nygenome/lancet

lancet does not build (Centos 6.9, gcc gcc-4.9.3)

jbsysadmin opened this issue · 2 comments

jbsysadmin commented

This is issue #23. It was closed before I could respond, and I didn't see a way to re-open.
I spotted your latest 1.0.7, then tried again. Same error on make:

[edit]

make[1]: Leaving directory /usr/local/installs/lancet-master-1.0.3/htslib-1.8' cd src; make; cp lancet ../; cd ../ make[1]: Entering directory /usr/local/installs/lancet-master-1.0.3/src'
g++ -std=c++0x -Wno-deprecated -Wall -O3 -fexceptions -g -Wl,-rpath,/usr/local/installs/lancet-master-1.0.3/bamtools-2.5.1/lib64/ -I/usr/local/installs/lancet-master-1.0.3/bamtools-2.5.1/include/bamtools -I/usr/local/installs/lancet-master-1.0.3/htslib-1.8/ -L/usr/local/installs/lancet-master-1.0.3/bamtools-2.5.1/lib64/ -L/usr/local/installs/lancet-master-1.0.3/htslib-1.8/ Lancet.cc Edge.cc Node.cc Graph.cc Microassembler.cc Ref.cc Path.cc ContigLink.cc align.cc util.cc sha256.cc VariantDB.cc Variant.cc -o lancet /usr/local/installs/lancet-master-1.0.3/htslib-1.8/libhts.a -llzma -lbz2 -lz -ldl -lpthread -lcurl -lcrypto -lbamtools
In file included from Variant.hh:34:0,
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:74:69: 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:74:69: 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;
^
/nfs/goldstein/software/binutils-2.26.1/bin/ld: /tmp/ccgNDtyg.o: undefined reference to symbol 'clock_gettime@@GLIBC_2.2.5'
/lib64/librt.so.1: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[1]: *** [lancet] Error 1
make[1]: Leaving directory /usr/local/installs/lancet-master-1.0.3/src' cp: cannot stat lancet': No such file or directory

jbsysadmin commented

Greetings.
I just spent several hours rebuilding tools for this.

Using a new gcc-6.4.0, binutils-2.29.1, and cmake-3.12.1, this lancet 1.0.7 build fails. The last excerpt from that attempt is below. Please advise.

-John

make[1]: Entering directory /usr/local/installs/lancet-1.0.7/src' g++ -std=c++0x -Wno-deprecated -Wall -O3 -fexceptions -g -Wl,-rpath,/usr/local/installs/lancet-1.0.7/bamtools-2.5.1/lib64/ -I/usr/local/installs/lancet-1.0.7/bamtools-2.5.1/include/bamtools -I/usr/local/installs/lancet-1.0.7/htslib-1.8/ -L/usr/local/installs/lancet-1.0.7/bamtools-2.5.1/lib64/ -L/usr/local/installs/lancet-1.0.7/htslib-1.8/ Lancet.cc Edge.cc Node.cc Graph.cc Microassembler.cc Ref.cc Path.cc ContigLink.cc align.cc util.cc sha256.cc VariantDB.cc Variant.cc -o lancet /usr/local/installs/lancet-1.0.7/htslib-1.8/libhts.a -llzma -lbz2 -lz -ldl -lpthread -lcurl -lcrypto -lbamtools 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; ^~~ /nfs/goldstein/software/binutils-2.29.1-x86_64/bin/ld: /tmp/ccqdQqAl.o: undefined reference to symbol 'clock_gettime@@GLIBC_2.2.5' /lib64/librt.so.1: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[1]: *** [lancet] Error 1 make[1]: Leaving directory /usr/local/installs/lancet-1.0.7/src'
cp: cannot stat `lancet': No such file or directory

jbsysadmin commented

Please close. Our group is no longer actively using Centos6 build environments.