v 1.0.7 not compiling on Mac
proukakis opened this issue · 2 comments
hi, still using OS El Capitan- I had problems before with 16 Gb RAM, having more helps
v_1.0.6 works fine, so not bothered- posting in case it helps others
i do
make CC=gcc-6 CXX=g++-6
seems OK until here
Microassembler.cc: In member function 'int Microassembler::processReads()':
Microassembler.cc:644:16: error: 'CLOCK_MONOTONIC' was not declared in this scope
clock_gettime(CLOCK_MONOTONIC, &start);
^~~~~~~~~~~~~~~
Microassembler.cc:644:39: error: 'clock_gettime' was not declared in this scope
clock_gettime(CLOCK_MONOTONIC, &start);
^
In file included from Variant.hh:36:0,
from Variant.cc:1:
FET.hh: In member function 'double Variant_t::compute_FET_score()':
FET.hh:71:22: warning: 'aux.FET_t::hgacc_t::n' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) {
~~~~^~~~~~~~
FET.hh:95:11: note: 'aux.FET_t::hgacc_t::n' was declared here
hgacc_t aux;
^~~
FET.hh:71:31: warning: 'aux.FET_t::hgacc_t::n1_' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) {
~~~~~~~~~~~~~^~~~~~~~~~
FET.hh:95:11: note: 'aux.FET_t::hgacc_t::n1_' was declared here
hgacc_t aux;
^~~
FET.hh:71:15: warning: 'aux.FET_t::hgacc_t::n_1' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) {
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FET.hh:95:11: note: 'aux.FET_t::hgacc_t::n_1' was declared here
hgacc_t aux;
^~~
FET.hh:72:25: warning: 'aux.FET_t::hgacc_t::n11' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (n11 == aux->n11 + 1) { // incremental
~~~~~~~~~^~~
FET.hh:95:11: note: 'aux.FET_t::hgacc_t::n11' was declared here
hgacc_t aux;
^~~
FET.hh:74:68: warning: 'aux.FET_t::hgacc_t::p' may be used uninitialized in this function [-Wmaybe-uninitialized]
* (aux->n_1 - aux->n11) / (n11 + aux->n - aux->n1_ - aux->n_1);
^
FET.hh:95:11: note: 'aux.FET_t::hgacc_t::p' was declared here
hgacc_t aux;
^~~
FET.hh: In member function 'double Variant_t::compute_SB_score()':
FET.hh:71:22: warning: 'aux.FET_t::hgacc_t::n' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) {
~~~~^~~~~~~~
FET.hh:95:11: note: 'aux.FET_t::hgacc_t::n' was declared here
hgacc_t aux;
^~~
FET.hh:71:31: warning: 'aux.FET_t::hgacc_t::n1_' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) {
~~~~~~~~~~~~~^~~~~~~~~~
FET.hh:95:11: note: 'aux.FET_t::hgacc_t::n1_' was declared here
hgacc_t aux;
^~~
FET.hh:71:15: warning: 'aux.FET_t::hgacc_t::n_1' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) {
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FET.hh:95:11: note: 'aux.FET_t::hgacc_t::n_1' was declared here
hgacc_t aux;
^~~
FET.hh:72:25: warning: 'aux.FET_t::hgacc_t::n11' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (n11 == aux->n11 + 1) { // incremental
~~~~~~~~~^~~
FET.hh:95:11: note: 'aux.FET_t::hgacc_t::n11' was declared here
hgacc_t aux;
^~~
FET.hh:74:68: warning: 'aux.FET_t::hgacc_t::p' may be used uninitialized in this function [-Wmaybe-uninitialized]
* (aux->n_1 - aux->n11) / (n11 + aux->n - aux->n1_ - aux->n_1);
^
FET.hh:95:11: note: 'aux.FET_t::hgacc_t::p' was declared here
hgacc_t aux;
^~~
make[1]: *** [lancet] Error 1
cp: lancet: No such file or directory
It seems like "clock_gettime()" is not available in macOS before Sierra. The link below provides a possible solution. Hope it helps.
https://stackoverflow.com/questions/5167269/clock-gettime-alternative-in-mac-os-x
thanks, will use 1.0.6 for now I think