HEASoft v6.29 - Known Issues

If you are using HEASoft v6.28 and don't want to upgrade to v6.29 just yet, see the HEASoft 6.28 Issues List.

Several packages track issues separately from this page:

• Swift
• CALDB
• XSPEC
• XSTAR
• HEASP
• XIMAGE
• XRONOS

The following is a list of known issues in v6.29 of HEASoft not covered by the above pages.

• MacPorts compiler libraries & rpath:
  
  MacPorts compiler libraries are (or may soon be) installed using an rpath location rather than a hard-coded directory path, so when using MacPorts compilers we recommend that - prior to configuring heasoft - you set the LDFLAGS environment variable to tell heasoft executables where to find these libraries at runtime, for example:

  
    $ export LDFLAGS="-Wl,-rpath,/opt/local/lib/gcc11"
  
  

  Note that the path may differ depending on your MacPorts installation and the compiler version, but the directory you use should contain for example "libgfortran.5.dylib" and "libgcc_s.1.1.dylib".
• Mac "gcc-11: error: unrecognized command-line option '-iwithsysroot'; did you mean '-isysroot'?":
  
  On newer macOS we have found that using the Apple Perl (/usr/bin/perl) alongside third-party GCC (Homebrew, MacPorts, etc.) may cause build problems as a result of flags ("-iwithsysroot") that Apple's Perl inserts into our C/Perl library configuration. So, we recommend that you install and use e.g. the matching Homebrew or MacPorts Perl.
• Mac "C compiler cannot create executables":

  The HEASoft configure script may fail with "C compiler cannot create executables", and one of the config.logs may show
  
  ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib/libSystem.tbd' for architecture x86_64
  
  or
  
  ld: library not found for -lSystem
  
  The former error may be resolved by putting /usr/bin at the front of your PATH environment variable (as recommended in our Mac installation guide), and the latter typically implies that your compiler suite (e.g. Homebrew or MacPorts) is out-of-synch with Apple XCode and its Command Line Tools (CLT), for example if you updated XCode but did not reinstall Homebrew after doing so. Since these third-party compilers use XCode as their starting foundation, they must typically be rebuilt/reinstalled whenever XCode is updated.

• Apple clang 12 (or newer):
  
  Builds of HEASoft using version 12 or newer of the Apple clang compiler are not supported, though we hope to be able to support clang again in a future release. Users are advised to follow the instructions in our Mac installation guide for using third-party compilers (Homebrew, MacPorts, etc.) instead.
• NICER nicerarf, nivigsum, nifpmsel & niextract-events:
  
  The NICERDAS tasks nicerarf, nivigsum, nifpmsel and niextract-events have been updated to fix an "off-by-one" TIMEZERO bug. The nicerarf task now requires "fixed" event files with a new NICTZFIX keyword, and has also been updated to fix a detector-dependent response weighting factor bug (see also this link).

  All of these issues are fixed in current downloads (2021 September 1), but users may update their older 6.29 (or 6.29a/b) installation by following these patch instructions (6.29c includes the 6.29a & 6.29b patches referred to elsewhere).

• extractor & event file TIMEZERO keyword: When writing an output event file, a long-standing bug in extractor creats a TIMEZERO keyword with value 0.0 instead of copying TIMEZERO from the input event file. Since event data are copied directly from the input to output event file, no time correction is made and therefore TIMEZERO should be left unchanged.
  
  To fix this issue in your source code distribution, please download this extractor patch, copy it into the directory containing your heasoft-6.29 source code tree (i.e. "above" the heasoft-6.29 folder), unpack it there, and then rebuild:

    1) Initialize HEASoft
  
    2) Rebuild & reinstall the heasp library:
  
       $ cd heasoft-6.29/ftools/heasarc/tasks/extractor
       $ hmake clean
       $ hmake all
       $ hmake install
  

• XTE fcollect task & vector columns: The XTE task fcollect or e.g. the xtefilt task that invokes it may generate an error ("Sorry, but this is a vector column...skipping") due to a string overflow when checking for vector columns. This is fixed in a new version of fcollect.
  
  To fix this issue in your source code distribution, please download this updated version of fcollect.c, and then rebuild:

    1) Copy the new fcollect.c into heasoft-6.29/ftools/xte/tasks/fcollect/
  
    2) Initialize HEASoft
  
    3) Rebuild & reinstall fcollect:
  
       $ cd heasoft-6.29/ftools/xte/tasks/fcollect/
       $ hmake clean
       $ hmake all
       $ hmake install
  

• NICER nicerl2 / nifpmsel & niextract-events:
  
  When running nicerl2 or nifpmsel to generate cleaned events, an error message of the form "Input GTI must be time-ordered for GTIOVERLAP" may appear (see also this link).

  Additionally, the task niextract-events may crash when handling empty event files.

  Both of these issues are fixed in current downloads (2021 September 1), but users may update their older 6.29 (or 6.29a) installation by following these patch instructions .

• HEASPTOOLS (ftrbnpha, ftaddarf, ftaddrmf):
  
  A few issues have been fixed in the heasptools:

  ftaddrmf: Added an explicit check for incompatible RMFs; now writes an error message if found instead of silently failing to do the addition. In the case of only EBOUNDS values differing, continue and write a warning message at the end. This issue can affect e.g. the addspec task which invokes ftaddrmf.

  ftaddarf: Added an explicit check for compatibility between arfs being summed.

  ftrbnpha: Fixed crash that occurred if using a binfile which starts by not including channels.

  All of these issues are fixed in current downloads (2021 September 1), but users may update their older 6.29 installation by following these patch instructions .

• NICER pipeline & nicaldbver:
  
  When running nicerl2 or niprefilter to generate a filter file, an error of the form "satellite has re-entered at YYYY/MM/DD" may appear due to an error in the task prefilter when using the new option "orbpropagate=YES" (see also this link). An update to prefilter allows it to more gracefully handle interpolation across large gaps in orbit files by adding the first derivative of mean motion for large gaps.

  Additionally, the NICER CALDB version-reporting task nicaldbver may incorrectly report "INDEF".

  Both of these issues are fixed in current downloads (2021 July 30), but users may update their older 6.29 installation by following these patch instructions . (Note that the 6.29a patch is included in the 6.29b patch, so there is no need to install them separately.)

• "Developer cannot be verified" or "unidentified developer" error on Macs:
  
  Some Mac users have reported problems configuring and/or running pre-compiled HEASoft binaries. To free HEASoft binaries from the Apple quarantine, use the xattr utility, e.g.:

  $ cd heasoft-6.29/x86_64-apple-darwin-19.6.0
  $ xattr -r -d com.apple.quarantine BUILD_DIR/configure lib/* bin/*
  

• Fortran compiler requirements:
  
  HEASoft now includes a new dependency on the FGSL library which requires a Fortran 2008 feature (c_loc for targeted arrays); therefore GNU Fortran compilers older than version ~5.x are unsupported.
• XIMAGE and gfortran 8.x (or newer) on macOS:
  
  When built with the Apple XCode C compiler (clang) paired with gfortran newer than version 8.0, ximage may generate "Invalid header key" messages and a Tcl error "Failed to run tcl: pgtk::upcopy MAP1 MAP9". Subsequent attempts to display the image may then result in a segmentation fault. Note that this problem will affect tasks that use ximage such as xrtpipeline or nupipeline. To get around this, we recommend avoiding the Apple XCode compilers and using only a third-party compiler suite instead, as noted in our Mac installation guide.


• Perl symbol lookup error, "undefined symbol: Perl_Gthr_key_ptr":

  If running a HEASoft Perl script generates an error similar to the above, it may result from a Perl version incompatibility (common when using the pre-compiled binaries), but it may also occur if you have the VERSIONER_PERL_PREFER_32_BIT environment variable set to "yes". If "echo VERSIONER_PERL_PREFER_32_BIT" returns "yes", then unset it:

     unset VERSIONER_PERL_PREFER_32_BIT
  
  or, in C-shell:
  
     unsetenv VERSIONER_PERL_PREFER_32_BIT
  

• Mac "configure failed..." Fortran compiler issue:

  The configure script may generate an error ("Configure failed in the AST package!", or "configure failed for heacore component fftw!") resulting from a MacPorts assembler (as) under /opt/local/bin being ahead of the default Apple /usr/bin/as in a user's PATH (which may result from an automated change made to .profile during a MacPorts installation). To get past this issue, put /usr/bin at the front of your PATH:

     export PATH="/usr/bin:$PATH"
  

• MacPorts "unexpected token" linker issue:

  If you are using MacPorts compilers in your build, 'make' may fail when building the HEASoft source code distribution with an error referring to a new Xcode linker ("ld") format ("tbd"), e.g.:

  ld: in '/System/Library/PrivateFrameworks/CoreEmoji.framework/Versions/A/CoreEmoji.tbd', unexpected token: !tapi-tbd-v2 ...
  

  The underlying issue is discussed here and here; it appears that when new versions of the XCode command line tools are released, problems such as this may affect MacPorts compilers until they catch up with Apple's changes. Users should be able to get around the error in our build by installing the MacPorts 'xcode' variant of the linker ld64 as a temporary measure:

  
      sudo port install ld64 +ld64_xcode
  
  

  and when MacPorts eventually supports the latest XCode command line tools, you can switch back to the latest ld64 with the following:

  
      sudo port install ld64 +ld64_latest
  
  

• Mac "suffix or operands invalid for 'movq'" Fortran compiler issue:

  When using the gnu.org gfortran binaries note their recommendation that when installing new versions of the compiler you should remove the previous gfortran installation first:

     $ sudo rm -r /usr/local/gfortran /usr/local/bin/gfortran
  

  Failure to do so may result in a corrupted compiler installation, leading to the "suffix or operands invalid for 'movq'" error.



• Ubuntu ds9 & HEASoft:

  After initializing HEASoft on Ubuntu Linux, the ds9 GUI (if installed) may fail to start up (mentioning "can't find package xml", "can't find package uri 1.1", or "package require base64""). This results from incompatibilities between the Tcl/Tk included with HEASoft and the Ubuntu system libraries. Until a more elegant solution can be devised, we recommend that users try one of the following options, depending on the file type of your ds9 (shell script or compiled executable - check the output from "file `which ds9`" to determine which it is):

  
  1) If ds9 is the shell script version, edit it to change the line
  
       exec wish8.6 -f ${DS9_HOME-/usr/share/saods9}/library/ds9.tcl $*
  
     to
  
       exec /usr/bin/env -u LD_LIBRARY_PATH /usr/bin/wish8.6 -f ${DS9_HOME-/usr/share/saods9}/library/ds9.tcl $*
  
  or
  
  2) If ds9 is the compiled executable version, create a new file
     "$HEADAS/bin/ds9" containing the following lines:
  
       #!/bin/sh
       exec /usr/bin/env -u LD_LIBRARY_PATH /usr/bin/ds9 "$@"
  
     (Note this assumes that `which ds9` = /usr/bin/ds9)
  
     To make the new script executable, run the following command:
  
       $ chmod +x $HEADAS/bin/ds9
  
     Then, as long as $HEADAS/bin is ahead of /usr/bin in your PATH, you
     should now be able to successfully run ds9 from the command line:
  
       $ rehash
       $ ds9
  
  




• "relocation R_X86_64_32 against `.rodata' can not be used when making a shared object":
  
  Users building HEASoft from the source code distribution may run into this error which refers to a "Bad value" in the file heacore/wcslib/C/cel.o, from which the linker "could not read symbols". It also suggests that you "recompile with -fPIC". This situation most likely occurrs when users perform a re-build after a previously unsuccessful build attempt. To get past this issue, try the following:

  
     $ cd heasoft-6.27.1/BUILD_DIR
     $ make distclean
  
  

  When that finishes, restart the build procedure beginning with "./configure", then "make", and let us know if this does not resolve the problem.



• fv - XPA_METHOD:
  
  Some users of the fv GUI may experience long delays at startup, or error messages of the type "XPA$WARNING: xpans needs to be running on this machine", or "XPA$ERROR: invalid host name specified: $host:$port" (when using the ds9 display device). These issues tend to occur on Macs with customized firewall settings, or on machines without valid IP addresses. This can be resolved by setting the XPA_METHOD environment variable to the value "local" (to use local/UNIX sockets instead of inet sockets):

  
          export XPA_METHOD=local          # Bourne shell (bash/sh)
  or
          setenv XPA_METHOD local          # C-shell (csh/tcsh)
  
  

• Perl version mismatch::
  
  Pre-compiled Perl libraries used extensively by mission software (Swift, Suzaku, NuSTAR) and other packages are not especially portable, so we generally recommend building HEASoft from the source code distribution.



• xspec / PLT - wenv, whead, wdata:
  
  Some GNU Fortran compilers (gfortran 4.4.x, 4.0.x, 4.1.x) appear to have internal issues which prevent the PLT commands wenv, whead and wdata from working unless an output file is specified; i.e. attempts at producing terminal output may fail with "Fortran runtime error: Invalid argument". To get around this, provide an output file name when using these commands, for example:

       wenv myFile1.qdp
       whead myFile2.qdp
       wdata myFile3.qdp
  




• HEASoft and other software packages (CIAO, XMM-SAS):
  
  

  Please note:

  Users may wish to download and run our hwrap script to create an alternate runtime environment for HEASoft to help avoid conflicts with other software packages, but if not, please take note of the potential pitfalls below:
  
  
  • CIAO:
    
    Please see the following notes at the CXC website regarding the potential dangers of using CIAO and HEASoft together in the same session:
    
    
    • FTOOLS & CIAO
      
  
  
  
  • XMM-SAS:
    
    The XMM-SAS setup typically adjusts your LD_LIBRARY_PATH environment variable (or DYLD_LIBRARY_PATH on macOS) to include the SAS library folders, one of which includes a copy of the C++ compiler library (libstdc++). This can cause problems building HEASoft, so we recommend that HEASoft be built in a session in which the SAS has not been initialized, or at least one in which your [DY]LD_LIBRARY_PATH is either empty or otherwise does not include the installed SAS directories.
    
    Similarly, after both SAS and HEASoft are installed, if they are initialized in the same session (terminal), C++-based tasks such as XSPEC may suffer runtime problems if the XMM-SAS library directories precede the one needed by XSPEC in [DY]LD_LIBRARY_PATH (as is the case if the SAS is initialized after HEASoft. As an example, if you compiled HEASoft on a Mac using the Homebrew compilers, XSPEC will need to have the Homebrew library path ahead of the SAS library directories in your DYLD_LIBRARY_PATH:

         For example:
    
         C-shell:
    
             setenv DYLD_LIBRARY_PATH "/usr/local/opt/gcc/lib/gcc/10:${DYLD_LIBRARY_PATH}
    
         Bourne shell:
    
             export DYLD_LIBRARY_PATH="/usr/local/opt/gcc/lib/gcc/10:${DYLD_LIBRARY_PATH}
      

    Additionally, when both the SAS & HEASoft are used in the same session and the SAS was initialized after HEASoft, the SAS setup changes the value of the environment variable PGPLOT_FONT with the result that plots in e.g. XSPEC may (or may not, depending on the software distributions in use) have no axis labels or values. Users can fix this by resetting PGPLOT_FONT to point to the HEASoft location:

         C-shell:
    
             setenv PGPLOT_FONT $HEADAS/lib/grfont.dat
    
         Bourne shell:
    
             export PGPLOT_FONT=$HEADAS/lib/grfont.dat
    
      

    or by simply re-initializing HEASoft:

         C-shell:
    
             source $HEADAS/headas-init.csh
    
         Bourne shell:
    
             . $HEADAS/headas-init.sh
      

    This may in turn have consequences for plotting in XMM-SAS, in which case users may need to return PGPLOT_FONT to the SAS setting when using it for data analysis.

Web page maintained by: Bryan K. Irby