undefined reference to `gzgets'

[macmanes]

root@ip-172-31-42-250:~/Lighter# make g++ -Wall -O3 -c -o main.o main.cpp main.cpp: In function ‘int main(int, char*)’: main.cpp:219:8: warning: variable ‘readId’ set but not used [-Wunused-but-set-variable] char readId/*, read, qual/ ; ^ g++ -Wall -O3 -c -o ErrorCorrection.o ErrorCorrection.cpp ErrorCorrection.cpp: In function ‘int ErrorCorrection(char, char, KmerCode&, int, char, Store_, int&, int&)’: ErrorCorrection.cpp:44:7: warning: variable ‘trusted’ set but not used [-Wunused-but-set-variable] bool trusted[MAX_READLENGTH] ; // Do not correct these makred positions. ^ g++ -Wall -O3 -c -o KmerCode.o KmerCode.cpp g++ -Wall -O3 -c -o GetKmers.o GetKmers.cpp GetKmers.cpp: In function ‘void StoreTrustedKmers(char, char, int, char, int, KmerCode&, Store, Store)’: GetKmers.cpp:261:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] int i, k ; ^ g++ -o lighter -Wall -O3 -lpthread -lz ErrorCorrection.o KmerCode.o GetKmers.o main.o main.o: In function GetGoodQuality(Reads&)': main.cpp:(.text+0x315): undefined reference togzgets' main.cpp:(.text+0x42b): undefined reference to gzgets' main.cpp:(.text+0x45a): undefined reference togzgets' main.cpp:(.text+0x477): undefined reference to gzgets' main.cpp:(.text+0x4a9): undefined reference togzgets' main.o:main.cpp:(.text+0x70d): more undefined references to gzgets' follow main.o: In functionFile::~File()': main.cpp:(.text._ZN4FileD2Ev[ZN4FileD5Ev]+0x25): undefined reference to gzclose' main.o: In functionFile::Printf(char const, ...)': main.cpp:(.text._ZN4File6PrintfEPKcz[_ZN4File6PrintfEPKcz]+0x10a): undefined reference to gzputs' main.o: In functionReads::~Reads()': main.cpp:(.text._ZN5ReadsD2Ev[_ZN5ReadsD5Ev]+0x95): undefined reference to gzclose' main.cpp:(.text._ZN5ReadsD2Ev[_ZN5ReadsD5Ev]+0xa8): undefined reference togzclose' main.cpp:(.text._ZN5ReadsD2Ev[_ZN5ReadsD5Ev]+0xfa): undefined reference to gzclose' main.cpp:(.text._ZN5ReadsD2Ev[_ZN5ReadsD5Ev]+0x13a): undefined reference togzclose' main.o: In function Reads::Rewind()': main.cpp:(.text._ZN5Reads6RewindEv[_ZN5Reads6RewindEv]+0x59): undefined reference togzrewind' main.cpp:(.text._ZN5Reads6RewindEv[_ZN5Reads6RewindEv]+0x6e): undefined reference to gzrewind' main.o: In functionmain': main.cpp:(.text.startup+0x9fe): undefined reference to pthread_create' main.cpp:(.text.startup+0xa14): undefined reference topthread_join' main.cpp:(.text.startup+0xb75): undefined reference to gzopen' main.cpp:(.text.startup+0xc95): undefined reference togzopen' main.cpp:(.text.startup+0xcd5): undefined reference to gzopen' main.cpp:(.text.startup+0xd0a): undefined reference togzgets' main.cpp:(.text.startup+0x10bd): undefined reference to gzgets' main.cpp:(.text.startup+0x10f1): undefined reference togzgets' main.cpp:(.text.startup+0x1396): undefined reference to gzgets' main.cpp:(.text.startup+0x13c9): undefined reference togzclose' main.cpp:(.text.startup+0x13e3): undefined reference to gzgets' main.cpp:(.text.startup+0x13fd): undefined reference togzgets' main.cpp:(.text.startup+0x1418): undefined reference to gzgets' main.cpp:(.text.startup+0x1432): undefined reference togzgets' main.cpp:(.text.startup+0x154d): undefined reference to pthread_create' main.cpp:(.text.startup+0x156b): undefined reference topthread_join' main.cpp:(.text.startup+0x176d): undefined reference to gzgets' main.cpp:(.text.startup+0x1bf1): undefined reference togzgets' main.cpp:(.text.startup+0x1c18): undefined reference to gzgets' main.cpp:(.text.startup+0x1c33): undefined reference togzgets' main.cpp:(.text.startup+0x1c48): undefined reference to gzgets' main.o:main.cpp:(.text.startup+0x1d6d): more undefined references togzgets' follow main.o: In function main': main.cpp:(.text.startup+0x1f36): undefined reference topthread_create' main.cpp:(.text.startup+0x1f51): undefined reference to pthread_join' main.cpp:(.text.startup+0x204d): undefined reference togzgets' main.cpp:(.text.startup+0x2064): undefined reference to gzgets' main.cpp:(.text.startup+0x207f): undefined reference togzgets' main.cpp:(.text.startup+0x2114): undefined reference to gzgets' main.cpp:(.text.startup+0x212f): undefined reference togzgets' main.o:main.cpp:(.text.startup+0x2149): more undefined references to gzgets' follow GetKmers.o: In functionSampleKmersThread(void)': GetKmers.cpp:(.text+0x3cb): undefined reference to pthread_create' GetKmers.cpp:(.text+0x443): undefined reference topthread_join' GetKmers.cpp:(.text+0x4d3): undefined reference to pthread_create' GetKmers.cpp:(.text+0x4e2): undefined reference topthread_join' GetKmers.cpp:(.text+0x523): undefined reference to pthread_join' GetKmers.o: In functionStoreKmersThread(void)': GetKmers.cpp:(.text+0x145d): undefined reference to gzgets' GetKmers.cpp:(.text+0x14f8): undefined reference togzgets' GetKmers.cpp:(.text+0x1513): undefined reference to gzgets' GetKmers.cpp:(.text+0x1529): undefined reference togzgets' GetKmers.cpp:(.text+0x1544): undefined reference to gzgets' GetKmers.o:GetKmers.cpp:(.text._ZN5Reads14NextWithBufferEPcS0_S0_bb[_ZN5Reads14NextWithBufferEPcS0_S0_bb]+0x15d): more undefined references togzgets' follow collect2: error: ld returned 1 exit status make: _* [lighter] Error 1

[mourisl]

It seems I messed up the Makefile some time ago. I just uploaded the fixed Makefile, can you test the new version?

Thanks.

[macmanes]

Yes, this solves the make issue

[mourisl]

Great!