make error

[WenfeiXiao]

make[1]: Entering directory '/newhome/xiaowf/peptide_design/freesasa-2.1.2'
Making all in src
make[2]: Entering directory '/newhome/xiaowf/peptide_design/freesasa-2.1.2/src'
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cc
mv -f .deps/main.Tpo .deps/main.Po
g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT cif.o -MD -MP -MF .deps/cif.Tpo -c -o cif.o cif.cc
mv -f .deps/cif.Tpo .deps/cif.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT classifier.o -MD -MP -MF .deps/classifier.Tpo -c -o classifier.o classifier.c
mv -f .deps/classifier.Tpo .deps/classifier.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT classifier_protor.o -MD -MP -MF .deps/classifier_protor.Tpo -c -o classifier_protor.o classifier_protor.c
mv -f .deps/classifier_protor.Tpo .deps/classifier_protor.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT classifier_oons.o -MD -MP -MF .deps/classifier_oons.Tpo -c -o classifier_oons.o classifier_oons.c
mv -f .deps/classifier_oons.Tpo .deps/classifier_oons.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT classifier_naccess.o -MD -MP -MF .deps/classifier_naccess.Tpo -c -o classifier_naccess.o classifier_naccess.c
mv -f .deps/classifier_naccess.Tpo .deps/classifier_naccess.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT coord.o -MD -MP -MF .deps/coord.Tpo -c -o coord.o coord.c
mv -f .deps/coord.Tpo .deps/coord.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT pdb.o -MD -MP -MF .deps/pdb.Tpo -c -o pdb.o pdb.c
mv -f .deps/pdb.Tpo .deps/pdb.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT log.o -MD -MP -MF .deps/log.Tpo -c -o log.o log.c
mv -f .deps/log.Tpo .deps/log.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT sasa_lr.o -MD -MP -MF .deps/sasa_lr.Tpo -c -o sasa_lr.o sasa_lr.c
mv -f .deps/sasa_lr.Tpo .deps/sasa_lr.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT sasa_sr.o -MD -MP -MF .deps/sasa_sr.Tpo -c -o sasa_sr.o sasa_sr.c
mv -f .deps/sasa_sr.Tpo .deps/sasa_sr.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT structure.o -MD -MP -MF .deps/structure.Tpo -c -o structure.o structure.c
mv -f .deps/structure.Tpo .deps/structure.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT node.o -MD -MP -MF .deps/node.Tpo -c -o node.o node.c
mv -f .deps/node.Tpo .deps/node.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT freesasa.o -MD -MP -MF .deps/freesasa.Tpo -c -o freesasa.o freesasa.c
mv -f .deps/freesasa.Tpo .deps/freesasa.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT nb.o -MD -MP -MF .deps/nb.Tpo -c -o nb.o nb.c
mv -f .deps/nb.Tpo .deps/nb.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT util.o -MD -MP -MF .deps/util.Tpo -c -o util.o util.c
mv -f .deps/util.Tpo .deps/util.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT rsa.o -MD -MP -MF .deps/rsa.Tpo -c -o rsa.o rsa.c
mv -f .deps/rsa.Tpo .deps/rsa.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT selection.o -MD -MP -MF .deps/selection.Tpo -c -o selection.o selection.c
In file included from /usr/include/string.h:495,
from freesasa_internal.h:10,
from selection.c:9:
In function ‘strncpy’,
inlined from ‘select_area_impl’ at selection.c:728:17:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
selection.c: In function ‘select_area_impl’:
selection.c:723:19: note: length computed here
723 | len = strlen(selection->name);
| ^~~~~~~~~~~~~~~~~~~~~~~
mv -f .deps/selection.Tpo .deps/selection.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT lexer.o -MD -MP -MF .deps/lexer.Tpo -c -o lexer.o lexer.c
mv -f .deps/lexer.Tpo .deps/lexer.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -g -O2 -MT parser.o -MD -MP -MF .deps/parser.Tpo -c -o parser.o parser.c
mv -f .deps/parser.Tpo .deps/parser.Po
rm -f libfreesasa.a
ar cru libfreesasa.a classifier.o classifier_protor.o classifier_oons.o classifier_naccess.o coord.o pdb.o log.o sasa_lr.o sasa_sr.o structure.o node.o freesasa.o nb.o util.o rsa.o selection.o lexer.o parser.o
ar: u' modifier ignored since D' is the default (see `U')
ranlib libfreesasa.a
g++ -std=gnu++14 -g -O2 -o freesasa main.o cif.o -lc++ libfreesasa.a -ldl -lm
/usr/bin/ld: cannot find -lc++
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:513: freesasa] Error 1
make[2]: Leaving directory '/newhome/xiaowf/peptide_design/freesasa-2.1.2/src'
make[1]: *** [Makefile:382: all-recursive] Error 1
make[1]: Leaving directory '/newhome/xiaowf/peptide_design/freesasa-2.1.2'
make: *** [Makefile:321: all] Error 2

[mittinatten]

Hmm, this must be a stricter warning set in newer versions of GCC. I had a quick look at the code, and I think it's not an actual error in this case. The quick fix should be configuring with ./configure CFLAGS="-g -O2 -Wno-stringop-overflow". I will see if I there's a way fix the underlying problem, but will probably take a while, because of summer holidays.

[WenfeiXiao]

Thanks a lot! Have a great summer.

[Azam-Shi]

Hmm, this must be a stricter warning set in newer versions of GCC. I had a quick look at the code, and I think it's not an actual error in this case. The quick fix should be configuring with ./configure CFLAGS="-g -O2 -Wno-stringop-overflow". I will see if I there's a way fix the underlying problem, but will probably take a while, because of summer holidays.

Hi,
I got the same error as WenfeiXiao.
When do you think you can solve the problem? It seems it is an actual error both for "make" and "make install" commands. Looking forward to fixing it.

Have a great summer holiday. :) 😊

[mittinatten]

I fixed the code on the line mentioned in the printout. My compiler doesn't throw this warning, so it could still be problem elsewhere. Can you see if the latest version of code works for you @WenfeiXiao ?