<div dir="ltr">Hi Xavier and Kevin,<br><br>H5Rdereference is defined in libhdf5. It is referenced but not defined in libhdf5_hl. <br><br>One thing that might be related to this problem is the fact that in HDF5 1.10.x H5Rdereference has become a macro that points to one of two different function signatures: H5Rdereference1 or H5Rdereference2, depending on various compiler flags and/or source code defines. H5dereference2 has one more argument and is the newer version intended for use with HDF5 1.10 and newer. <br>If you were compiling against 1.8.x header files but linking against 1.10 libraries, then that could be a scenario where H5Rdereference would show up as an undefined symbol. I'm not sure if this is a plausible explanation, but, if not, it is an interesting coincidence that this is one of only two cases where a function name was changed to a macro in the migration from 1.8.x to 1.10.x.<div><br>See <a href="https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html">https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html</a></div><div><br> -dave<br><br><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, May 15, 2017 at 6:31 PM, Kevin Hallock <span dir="ltr"><<a href="mailto:hallock@ucar.edu" target="_blank">hallock@ucar.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Xavier,<div><br></div><div>First of all, thank you for maintaining this package on the AUR. I use Arch Linux at home, so it’s great to see someone supporting this!</div><div><br></div><div>I tried makepkg’ing the PKGBUILD you provided, but I encountered the same H5Rdereference error. I noticed that the hdf5_18 package is listed as a dependency, and then noticed that /usr/lib/hdf5_18 does not include libhdf5_hl.so. Someone reported this for a previous version of hdf5_18, but it doesn’t appear to have been fixed since then: <a href="https://bugs.archlinux.org/task/51902" target="_blank">https://bugs.archlinux.<wbr>org/task/51902</a> </div><div><br></div><div>I also found that the newer hdf5 package was installed as a dependency for both gdal and netcdf, with its libs and includes directly in /usr/lib and /usr/include (as opposed to /usr/{lib,include}/hdf5_18 for hdf5_18); the libs and includes seem to be duplicated between the two packages (except the libhdf5_hl.so* files mentioned above), so I wonder if perhaps having both of these installed is causing a conflict?</div><div><br></div><div>Also, I noticed that the Site.local you provided has “<font face="Menlo">-I/usr/include/hdf5_18</font>” in IncSearch, but no corresponding “<font face="Menlo">-L/usr/lib/hdf5_18</font>” in LibSearch. I tried adding “<font face="Menlo">-L/usr/lib/hdf5_18</font>”, but the build still failed.</div><div><br></div><div>For what it’s worth, /usr/lib/hdf5_18/libhdf5.so <i>does</i> seem have a reference to H5Rdereference:</div><div><font face="Menlo">$ nm -D /usr/lib/hdf5_18/libhdf5.so | grep H5Rdereference<br>000000000016cfb0 T H5Rdereference</font></div><div><br></div><div>I hope this helps!</div><div>Kevin</div><div><br></div><div>PS - I currently run NCL 6.4.0 on Arch using conda: <a href="http://ncl.ucar.edu/Download/conda.shtml" target="_blank">http://ncl.ucar.edu/<wbr>Download/conda.shtml</a> </div><div><br><div><blockquote type="cite"><div><div class="h5"><div>On May 15, 2017, at 3:06 PM, Xavier Corredor Llano <<a href="mailto:xcorredorl@unal.edu.co" target="_blank">xcorredorl@unal.edu.co</a>> wrote:</div><br class="m_-5695297029999725325Apple-interchange-newline"></div></div><div><div><div><div class="h5">hi everyone, <br><br>I'm the maintainer of the NCL packages for Archlinux [1], I have some issues for build the new version 6.4.0, the error is:<br><br>NclNewHDF5.o: In function `_checkH5attribute':<br>NclNewHDF5.c:(.text+0x2818): undefined reference to `H5Rdereference'<br>NclNewHDF5.c:(.text+0x3552): undefined reference to `H5Rdereference'<br>NclNewHDF5.o: In function `_region2string':<br>NclNewHDF5.c:(.text+0x4c89): undefined reference to `H5Rdereference'<br>NclNewHDF5.o: In function `_mem2string':<br>NclNewHDF5.c:(.text+0x4de1): undefined reference to `H5Rdereference'<br>NclNewHDF5.o: In function `_readH5dataInfo':<br>NclNewHDF5.c:(.text+0x64aa): undefined reference to `H5Rdereference'<br>collect2: error: ld returned 1 exit status<br>make[4]: *** [Makefile:707: ncl] Error 1<br>make[4]: Leaving directory '/build/ncl/src/ncl_ncarg-6.4.<wbr>0/ni/src/ncl'<br><br>using hdf5 version 1.8.18, the build instructions (PKGBUILD) and completed build log can found in [2].<br><br>Thanks for any help!<br><br>Xavier<br><br>[1] <a href="https://aur.archlinux.org/packages/ncl/" target="_blank">https://aur.archlinux.org/<wbr>packages/ncl/</a><br></div></div>[2] <a href="https://drive.google.com/drive/folders/0B2KQf7Dbx7DUNkZXRVRwOEVLcm8_______________________________________________" target="_blank">https://drive.google.com/<wbr>drive/folders/<wbr>0B2KQf7Dbx7DUNkZXRVRwOEVLcm8__<wbr>______________________________<wbr>_______________</a><br>ncl-install mailing list<br>List instructions, subscriber options, unsubscribe:<br><a href="http://mailman.ucar.edu/mailman/listinfo/ncl-install" target="_blank">http://mailman.ucar.edu/<wbr>mailman/listinfo/ncl-install</a><br></div></div></blockquote></div><br></div></div><br>______________________________<wbr>_________________<br>
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