dextrac errors

[liguiyang410]

hi, dear Dr. Xiao, I install the dextract and showed some errors as　ｆｏｌｌｏｗｓ：　Ｈｏｗ　ｃａｎ　Ｉ　ｄo?

make -f dextract_makefile gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -I/home/ubuntu/Softwares/hdf5-1.8.15-patch1/mecat_hdf5/hdf5/include -L/home/ubuntu/Softwares/hdf5-1.8.15-patch1/mecat_hdf5/hdf5/lib -o dextract dextract.c DB.c QV.c -lhdf5 /tmp/ccUmaBqB.o: In function main': dextract.c:(.text.startup+0x141): undefined reference toparse_filter' dextract.c:(.text.startup+0x228): undefined reference to initBaxData' dextract.c:(.text.startup+0x2eb): undefined reference tosam_open' dextract.c:(.text.startup+0x305): undefined reference to sam_header_process' dextract.c:(.text.startup+0x34e): undefined reference tosam_record_extract' dextract.c:(.text.startup+0x361): undefined reference to SAM_EOF' dextract.c:(.text.startup+0x374): undefined reference toevaluate_bam_filter' dextract.c:(.text.startup+0x85e): undefined reference to getBaxData' dextract.c:(.text.startup+0x875): undefined reference tonextSubread' dextract.c:(.text.startup+0x894): undefined reference to nextSubread' dextract.c:(.text.startup+0x8b0): undefined reference toevaluate_bax_filter' dextract.c:(.text.startup+0xe61): undefined reference to sam_close' dextract.c:(.text.startup+0x107f): undefined reference tosam_open' dextract.c:(.text.startup+0x1352): undefined reference to parse_filter' dextract.c:(.text.startup+0x13b2): undefined reference togetBaxData' dextract.c:(.text.startup+0x160c): undefined reference to `printBaxError' collect2: error: ld returned 1 exit status dextract_makefile:7: recipe for target 'dextract' failed make: *** [dextract] Error 1

[Jianbing-Hu]

I just got essentially the same failure with the same error messages. Do you have any solution to this problem.If so, please contact hu.jianbing@yahoo.com Thank you!

[githubwangqiqi]

@Hu-Jianbing ，the solution is：https://github.com/xiaochuanle/MECAT/issues/19

edit the dextractor_makefile (line 7) : ${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -L$(HDF5_LIB) -o dextract dextract.c sam.c bax.c expr.c DB.c QV.c -lhdf5 -lz

[Jianbing-Hu]

Thanks a lot, my problem has been solved.

[liguiyang410]

edit the dextractor_makefile (line 7) : ${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -L$(HDF5_LIB) -o dextract dextract.c sam.c bax.c expr.c DB.c QV.c -lhdf5 -lz

At 2019-01-04 09:19:55, "Hu-Jianbing" notifications@github.com wrote:

I just got essentially the same failure with the same error messages. Do you have any solution to this problem.If so, please contact hu.jianbing@yahoo.com Thank you!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[MeHelmy]

Hi!

I changed line 7 as suggested now I have this error:

gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -I/users/mmahmoud/home/source/MECAT/hdf5/include -L/users/mmahmoud/home/source/MECAT/hdf5/lib -o dextract dextract.c sam.c bax.c expr.c DB.c QV.c -lhdf5 -lz sam.c: In function ‘sam_open’: sam.c:147: warning: implicit declaration of function ‘gzbuffer’ At top level: cc1: warning: unrecognized command line option "-Wno-unused-result" /tmp/cclRV9H3.o: In function sam_open': sam.c:(.text+0x1d8): undefined reference togzbuffer' collect2: ld returned 1 exit status make: *** [dextract] Error 1

Any suggestions?

[2017-ambMicrobiome]

Hi!

I changed line 7 as suggested now I have this error:

gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -I/users/mmahmoud/home/source/MECAT/hdf5/include -L/users/mmahmoud/home/source/MECAT/hdf5/lib -o dextract dextract.c sam.c bax.c expr.c DB.c QV.c -lhdf5 -lz sam.c: In function ‘sam_open’: sam.c:147: warning: implicit declaration of function ‘gzbuffer’ At top level: cc1: warning: unrecognized command line option "-Wno-unused-result" /tmp/cclRV9H3.o: In function sam_open': sam.c:(.text+0x1d8): undefined reference togzbuffer' collect2: ld returned 1 exit status make: *** [dextract] Error 1

Any suggestions?

Can we bumb this, I have the exact same issue.