine.

• If you have SuperMongo (SM), you can request the new version. It has jumped from version SM 2.4.16 to SM 2.4.26. I don’t have a license for SuperMongo, so I can’t report much beyond this. This version of SM has Aquaterm support.
• FV, the FITS file viewer, was updated to version 5.1 from version 4.4 (they changed numbering conventions, I think). The CONTENTS file accidentally lists it as version 1.1.
• Numpy (which is used in PyRAF extensively) was updated from version 1.0.3 to the current version 1.0.4.
• stsci_python (which is also used in PyRAF extensively) went from version 2.5 to the current version 2.6.
• The mkiraf command line program that creates user’s IRAF directories appears to have been fixed for c-shell users. The bug (along with a fix) had been noted by Nor Pirzkal on his blog, so I am not surprised it was rolled into this release.
• The IRAF external packages STSDAS and TABLES when from version 3.7 to current version 3.8. The change in STSDAS includes a new package for processing WFC3 data (since I don’t use HST, I’m not that excited at the moment by this change, but I am sure someone is).
• The ESO-MIDAS version is listed as unchanged from the last release of SciSoft OSX, although the release notes just noted that “[t]his version includes a recompiled version of MIDAS (which was not tested under 10.4)”. The installed version is listed as 07FEBpl1.1 whereas the current version is 08FEBpl1.1.
• The version of DS9 included with this install of SciSoft is the current version 5.1 Aqua. This replaces the X11-based version previously included. I haven’t checked to see if it works in previous MacOS X installs, but it works fine in MacOS 10.5.2 (aka Leopard). If you do need to install a version of ds9 more appropriate to your MacOS X or if you are like me and prefer the X11 version of ds9, you can easily change the installed version.
  • If you are using an earlier MacOS X than Leopard and find the Aqua version of DS9 isn’t working, you can download an appropriate DS9 for you at http://hea-www.harvard.edu/RD/ds9/ and install it within SciSoft by noting that SciSoft OSX places the DS9 application at /scisoft/i386/Applications/SAOImage DS9.app. You could rename the installed DS9 application via the Finder or from the command line,

    mv /scisoft/i386/Applications/SAOImage\ DS9.app /scisoft/i386/Applications/SAOImage\ DS9\ \(Disabled\).app

    then if you want the Tiger (Aqua) version there, just place it in the /scisoft/i386/Applications/ directory.
  • I happen to prefer the X11 version of DS9 usually because I use pipe files to connect my IRAF session to my DS9 session and I have found that the Aqua version of ds9 doesn’t seem to play nicely in this regard. Its for that reason I installed the X11 version over the command line ds9. To do this, I noticed the command line ds9 is at /scisoft/i386/bin/ds9 and is just a symbolic link to the ds9 binary within the Application. You can just rename this symbolic link at /scisoft/i386/bin/ds9 from the command line:

    mv /scisoft/i386/bin/ds9 /scisoft/i386/bin/ds9.old

    and place the executable ds9 file that is in the X11-version tarball of ds9 there instead.

    mv ds9 /scisoft/i386/bin/ds9

    This has the added advantage of leaving the Aqua version of DS9 completely intact.
• I noticed this version of SciSoft OSX does install with me as the owner (instead of user 502). I don’t know if that is because it is defaulting to user 501 or because a change occurred in the SciSoft OSX installer, but its a welcome change.

Scisoft Intel 2008.3.1 is available. This version includes a recompiled version of MIDAS (which was not tested under 10.4), updates to STSDAS/TABLES and a few other packages such as FV, STScI_Python, and DS9 Aqua.

I’ve placed a copy Scisoft OSX Intel 2008.3.1 on the online mirror, but I will also keep last few versions around for a while until I can evaluate this one. I suspect users may this version of SciSoft OSX may have issues running under 10.4, given the comment above in the release notes. I believe if you install DS9 yourself, you have to install the version specific to your MacOS version.

• Certain links to libraries that I have previously noted had to be manually fixed have been fixed.
• The IRAF within SciSoft OSX has been updated to the latest release, version 2.14. However, as noted in his February 25 post, Nor notes if mkiraf fails to create a proper login.cl, you should do the following:

  edit /scisoft/all/packages/iraf/iraf/unix/hlib/mkiraf.csh
  and replace the first two uncommented lines with
  
  set iraf = "/scisoft/all/packages/iraf/iraf/"
  set imdir = "/scisoft//all/packages/iraf/imdirs"

• SAO Image DS9 is still at version 4.13 and not the current version 5.1. This is an issue mostly for Leopard users, since the older version of DS9 doesn’t run under Leopard without some tweaks. This is an easy enough upgrade.
• fv (an interactive FITS file viewer) is still at version 4.4 instead of the current version 5.1. You can download the current version and replace the one in the /scisoft/i386/Applications directory in case you view this as necessary.
• It installs /scisoft with permissions set such that the owner is the second user account created on most Macs (User 502). Previously it installed as owned by the first user account (user 501). This is not a huge issue if you have “sudo” privileges on the Mac (any “Administrative” user does, its the default on the first account created), just type the following on the command line:

  sudo chown -R root:admin /scisoft

  and enter your password when prompted. This will set the root account to own the files, which is appropriate in a multiuser situation. If you are the only user, you could set yourself up as owner by replacing ‘root’ above with your username (you can determine your username by typing “whoami” on the command line).

• If you want the Aqua (MacOS X native version, download the appropriate one of the following files. If you want to use the Aqua-native version from IRAF, you will need to access the command-line binary within the SAOImage DS9.app application bundle as “SAOImage\ DS9.app/Contents/MacOS/ds9“.
  • MacOSX 10.4 Tiger Aqua Interface, Universal (PPC and Intel)
  • MacOSX 10.5 Leopard Aqua Interface, Universal (PPC and Intel)
• If you want the X11-based command line driven version
  • Darwin PPC 10.4 Tiger version
  • Darwin Intel 10.4 Tiger version
  • Darwin PPC 10.5 Leopard version
  • Darwin Intel 10.5 Leopard version

More detailed release notes are available here. See my previous post on SAOImage DS9 5.0 to see how it is possible to upgrade the binaries included with SciSoft OSX.

Just to let you know that I just implemented your changes in 2007.11.2b. Thanks again.

So it looks like these bugs will be fixed when Scisoft OSX 2007.11.2b is released soon. I have to hand it to them, Nor is pretty quick to respond to these bugs, given he has a full time job which doesn’t involve maintaining SciSoft OSX!

This version updated Python to version 2.5.1 and correct some minor issue with the bash version of the irafuser.bash script when running under OSX 10.5 Leopard. Missing GCC runtime fortran libraries are also now included. This version was test under OSX 10.5 and seems to run fine. Note that 10.5 does deal with X11 applications slightly differently. Once the Setup.bash script has been source[d], you should add the following line to your .bash_profile: export DISPLAY=127.0.0.1:0.0 This will enable all Scisoft X11 applications to start from Terminal.app

• I did notice this new version of Scisoft OSX doesn’t appear to link its IRAF install with the rvsao IRAF package (used for radial velocity computations). Doesn’t matter to me to much since I compiled the newer version and linked to it, but it is funny they include the rvsao package at /scisoft/all/packages/iraf/extern/rvsao but don’t link to it in the $hlib/extern.pkg file, which I do believe they did in the older versions.
• I may not have noticed this earlier, but in the libraries directory /scisoft/i386/lib, some of the symbolic links are broken. Specifically:
  • All the items in this directory linking to the OpenMotif library items are not linked, it appears /scisoft/i386/Packages/OpenMotif-2.3.0/lib doesn’t exist. However, /scisoft/i386/Packages/OpenMotif-2.3.0/lib.org does. So I symbolically linked lib to lib.org via:

    cd /scisoft/i386/Packages/OpenMotif-2.3.0/
    ln -s lib.org/ lib

    And now all the links to the OpenMotif libraries within /scisoft/i386/lib work.
  • The CFITSIO library is mis-linked to an older version which no longer is installed. So I needed to:

    cd /scisoft/i386/lib/
    rm libcfitsio.a
    ln -s ../Packages/cfitsio-3.040/lib/libcfitsio.a libcfitsio.a

    and the CFITSIO library was properly linked again.
  • libpng.so was apparently not compiled within /scisoft/i386/Packages/libpng-1.2.10/lib, so there is no quick fix for that broken link.
  • I removed a link to python2.4 in /scisoft/i386/lib and replaced it with a link to python 2.5:

    cd /scisoft/i386/lib/
    rm python2.4
    ln -s ../Packages/pygtk-2.8.6/lib/python2.5/ python2.5

• All the CFITSIO headers in /scisoft/i386/include/ are linking to an older version (3.006) instead of the current installed version (3.040). Fixed via:
• There are symbolic links in the /scisoft/i386/bin directory to a variety of executables from the sm plotting package which doesn’t appear to have been installed as part of the Scisoft OSX distribution.
• Not really a bug, but the version of SAOImage DS9 is version 4.1.3 and not the current version 5.0.0. Of course, given the long history of dangerous version X.0.0 software, this maybe safer that way.

• MacOSX 10.4.x (Universal)
• Darwin PPC 10.4.x
• Darwin Intel

• MacOSX Aqua Support: DS9 has been ported to MacOSX Aqua and is an universal application which no longer requires X11.
• Compressed FITS Support: DS9 supports compressed FITS images using RICE compression.
• Mask Support: DS9 supports overlay masks. A mask is defined as a valid FITS image, in which a non zero value indicates that the selected mask color is to be displayed instead of the data value color.
• SkyView Support: DS9 provides support for HEASARC’s image cutout service, SkyView. This site provides image cutout service for a number of image surveys, including SDSS.
• Multi-Language Support: DS9 provides multi-language support. By default, the language used for menus and dialog boxes is based on the value of the operating system locale variable. The user may override the default value by selecting the desired language in the preferences or by the -language command line option.
• Preferences: Preferences are automatically saved when a user changes an option. Selecting the saving preferences menu item is no longer needed.

1. Decompress the command line version of ds9 via the terminal using tar xzvf ds9.darwinppc.5.0.tar.gz (PPC version) or tar xzvf ds9.darwinintel.5.0.tar.gz (Intel version). When the decompression is done, all you have is an executable called ds9.
2. Next, from the terminal, go to the /scisoft/bin directory (on PPC) or /scisoft/i386/bin/ directory (on Intel) and rename the old ds9 executable to something like ds9_old (using something like mv ds9 ds9_old).
3. Copy your newly decompressed ds9 executable into the SciSoft OSX binary directory. I should note the command line version of ds9 still requires X11.

This version contains an updated [ESO-]MIDAS package.         

I checked the list of packages included and sure enough, the only change was in the ESO-MIDAS package (whose current version is actually 07SEPpl1.0).

• MIDAS 07FEBpl1.1 (previously MIDAS 06FEBpl1.0)

I don’t use ESO-MIDAS, which is an image reduction package aimed as users of ESO’s La Silla facilities and the VLT at Paranal, so I can’t really comment as to the usefulness of this update. As with previous versions of Scisoft, the release notes warn if you use Aquaterm devices for PGPLOT, GNUPLOT, or any other packages that you “must manually run /scisoft/i386/Applications/Aquaterm.app once first to enable the aquaterm devices.”

I have also confirmed that this release also fixes the IRAF problem with symbolic linking to mkpkg and xc in /scisoft/i386/bin/ I referred to earlier in my blog.   Thanks for the fix guys!

Finally, as I noted with the last release of Scisoft, my standard method for updating Scisoft OSX is to move my existing /scisoft directory to /scisoft_old and then I unpack the new version. That way, in case anything goes wrong, I can always switch back.

During my adventures compiling the hectospec-related IRAF packages, I was using Scisoft OSX and discovered there were a couple of issues with the symbolic links for the mkpkg command necessary for compiling new IRAF packages.

• In the Scisoft OSX PPC Beta (2006.11.1b) mkpkg appears to be mis-linked, so it can’t be executed. So I did the following in the terminal:

  cd /scisoft/binsudo rm mkpkgsudo ln -s ../iraf/iraf/unix/bin.macosx/mkpkg.e mkpkg

• In the Scisoft OSX MacIntel version (2007.1.1) and Scisoft OSX MacIntel version (2007.7.1), there are some missing symbolic links to mkpkg and xc in the directory for MacIntel binaries.  As a result, both mkpkg and xc were instead pointing to PowerPC binaries. I fixed this as follows (again, from the command line):

  cd /scisoft/i386/bin/sudo ln -s /scisoft/all/packages/iraf/iraf/unix/bin.macintel/mkpkg.e mkpkgsudo ln -s /scisoft/all/packages/iraf/iraf/unix/bin.macintel/xc.e xc

  This mis-linking certainly didn’t help getting things to compile under MacIntel, since IRAF was attempting to compile MacIntel code using PowerPC versions of mkpkg and xc.

Thanks for Nor Pirzkal for giving me some feedback on fixing this problem.  He tells me he has made the appropriate changes so that the next version of Scisoft OSX will not have this  issue.By the way, my complaint here should in no way be construed as a critique of the efforts of Francesco Pierfedericki and Nor Pirzkal in putting together Scisoft OSX. They have done a great deal of work to put together an awesome package. For two people to track over 2 GB of software and not expect some glitches is unrealistic. And I for one am extremely grateful that his efforts have saved me a lot of time.