problem installing under cygwin

[jchenpku]

when I comiled the source under cygwin, I met the following error: anything missing? { RSEM-master } » make cygwin=true /cygdrive/g/NGS/bin/RSEM-master 2 g++ -pthread -o rsem-parse-alignments parseIt.o samtools-1.3/htslib-1.3/libhts.a -lz parseIt.o:parseIt.cpp:(.text+0x256e): undefined reference to bam_hdr_destroy' parseIt.o:parseIt.cpp:(.text+0x2576): undefined reference tohts_close' parseIt.o:parseIt.cpp:(.text+0x257f): undefined reference to bam_destroy1' parseIt.o:parseIt.cpp:(.text+0x26d6): undefined reference tosam_read1' parseIt.o:parseIt.cpp:(.text+0x29bb): undefined reference to bam_aux_get' parseIt.o:parseIt.cpp:(.text+0x29cc): undefined reference tobam_aux2i' parseIt.o:parseIt.cpp:(.text+0x2c68): undefined reference to sam_read1' parseIt.o:parseIt.cpp:(.text+0x2eeb): undefined reference tobam_aux_get' parseIt.o:parseIt.cpp:(.text+0x2efc): undefined reference to bam_aux2i' parseIt.o:parseIt.cpp:(.text+0x317d): undefined reference tosam_read1' parseIt.o:parseIt.cpp:(.text+0x3195): undefined reference to sam_read1' parseIt.o:parseIt.cpp:(.text+0x37fb): undefined reference tobam_aux_get' parseIt.o:parseIt.cpp:(.text+0x380c): undefined reference to bam_aux2i' parseIt.o:parseIt.cpp:(.text+0x38bb): undefined reference tobam_aux_get' parseIt.o:parseIt.cpp:(.text+0x38c8): undefined reference to bam_aux2i' parseIt.o:parseIt.cpp:(.text+0x3d68): undefined reference tosam_read1' parseIt.o:parseIt.cpp:(.text+0x3d80): undefined reference to sam_read1' parseIt.o:parseIt.cpp:(.text+0x43cb): undefined reference tobam_aux_get' parseIt.o:parseIt.cpp:(.text+0x43dc): undefined reference to bam_aux2i' parseIt.o:parseIt.cpp:(.text+0x455b): undefined reference tobam_aux_get' parseIt.o:parseIt.cpp:(.text+0x4568): undefined reference to bam_aux2i' parseIt.o:parseIt.cpp:(.text+0x678d): undefined reference tohts_open' parseIt.o:parseIt.cpp:(.text+0x67a5): undefined reference to hts_set_fai_filename' parseIt.o:parseIt.cpp:(.text+0x67ad): undefined reference tosam_hdr_read' parseIt.o:parseIt.cpp:(.text+0x67d5): undefined reference to bam_init1' parseIt.o:parseIt.cpp:(.text+0x67de): undefined reference tobam_init1' parseIt.o:parseIt.cpp:(.text+0x258e): undefined reference to `bam_destroy1' collect2.exe: error: ld returned 1 exit status Makefile:81: recipe for target 'rsem-parse-alignments' failed make: *** [rsem-parse-alignments] Error 1

[bli25wisc]

@jchenpku , Sorry for my late reply. Have you built "samtools-1.3/htslib-1.3/libhts.a" under Cygwin? Or you have it ready before you typed 'make'?

[jchenpku]

thank you for your reply. I got the error when using babun and then I found that there might be some problem with my babun so I switched to the original cygwin. Now I have successfully built RSEM.

[bli25wisc]

@jchenpku Great to hear!