include/external_libs.h | 25 21 + 4 - 0 !
src/lib/Makefile | 24 2 + 22 - 0 !
src/make-include.mk | 6 1 + 5 - 0 !
3 files changed, 24 insertions(+), 31 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

src/dless/dless.c | 4 2 + 2 - 0 !
src/dless/dlessP.c | 4 2 + 2 - 0 !
src/exoniphy/exoniphy.c | 4 2 + 2 - 0 !
src/phastCons/phastCons.c | 4 2 + 2 - 0 !
src/phastMotif/phastMotif.c | 4 2 + 2 - 0 !
src/phastOdds/phastOdds.c | 4 2 + 2 - 0 !
src/phyloBoot/phyloBoot.c | 4 2 + 2 - 0 !
src/phyloFit/phyloFit.c | 4 2 + 2 - 0 !
src/phyloP/phyloP.c | 4 2 + 2 - 0 !
src/prequel/pbsDecode.c | 4 2 + 2 - 0 !
src/prequel/pbsEncode.c | 4 2 + 2 - 0 !
src/prequel/pbsScoreMatrix.c | 4 2 + 2 - 0 !
src/prequel/pbsTrain.c | 4 2 + 2 - 0 !
src/prequel/prequel.c | 4 2 + 2 - 0 !
src/util/all_dists.c | 4 2 + 2 - 0 !
src/util/base_evolve.c | 4 2 + 2 - 0 !
src/util/chooseLines.c | 4 2 + 2 - 0 !
src/util/clean_genes.c | 4 2 + 2 - 0 !
src/util/consEntropy.c | 4 2 + 2 - 0 !
src/util/convert_coords.c | 4 2 + 2 - 0 !
src/util/display_rate_matrix.c | 4 2 + 2 - 0 !
src/util/draw_tree.c | 4 2 + 2 - 0 !
src/util/eval_predictions.c | 4 2 + 2 - 0 !
src/util/hmm_train.c | 4 2 + 2 - 0 !
src/util/hmm_tweak.c | 4 2 + 2 - 0 !
src/util/hmm_view.c | 4 2 + 2 - 0 !
src/util/indelFit.c | 4 2 + 2 - 0 !
src/util/indelHistory.c | 4 2 + 2 - 0 !
src/util/maf_parse.c | 5 3 + 2 - 0 !
src/util/makeHKY.c | 4 2 + 2 - 0 !
src/util/modFreqs.c | 4 2 + 2 - 0 !
src/util/msa_diff.c | 4 2 + 2 - 0 !
src/util/msa_split.c | 4 2 + 2 - 0 !
src/util/msa_view.c | 5 3 + 2 - 0 !
src/util/phastBias.c | 4 2 + 2 - 0 !
src/util/refeature.c | 4 2 + 2 - 0 !
src/util/stringiphy.c | 4 2 + 2 - 0 !
src/util/treeGen.c | 4 2 + 2 - 0 !
src/util/tree_doctor.c | 4 2 + 2 - 0 !
39 files changed, 80 insertions(+), 78 deletions(-)

 make char signed wherever necessary to avoid invalid comparisions
Last-Changed: October 3, 2020