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---+!! HIPE known issues

| %ICON{"help"}% *Welcome to the known issues page. Please take a look at the table of contents below. You can find known issues for each HIPE version, in addition to [[#Installation_and_uninstallation][installation/uninstallation]], [[#General_HIPE_startup_issues][startup]], [[#General_Help_System_issues][help]], [[#Herschel_Science_Archive_issues][Science Archive]] and [[#Other_issues][other]] issues common to different HIPE versions.* |

| %X% *This page is for known issues in the HIPE software. For known issues in data products see [[DpKnownIssues][this page]].* |

%TOC%

Please note that some issues detected in previous versions may still be present in HIPE 10. Scroll down and check earlier versions if you do not see your particular issue listed for HIPE 10. 

---++ Installation and de-installation issues

   * *Cannot install on Mac OS X 10.8 "Mountain Lion".* HIPE user installers do not work on Mac OS X 10.8 due to additional security checks implemented by this operating system. *Note that HIPE is not yet officially supported on Mac OS X 10.8.* There are two workarounds:
      * In a terminal window, use the ==chmod u+x== command to change the permissions of the file ==HIPE_9_1_0_INSTALLER.app/Contents/MacOS/HIPE_9_1_0_INSTALLER==. Change the file name according to the HIPE version you are installing.
      * In Mac OS X, from _System Preferences --> Security & Privacy --> General --> Allow applications downloads from_ select _ANYWHERE_.
   * *The installer for Mac complains about write permissions. Why?* You need write permissions for the directory where you want to install HIPE. For example, you need Administrator privileges to install in ==/Applications==. If you have installed HIPE successfully in the past, and are now experiencing write permission problems, it may be that some other application changed the permissions in the meantime. There have been cases of scientific applications such as _SciSoft_ doing this. Once you revert write permissions to their correct values, HIPE installation should succeed.
   * *The installer for Windows does not start and issues the error message _Not a valid Win32 application_. Why?* This problem has been encountered under Windows Vista because the installer had not been downloaded correctly, resulting in an empty file. The exact cause is not yet known. As a workaround, try downloading the installer in a different way (for instance, via command line FTP rather than a web browser) or from another computer.
   * *Why does the uninstaller leave some icons and files/directories behind?* This incomplete uninstallation is a known issue and may be caused by a corrupted _InstallAnywhere_ global registry. As a workaround, try renaming the _InstallAnywhere_ registry file. See point 7 in the [[http://herschel.esac.esa.int/hcss-doc-11.0/load/hcss_drm/installer/installAnywhereIssues.html][InstallAnywhere issues page]] for detailed information. If you add files (such as Jython scripts) into HIPE directories after installation, these will not be removed by the uninstaller.
   * For other issues affecting the installer, check [[InstallerKnownIssues][this page]].


---++ Known issues in HIPE 10.1

There are no changes with respect to the 10.0 issues detailed below.


---++ Known issues in HIPE 10.0

---+++!! Can't open plug-ins panel under KDE or Gnome 3

The Plug-ins panel cannot be opened (from the Tools menu) if you're working under Linux and you don't have the Gnome 2 library installed. Gnome 2 is a desktop environment, and typically if you use a different desktop environment (Gnome 3, KDE, Unity, etc), then you will not have this library.

In both cases, the problem can be solved by installing the Gnome 2 library. For example on Ubuntu (or Kubuntu), the command is:

sudo apt-get install libgnome2-0

A patch is planned for this issue in HIPE 10.2.

---+++!! Clicking on the 'plug-in' button to add the cassis plugin, nothing happens and you see multiple java exceptions

The "Desktop API", which is used to access the browser when you click "Find more.." button in the HIPE plugin dialogue, is not supported on KDE. It "was designed to work on Windows and Gnome". However, you can also open it directly by pointing your browser directly to http://herschel.esac.esa.int/twiki/bin/view/Public/DpHipePlugins, and copying the URL to the respective .jar files for the particular plugin you are interested in and pasting it in the HIPE plugins dialog to install it.

If you would like to have the "Find more.." button working, all you need is to have the Gnome libraries installed.

Some instructions:
 - To install Gnome 3 libraries on Ubuntu (http://www.filiwiese.com/installing-gnome-on-ubuntu-12-04-precise-pangolin/). Note that if you're using version 11.10 or later, you probably don't need the first command (sudo apt-add-repository ...). I would just skip it and if the last command does not complain about "package not found" or something similar, then all is well.
 - To install Gnome 2 libraries on Ubuntu: http://askubuntu.com/questions/123690/how-to-install-gnome2-on-ubuntu-11-10

A patch is planned for this issue in HIPE 10.2.

---+++!! Pools unreadable with _Unknown format version: -11_ error

If you installed a developer build of HIPE 10 between 10.0.2069 and 10.0.2674 and modified any of your pools you will find those pools are no longer readable in any other HIPE version; when trying to load a pool with ==getObservation== you will get the following error message:

<pre>
herschel.ia.task.TaskException: Error processing getObservation task: Unknown format version: -11
</pre>

See the [[http://herschel.esac.esa.int/hcss-doc-10.0/index.jsp#howtos:Dag.DataIO.UnknownFormatVersion][Data Analysis Guide]] for a recovery procedure. You can download from this page the [[%ATTACHURL%/firstScript.py.txt][first]] and [[%ATTACHURL%/secondScript.py.txt][second]] script mentioned in the procedure. Change the extension from ==.py.txt== to ==.py== after downloading.

---+++!! The WCS explorer for cubes does not work with PACS and SPIRE cubes

The WCS explorer does not work on cubes for which ==ImageIndex== is used to specify the wavescale axis. This is true for SPIRE and PACS cubes. If ==crpix3==, ==crval3== and ==cdelt3== are used instead, the WCS explorer works. *To be fixed in HIPE 11*.

---+++!! Issues with reading text files from SExtractor or Topcat

While reading files from SExtractor or Topcat you may encounter the following issues:    

   * Some SExtractor headers are not read successfully, due to an issue with the column position of units in the file header. Workaround: read the file with the ==tableType== parameter set to _SPACES_. You can then fill any missing information by hand.
   * Some Topcat files are not read successfully, due to an issue with quoted cells with spaces. Workaround: export the data from Topcat in FITS format, then read the FITS file back into HIPE. For information about reading FITS files into HIPE, see the [[http://herschel.esac.esa.int/hcss-doc-10.0/#howtos:Dag.Sec.ImportingNonHerschelFits][Data Analysis Guide]].

---+++!! Format change for exported variables

The file format of variables exported with _File --> Session --> Export_ has changed in HIPE 10. This means that HIPE 10 will not be able to read session variables exported with HIPE 9, and vice-versa.<br/>If you exported variables with HIPE 9 or a previous version, follow this workaround to read them in HIPE 10:

   1. Open HIPE 9 and import the exported variables with _File --> Session --> Import_.
   1. Set _Save variables on exit_ in the _Preferences_ dialogue window, under _General --> Startup & Shutdown_.
   1. Exit HIPE 9.
   1. Open HIPE 10. The variables shall be restored in the _Variables_ view.
   1. Export the variables with the new format of HIPE 10, with _File --> Session --> Export_.

---+++!! HIPE cannot send data to an external application via SAMP

When you try to send data to an external application via the SAMP Virtual Observatory protocol, the following window may appear:

%ATTACHURL%/vospec.png

The reason is that HIPE tries to send data before the external application has initialised properly. This issue seems to occur more frequently with VOSpec.

The solution is to send the data again without closing the external application.

---+++!! Separate, undocked instances Cube Toolbox talk to each other

If you have two or more separate Spectrum Explorer GUIs open and at least one is undocked, when using its Cube Toolbox the separate SE instances talk to each other--spectra or new cubes you create in one instance will also appear in the other one.

---+++!! New PACS calibration version 45 should not be used with HIPE 10

In HIPE 10 a new spectroscopy telescope background calibration was introduced. This update is not compatible with the code in HIPE 9.

You can alway check the calibration version that you are using with the following command:

    ==print getCalTree().version==

If you use HIPE 10, you should update to version 45 of the calibration tree to make use of several new calibration files.

---+++!! Generating a co-moving frame for HIFI mapping observations of solar system objects

There is a task in HIPE that allows you to transform level-2 coordinates into a coordinate system co-moving with the target ephemeris.  That task is called doOffset, 

http://herschel.esac.esa.int/hcss-doc-10.0/index.jsp#hifi_um:hdrg_offsetposn_use

A typical code snippet would be:

comet = getObservation(1342227173, useHsa=True)

htp=comet.refs["level2"].product.refs["WBS-H-USB"].product # extract USB, pol H

htp2=doOffset(htp=htp, overwrite=0, relative=1) # make coordinates relative to ephemeris

HiClassTask()(product=htp2, fileName='cometHUSB_relativeCoords.fits') # export in CLASS-readable format

However,  the target ephemeris inside HIPE doesn't get updated.  I.e., doOffset uses the ephemeris current as of observation uplink to the spacecraft.  Work is in progress to automatically update target ephemerids.  If your target ephemeris was very uncertain at observation time (and if it has improved since), then you may be better off using a manual approach of downloading the Horizons ephemeris for each target.

---+++!! Printing a HIPE script to a file in Snowleopard sends the job to a printer instead

When a user tries to print a script to a file on disk, HIPE sends it to the printer instead. A patch will be issued for this problem in HIPE 11 and a definitive fix included in HIPE 12. 

---++ Known issues in HIPE 9.2

---+++!! New PACS calibration version 45 should not be used with HIPE 9

In HIPE 10 a new spectroscopy telescope background calibration was introduced. This update is not compatible with the code in HIPE 9.

If you use the background normalisation ipipe script for chopped spectroscopy in HIPE 9, you should not update the PACS calibration tree to version 45.  You should keep using the calibration set 41 and cancel the update when the automatic calibration updater in HIPE asks to install set 45.

If you have updated to set 45 and want to use the background normalisation in HIPE 9, you can switch back to version 41 in two ways:

   * With the command ==getCalTree(version=41)==.
   * By removing the file ==PCalBase_TimeDependency_FM_v45.fits== from the directory ==~/.hcss/data/pcal-community==.

You can alway check the calibration version that you are using with the following command:

    ==print getCalTree().version==

If you use HIPE 10, you should update to version 45 of the calibration tree to make use of several new calibration files.

---+++!! Issues with computePVMap task

The [[http://herschel.esac.esa.int/hcss-doc-9.0/index.jsp#hcss_urm:herschel.ia.toolbox.cube.ComputePVMapTask][computePVMap]] task has the following issues:

   * There are remaining aesthetic issues regarding the pvMap aspect ratio modification in the task.
   * There is a known error when extracting a pvMap with row &lt; col (velocity dimension &lt; spatial dimension). Workaround: set the ==correctAspectRatio== parameter to ==False== (in the graphical interface, untick the corresponding checkbox).

---++ Known issues in HIPE 9.1

_None known in addition to those listed for HIPE 9.0._

---++ Known issues in HIPE 9.0


---++ Installation and de-installation issues

There is a known problem with the InstallAnywhere installer observed on a Linux 64 bits, Debian wheezy/sid, java 1.6.0_24 computer. Installation fails with the following error:

"Configuring the installer for this system's environment...

strings: '/lib/libc.so.6': No such file"

Un-setting the PS1 envar solves the problem. Further details of the InstallAnywhere issue can be found here: http://kb.flexerasoftware.com/selfservice/viewContent.do?externalID=Q112941

This issue is still present in HIPE 10.0.

---+++!! Performance issues of convolution task with !NaN values

 The performance of the [[http://herschel.esac.esa.int/hcss-doc-9.0#hcss_urm:herschel.ia.toolbox.image.ImageConvolutionTask][imageConvolution]] task is severely degraded when !NaN values are found in input data. HIPE 8.3 is not affected by this problem. *Fixed in HIPE 9.1.*

---+++!! Performance issues with very large images

Images larger than about 100 MB in FITS format can still take over a minute to load. During such time HIPE is unresponsive. Image analysis operations, such as cropping and adding contours, also take a long time on large images.

---+++!! Problem with PACS background normalization script

The ==ChopNodBackgroundNormalizationRange== interactive pipeline script (_Pipelines --> PACS --> Spectrometer --> Chopper large range scan SED --> Background Normalization_) is missing a definition of the variable ==target==. After loading the observation, assuming it is stored in a variable called ==obs==, you can define the missing ==target== variable as follows: 
<verbatim>
target = obs.meta["object"].value.replace(" ","_")
</verbatim>

---+++!! PACS task [[http://herschel.esac.esa.int/hcss-doc-9.0#pacs_urm:herschel.pacs.toolboxes.spec.SpecFlatFieldLine.py][specFlatFieldLine]] problem with !NaN values

The ==specFlatFieldLine== task cannot handle !NaNs in the fluxes of ==PacsCube== products. This affected one observation as far as we tested. If you encounter this problem then you can mask the !NaNs by running the function shown below. Copy and paste the function code in a new Jython script window in the _Editor_ view of HIPE, then click the green double arrow icon in the HIPE toolbar to run the script. After that you can call the function from the _Console_ view, passing the variable contaning your cube as argument: ==addInvalidMask(_myCube_)==.
<verbatim>
def addInvalidMask(slicedCube):
    for i in range(0,slicedCube.numberOfSlices):
    	cube = slicedCube.get(i)
    	invalid = IS_NAN(cube.flux)
    	if not cube.containsMask("INVALID"):
    		cube.addMask("INVALID","Invalid signal values")
    	cube.setMask("INVALID",invalid)
    	slicedCube.replace(i,cube)
</verbatim>

---+++!! HIPE hangs when pressing the activate/deactivate button in the mask panel of the Spectrum Explorer PACS extensions

This button is enabled only when you change the state of one or more masks. *Fixed in HIPE 9.1.* <!-- PACS-4626 -->

---+++!! Image analysis tasks start only from _Applicable_ section

Image analysis tasks will open only from the _Applicable_ folder of the _Tasks_ view. These tasks will not open when selected from the _All_ or _By Category_ folders. Note that you must select an image variable in the _Variables_ view for the _Applicable_ folder to be filled with the available tasks. *To be fixed in HIPE 10.* The problem affects the following tasks:
   * ==annularSkyAperturePhotometry==
   * ==circleHistogram==
   * ==crop==
   * ==ellipseHistogram==
   * ==fixedSkyAperturePhotometry==
   * ==polygonHistogram==
   * ==profile==
   * ==rectangleHistogram==
   * ==rectangularSkyAperturePhotometry==
   * ==sourceFitting==

---+++!! PV diagrams created with computePVMap on HIFI cubes cannot be easily viewed

HIFI cubes have in general a small number of rows and columns, while the spectral dimension is rather large (thousands of channels). The PV map is very narrow in the x direction and really wide in the y-direction, so that it does not fit in the Spectrum panel. When displaying the y-axis values, at its smaller zoom, only a small number of channels can be seen. Workaround:  open the variable created from the variables pane and use the full Display/Image Viewer.
<!-- use the old Cube Spectrum Analysis Toolbox, still available in HIPE 9. Legacy documentation is available in [[http://herschel.esac.esa.int/hcss-doc-9.0#howtos:Dag.SpectralAnalysis.App][Appendix C]] of the _Data Analysis Guide_. For position-velocity diagrams, see subsection C.6.8.1.-->

---+++!! HIPE crash linked to JAMA (Java Matrix) library

HIPE may crash without warning when executing parts of the bundled JAMA library. If you experience a sudden crash when running a script, this may be the cause, even if there are no obvious references to matrices in the script. Take the following steps to prevent the crash from happening:
   1. Go to the ==.hcss== directory in your open directory. Open the ==hipe.props== file, or create it if it does not exist.
   1. Add the following line to the file:<br/>java.vm.options = -XX:CompileCommand=exclude,Jama/LUDecomposition,&lt;init&gt;
   1. Restart HIPE.

---+++!! Problem with transpose task

In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur. *To be fixed in HIPE 10.*

---+++!! Velocity map creation in _Legacy_ Cube Spectrum Analysis Toobox (CSAT) fails

The creation of velocity maps with the _Legacy CSAT_ fails; the task will hang  without an error message.  CSAT is no longer supported and the new cube toolbox, which uses an improved algorithm for velocity map making, should be used instead.  See [[http://herschel.esac.esa.int/hcss-doc-9.0/load/howtos/html/Dag.Sec.CubeMapsCSAT.html#Dag.Sec.CubeVelMapCSAT 6.8.3]] in the Herschel Data Analysis Guide for information about using the new cube toolbox.

---+++!! Flag set in HIFI's flagTool task do not appear to be used by the fitBaseline task

This is a display issue only, the flags set by flagTool are, in fact, used.

---+++!! PACS specific: ==convertL1ToScanam== fails 

*convertL1ToScanam* fails because of a missing import for the calibration tree, when assignRaDec is set to True. The work around solution is :  

<verbatim>
calTree = getCalTree(time=frames.startDate)
frames=photAssignRaDec(frames,calTree=calTree)
convertL1ToScanam(frames,assignRaDec=False)
</verbatim>

*Fixed in HIPE 9.2.*

---++ Older HIPE versions

Known issues for older HIPE versions are listed in a [[HipeKnownIssuesOld][separate page]].

---++ General HIPE startup issues

---+++!! HIPE does not start at all, without giving error messages. What's wrong?

This can happen for different reasons, that are explored in the next entries. When you start HIPE by clicking on its icon and a problem occurs, you may only see a terminal/command window appear for a fraction of a second, leaving you without information on the error.

To obtain more information about the error, try invoking HIPE directly from a terminal/command window (==[installation_dir]/apps/hipe==) and examine the text output. Note that the output from some errors can be quite lengthy, so you may need to scroll up to discover the root cause.

The next entries list some common problems that prevent HIPE from starting.

---+++!! HIPE cannot start: the JVM cannot reserve enough memory
	
This only applies if you installed HIPE using the installer, and not downloading a developer build from the Continuous Integration System.

The cause is that the Java virtual machine is unable to start with the designated amount of memory.

The terminal/command window from which you invoke HIPE shows the following error message that indicates insufficient memory:

<verbatim>
Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.
</verbatim>

To fix this error you have to modify two properties in the ==installed.properties== file within your HIPE installation directory. _There is no need to reinstall HIPE._

The properties you need to modify are the following. You have to lower the amount of allocated memory:

<verbatim>
java.vm.memory.max
java.vm.options=-XX:PermSize
</verbatim>

Possible values are the following:

<verbatim>
java.vm.memory.max=1024m
java.vm.options=-XX:PermSize=128m
</verbatim>

Try running HIPE after modifying the values until it successfully starts.

| %X% You may have the same properties defined in a ==hipe.props== or ==user.props== file, located in the ==.hcss== directory within your home directory. In this case, any values set in ==hipe.props== override those in ==user.props==, which override those in ==installed.properties==. Make sure to edit the properties in the file with highest proprity for your changes to take effect. See [[http://herschel.esac.esa.int/hcss/install.php#howdoi][this page]] for more information on property files and their precedence order.|

---+++!! HIPE cannot start: ==SAXNotRecognizedException==

The terminal/command window from which you invoke HIPE shows a ==SAXNotRecognizedException==.

To solve this issue, add the following line to the installed.properties file in your HIPE installation directory:

==java.vm.options = -Djavax.xml.parsers.SAXParserFactory=com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl==

---+++!! HIPE cannot start: exception access violation.

The terminal/command window from which you invoke HIPE shows an ==EXCEPTION_ACCESS_VIOLATION== error related to a class in ==org.apache.xerces==.

Restart HIPE to resolve the issue.

This error is probably due to a bug in the Java Virtual Machine, and has so far been found only on Windows XP 32 bit.

---+++!! I get startup messages about missing HIFI/PACS/SPIRE modules. Is that serious?

You are probably referring to messages such as the following (for HIFI; messages for PACS and SPIRE are the same):

<verbatim>
Import "from herschel.hifi.all import *" returns:
          Import Error -> No module named hifi
</verbatim>

Such messages are harmless and just reflect the fact that you have not installed the software related to the specified instruments.

---++ General Help System issues

---+++!! The help does not work anymore! What's wrong?

First, check if your issue is that described below, in _Why is the HIPE Help System suddenly unable to connect to any help page?_
If not, you have probably encountered a bug. The following are known issues that can prevent you from viewing the documentation, resulting either in a blank page or an error message:

   * A caching bug in Safari 4.0 can be solved by clearing the browser cache. Alternatively, open the help page with another web browser: copy and paste the address (something like _http://127.0.0.1:8082/index.jsp?mark=null_) to the address bar of the other browser.
   * A problem with Mac OS X can result in error messages when viewing the documentation of any installed HIPE version. In particular, you may get an _HTTP ERROR: 404 NOT FOUND_ message in your browser, and a message about ==index.jsp== not found in the command line terminal. Rebooting the computer solves the issue.
   * Older browser versions may not display documentation correctly. For example, links from HIPE to the Help System, like the _Help in URM_ menu entries for tasks, work in Firefox 3.6.x but not in Firefox 3.0.x. Other legacy browsers may have similar problems.
   * If you are using Linux and get an error message like *Firefox can not contact the server www.%u.com*, change your default browser from ==firefox %u== to ==firefox %s== (same if ==mozilla== is your default browser). See the documentation of your Linux distribution for how to change default web browser. Alternatively, in HIPE choose _Edit --> Preferences_, go to _Help &amp; Documentation_ and enter the path to Firefox, or to another browser on your system, in the _Browser_ field. Click _Test_ to check if it works.
   * In general, when you encounter a problem with the Help System you should follow these steps:</para>
      * See if the help works with another browser. If possible, upgrade your browser to the latest version.
      * Clear the browser cache
      * Delete the browser cookies
      * Reboot the computer
If none of the above works, please raise a ticket with the Helpdesk.

---+++!! Is there a way to open the HIPE Help System without starting HIPE?

Yes, via the ==hipe_help== command, which resides in the ==apps== folder in your HIPE installation. The ==hipe_help== command will start a standalone Help System in a window called _Yet Another JAva Help System_. Press the _Display_ button to open the Help initial page in your default browser.

---+++!! The Help System opens in my web browser. Does it mean I need to be connected to the Internet?

No, the Help System resides on your computer and does not need Internet connection, except of course for links to online resources, such as !YouTube videos and pages hosted on the Herschel Wiki website, including the _What's New_ and _Known Issues_ documents. 

---+++!! Why does searching the documentation take such a long time?

When you execute the first search with a new HIPE version, HIPE has to index the contents of the documentation. This can take up to several minutes, depending on the performance of your system. Indexing of the documentation is _only done for the first search_. Subsequent searches will be much faster.

We are investigating ways to include pre-built indexes in the documentation shipped with HIPE, so you will not have to wait for the results of your first search.

---+++!! Why is the HIPE Help System suddenly unable to connect to any help page?

The Help System relies on a local web server to display help pages. If you close the application that started the web server, the server will shut down as well:

   * If you started the Help System from HIPE, quitting HIPE will stop the Help System.
   * If you started the Help System with the <command>show_help</command> command, closing the <emphasis>Yet Another JAva Help System</emphasis> window will stop the Help System.

Note that when the Help System stops, any browser window or tab showing help pages _will remain open_, but links on them will not work anymore.

---+++!! Why are several important packages missing from the Javadoc?

You are probably looking at the _static_ Javadoc located in the ==doc/api/== folder of your HIPE installation. The complete Javadoc can now be accessed from the HIPE Help System by clicking on _HCSS Developer's Reference Manual (API)_ in the _Developer Reference_ section. The plan is to remove the static version of the Javadoc completely.

---+++!! Is it possible to have the traditional, frame-based Javadoc layout?

Javadoc pages appear within the HIPE Help System frame structure. If you click on the _FRAME_ link on any Javadoc page, you will obtain the traditional Javadoc layout. To go back to the HIPE Help System layout you will have to use the _Back_ button of your browser (clicking on the _NO FRAMES_ link will not work). To avoid losing the HIPE Help System layout, you may want to right-click on the _FRAMES_ link to open the traditional Javadoc layout into a new tab of your web browser.

---+++!! How can I provide feedback/requests regarding HIPE documentation?

You can leave a comment using the box at the bottom of any documentation page in the HIPE Help System. You must be connected to the Internet to view and submit comments.

Alternatively, you can click the envelope icon on the top toolbar of any help page. This opens a new message in your email client, where you can add your feedback. 

If you want your issue to be officially tracked and supported, please raise a ticket with the Helpdesk of the Herschel Science Centre.

---+++!! Other help issues

   * *URM categories:* Some entries in the three instruments _User's Reference Manuals_ have wrong or missing categories.
   * *URM examples*: Some examples in the _User's Reference Manuals_ may not work as expected. Please use the feedback icon in the HIPE Help System to let us know about broken examples.
   * *JIDE vs HIPE*: The documentation shipped with HIPE may still mention JIDE in some places. JIDE was the data reduction application that came before HIPE and is no longer supported. All references to JIDE can be applied to HIPE.

---++ Herschel Science Archive issues



---+++!! I have downloaded FITS files in a tar archive from the HSA, but they are corrupted. How can I fix them?

You may have used !WinZip under Windows. !WinZip has an option called _TAR file smart CR/LF conversion_, in the _Miscellaneous_ tab of the _Configuration_ dialogue window (at least up to version 15.0), that is enabled by default and causes the corruption. Disable the option to solve this problem. You can also use other software such as 7-Zip. 

---+++!! In the HSA user interface I can query and select observations, but I do not get the option in the HSA to pass the data to HIPE, or in HIPE to load the selected products. Why?
	
If you are using Windows, the problem might be that you instructed your browser to auto-detect proxy settings. In Windows this is a system-wide setting which affects any application connecting to the Internet, including HIPE.

You can change proxy settings for HIPE by following the instructions in the [[http://herschel.esac.esa.int/hcss-doc-10.0/#hipeowner:site.hipe.proxy][HIPE Owner's Guide]]. 

---+++!! When I click _Send to external Application_ in the HSA interface, nothing seems to happen. What is going on?

The data is being transferred in the background. Clicking _Send to external Application_ should bring to the front the main HIPE window, which will tell you that data is indeed being received. In some cases however the HIPE window does not appear. Bring it to the front manually to follow the progress of your action. 

---+++!! When I try to retrieve data from the HSA I get an error message in the console about an invalid magic number for FITS file. What is going on?

The reason is that the "data" being downloaded is in reality a small file containing an error message. Two issues have been shown to cause this problem:

   * Your HSA password has non-alphanumeric characters in it. Change it to a password containing only letters and numbers.
   * Your HSA username has uppercase characters. Write it using only lowercase letters.

---++ Other issues

---+++!! HIPE crashed/froze! What do I do?

If you cannot find a solution in this document, you may have found a bug in HIPE. Please report it by opening a [[http://herschel.esac.esa.int/esupport/][Helpdesk ticket]]. If the system produced a dump file when the crash happened, make sure to include it in your ticket. For more information about dump files and where to look for them, see the [[http://herschel.esac.esa.int/hcss-doc-10.0/load/hipeowner/html/Hipeowner.Sec.Feedback.html#sec-when-things-go-wrong][HIPE Owner's Guide]]. 

---+++!! Cannot open a FITS file created by HIPE

If you export a FITS file from HIPE and modify it with an external program, HIPE may not be able to import it anymore. If this happens, follow these steps:
 
   1. Open the FITS file with a FITS editing program such as *fv*.
   1. Delete the ==HCSS____== keyword from the header of _all extensions_.
   1. Save the file.
      
HIPE should now be able to read the file.

---+++!! Cannot run !WebStart applications on Mac OS Lion or Mountain Lion because of security settings

!WebStart applications that can be opened from within HIPE include the HSA User Interface, Aladin, VOSpec and so on. When trying to open one of such applications, a window like the following may appear:

%ATTACHURL%/topcat.png

This is caused by the security settings of the _Gatekeeper_ feature of Mac OS. For more information about Gatekeeper, see the [[http://support.apple.com/kb/HT5290][Apple support website]].

To allow a !WebStart application that is blocked, change the _Allow applications downloaded from_ option in Gatekeeper from _Mac App Store_ to one of the two less restrictive options. If the application has a valid certificate, the _Mac App Store and identified developers_ option will suffice. Otherwise you will need to select the _Anywhere_ option.

---+++!! "Invalid context" errors on Mac OS X Lion 

When you start HIPE form a Terminal window on Mac OS X Lion, you may see errors such as these:

<verbatim>
java[40745] <Error>: CGContextGetCTM: invalid context
</verbatim>

These errors are harmless and can be safely ignored.

---+++!! Jython bug when comparing !NaN values with numbers

Jython behaves differently from Python when comparing ==NaN== values with numbers.

In Python 2.4 or 2.5:

<verbatim>
nan = float("nan")
print 0 < nan
# False
print 0 > nan
# False
</verbatim>

In Jython 2.5.2:

<verbatim>
nan = float("nan")
print 0 < nan
# False
print 0 > nan
# True
</verbatim>

An [[http://bugs.jython.org/issue1840][issue]] has been opened on the Jython bug tracker.

---+++!! "Can't connect to X11" error when using the jylaunch command

Executing a script outside HIPE with the ==jylaunch== command may fail with a ==java.lang.InternalError: Can't connect to X11 window server== error. This may happen even if the script does not open any graphical window, since it may indirectly call components that require an X11 server. The workaround is to run the script with the command ==jylaunch -Djava.awt.headless=true== instead of just ==jylaunch==.

---+++!! Problems saving observations to NFS-mounted disks and FAT32 disks

When saving observation to your computer, you may experience problems in the following cases:
   * When saving data to NFS-mounted disks (you may get an ==IllegalMonitorStateException==).
   * When saving data to a FAT32 filesystem from a Mac (you may get an ==OverlappingFileLockException==).
Both problems are solved by setting the following property:
<verbatim>
hcss.ia.pal.pool.lstore.lock = simple
</verbatim>
See the [[http://herschel.esac.esa.int/hcss-doc-10.0/index.jsp#hipeowner:site.hipe.props][HIPE Owner's Guide]] for information on how to set properties.

---+++!! Why do I get a !ClassCastException when trying to save an observation with the saveObservation command?

You probably retrieved the observation without having the corresponding instrument software installed (for instance, you retrieved a PACS observation without having the PACS modules in HIPE).

To solve this problem follow these steps:

   1. Reinstall HIPE, including the software of the desired instrument.
   1. Delete the following directories (==home== being your home directory):
      * ==home/.hcss/lstore/hsa_cache==
      * ==home/.hcss/pal_cache/hsa==
   1. Retrieve the observation again.

---+++!! I get an ==OutOfMemoryError== related to _PermGen_ space. What can I do?

Add or edit the following property in your ==hipe.props== property file:

<verbatim>
java.vm.options = -XX:MaxPermSize=256m
</verbatim>

Note that this parameter is specific to the Sun/Oracle Java implementation, which is the only one officially supported by HIPE.

For more information about property files, see the [[http://herschel.esac.esa.int/hcss-doc-10.0/index.jsp#hipeowner:site.hipe.props][HIPE Owner's Guide]].

---+++!! There are PACS files I cannot delete! Why?

It might not be possible to delete the following files on Windows because their full path exceeds the 260 characters limit.

   * ==PCalSpectrometer_RelCalSourceFlux_FM_v1.fits_2009...80Z.fits==
   * ==PCalSpectrometer_RelCalSourceFlux_FM_v2.fits_2009...55Z.fits==
   * ==PCalSpectrometer_RelCalSourceFlux_FM_v2.fits_2009...14Z.fits==
   * ==PCalSpectrometer_RelCalSourceFlux_FM_v2.fits_2009...21Z.fits==
   * ==PCalSpectrometer_RelCalSourceFlux_FM_v2.fits_2009...58Z.fits==

You can avoid this problem by installing HIPE with a short initial path, such as ==C:\hipe==, so that full paths remain below the limit.

---+++!! HIPE does not accept keyboard input anymore! What's wrong?

If you are running Linux, this could be due to a compatibility problem between Java and SCIM (Smart Common Input Method). A workaround is to stop SCIM or uninstall it. Please refer to the documentation of your distribution for how to do so.

The problem is described in more detail on these pages:

   * http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6506617
   * http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6299259

---+++!! What are all the ==tmp_product_sink_*== pools in my local store directory?

You may find these pools in your local store directory (by default ==.hcss/lstore== in your home directory) after reducing data with HIPE. These are temporary pools that are not deleted upon quitting HIPE due to a known bug. You can safely delete them by hand after quitting HIPE.

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