[Help] unifrac-tools: symbol `_ZTVN2H511IdComponentE' can not be used when making a shared object; recompile with -fPIC

Hi, the new version of package unifrac needs unifrac-tools. I've tried to build this package[1] but it fails with: h5c++ -shared -fopenmp -o libssu.so tree.o biom.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 -llapacke -lblas -L/lib /usr/bin/ld:

Re: [Help] unifrac-tools: symbol `_ZTVN2H511IdComponentE' can not be used when making a shared object; recompile with -fPIC

Andreas Tille writes: > h5c++ -shared -fopenmp -o libssu.so tree.o biom.o unifrac_internal.o > unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 > -llapacke -lblas -L/lib > /usr/bin/ld: > /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.a(H5Exception.o): warning: > rel

Re: [Help] unifrac-tools: symbol `_ZTVN2H511IdComponentE' can not be used when making a shared object; recompile with -fPIC

Hi Aaron, Am Wed, Jul 27, 2022 at 07:44:28AM -0400 schrieb Aaron M. Ucko: > > Please try arranging to add -shlib to the h5c++ command line to override > that script's preference for static HDF5 libraries. Thanks a lot - this did the trick. Kind regards Andreas. -- http://fam-tille.de

Finishing ncbi-vdb and sra-sdk

Hi Aaron, I think ncbi-vdb version 3.0.0 is finished in Git. I'm just uploading it to experimental (needs to pass new queue due to the changed binary names). I tried building sra-sdk 3.0.0 against these packages but here the configure step with cmake fails with -- Found Java: /usr/bin/java (fo

Re: Finishing ncbi-vdb and sra-sdk

Andreas Tille writes: > I think ncbi-vdb version 3.0.0 is finished in Git. I'm just uploading it to > experimental (needs to pass new queue due to the changed binary names). I Thanks, but I still have some unpushed changes from some time back. As noted at the time, I went to +dfsg2 to sideste

Re: Finishing ncbi-vdb and sra-sdk

Hi Aaron, Am Wed, Jul 27, 2022 at 02:21:11PM -0400 schrieb Aaron M. Ucko: > Andreas Tille writes: > > > I think ncbi-vdb version 3.0.0 is finished in Git. I'm just uploading it to > > experimental (needs to pass new queue due to the changed binary names). I > > Thanks, but I still have some u

Re: Upgrading invesalius

Hi Thiago, I noticed that you pushed some patch and have build invesalius. When I've started the executable it seems to work. Thus I uploaded now. I've also added a superficial autopkgtest. When doing so I've spotted the --no-gui option. This makes me wonder whether you could rather add a *rea