из-за чего ломается dist-upgrade:

file /usr/lib64/hdf5-seq/bin/nccopy from install of libnetcdf11-seq-4.4.1.1-alt2.x86_64 conflicts with file from package libnetcdf7-seq-4.3.2-alt1.x86_64
        file /usr/lib64/hdf5-seq/bin/ncdump from install of libnetcdf11-seq-4.4.1.1-alt2.x86_64 conflicts with file from package libnetcdf7-seq-4.3.2-alt1.x86_64
        file /usr/lib64/hdf5-seq/bin/ncgen from install of libnetcdf11-seq-4.4.1.1-alt2.x86_64 conflicts with file from package libnetcdf7-seq-4.3.2-alt1.x86_64
        file /usr/lib64/hdf5-seq/bin/ncgen3 from install of libnetcdf11-seq-4.4.1.1-alt2.x86_64 conflicts with file from package libnetcdf7-seq-4.3.2-alt1.x86_64
E: Error while running transaction

В спеке [1] указан конфликт (Conflicts: %sname%sover < %version-%release), но соверсия подставляется текущая.
Т.к. в спеке есть Provides: %sname = %version-%release, то решением проблемы будет Conflicts: %sname < %version-%release

Лучше также везде заменить %version-%release на %EVR.

P.S. В похожем пакете libnetcdf11-mpi выставлен правильный конфликт.

[1] http://git.altlinux.org/gears/l/libnetcdf11-seq.git?p=libnetcdf11-seq.git;a=blob;f=.gear/libnetcdf.spec;h=2135a013cb197a57948a77be48d21df5bf3e50c0;hb=fdcbcbad0cda3c95be582c972149f8cc2a6c9480#l24