Makefile | 8 4 + 4 - 0 !
1 file changed, 4 insertions(+), 4 deletions(-)

 accept the hardening flags

Makefile | 22 9 + 13 - 0 !
1 file changed, 9 insertions(+), 13 deletions(-)

 use debian packaged samtools

pRSEM/Gene.py | 4 2 + 2 - 0 !
pRSEM/Param.py | 4 2 + 2 - 0 !
pRSEM/Prsem.py | 8 4 + 4 - 0 !
pRSEM/Transcript.py | 8 4 + 4 - 0 !
pRSEM/Util.py | 6 3 + 3 - 0 !
pRSEM/prsem-calculate-expression | 2 1 + 1 - 0 !
pRSEM/prsem-prepare-reference | 2 1 + 1 - 0 !
pRSEM/prsem-testing-procedure | 2 1 + 1 - 0 !
rsem-gff3-to-gtf | 2 1 + 1 - 0 !
rsem-refseq-extract-primary-assembly | 2 1 + 1 - 0 !
10 files changed, 20 insertions(+), 20 deletions(-)

 use 2to3 to port to python3
Bug-Debian: https://bugs.debian.org/938415

Makefile | 2 1 + 1 - 0 !
PairedEndHit.h | 2 1 + 1 - 0 !
SingleHit.h | 2 1 + 1 - 0 !
buildReadIndex.cpp | 8 4 + 4 - 0 !
4 files changed, 7 insertions(+), 7 deletions(-)

 port codebase to gnu++11.
 Since boost 1.83, it is necessary to build rsem with C++ 2011 standard.  This
 patch bumps the -std=gnu++98 passed by upstream Makefil to -std=gnu++11.  It
 should become unnecessary once upstream bumped to C++ 2011 or later, or when
 the package will not depend on boost anymore, in case this is in upstream's
 agenda; there is a merge request open upstream to bump to -std=gnu++17 in the
 meantime.