src/lib/Makefile | 24 2 + 22 - 0 !
src/make-include.mk | 6 1 + 5 - 0 !
2 files changed, 3 insertions(+), 27 deletions(-)

 use debian package for blas/lapack (instead of obsolete clapack)
 - Use -lblas instead of -lblaswr
 - Use -ltmglib instead of -ltmg
 - Do not use f2c, not needed
 - Introduce prototypes for LAPACK functions used in the package
   (those are documented in the manpages from the liblapack-doc package)

src/Makefile | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 packages should not install anything to /opt

src/lib/Makefile | 2 1 + 1 - 0 !
src/make-include.mk | 4 2 + 2 - 0 !
2 files changed, 3 insertions(+), 3 deletions(-)

 use debian packaged libpcre

src/Makefile | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 debian packaged help2man creates better results

src/make-include.mk | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 propagate hardening options

test/Makefile | 62 31 + 31 - 0 !
test/hmrc_summary_correct | 3 0 + 3 - 0 !
2 files changed, 31 insertions(+), 34 deletions(-)

 test suite makefile has syntax errors and there
 was at least one buggy data file which was fixed.
 .
 With these changes `make msa_view` works but other targets are
 throwing errors.  This needs to be investigated

include/phast/stringsplus.h | 20 9 + 11 - 0 !
src/dless/dlessP.c | 2 1 + 1 - 0 !
src/lib/base/phast_misc.c | 2 1 + 1 - 0 !
src/lib/base/phast_stringsplus.c | 39 22 + 17 - 0 !
src/lib/feature/phast_bed.c | 2 1 + 1 - 0 !
src/lib/feature/phast_category_map.c | 10 5 + 5 - 0 !
src/lib/feature/phast_gff.c | 6 3 + 3 - 0 !
src/lib/motif/phast_tfbs.c | 6 3 + 3 - 0 !
src/lib/msa/phast_local_alignment.c | 2 1 + 1 - 0 !
src/lib/msa/phast_msa.c | 6 3 + 3 - 0 !
src/lib/msa/phast_multi_msa.c | 6 3 + 3 - 0 !
src/lib/msa/phast_sufficient_stats.c | 2 1 + 1 - 0 !
src/lib/phylo/phast_phylo_p_print.c | 2 1 + 1 - 0 !
src/make-include.mk | 2 1 + 1 - 0 !
src/prequel/phast_pbs_code.c | 2 1 + 1 - 0 !
src/util/msa_view.c | 2 1 + 1 - 0 !
16 files changed, 57 insertions(+), 54 deletions(-)

 port from pcre3 to pcre2
Bug-Debian: https://bugs.debian.org/1000000