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Old 05-16-2014, 01:29 PM   #1
Location: Boston

Join Date: Jun 2012
Posts: 33
Default zlib problem in Samtools compilation


Recently, I upgraded several of our cluster's RHEL packages for a new library that I wanted to use. One of these was Samtools, another was zlib.

In order to recover from some of the problems with the installation, I decided to reinstall samtools-0.1.19, and downgrade the zlib installation.

Our is version 1.2.3, but I'm not sure what it was before being upgraded. The latest is 1.2.8 and I've read that this caused problem when compiling samtools. So I think this needs to be downgraded.

Second, I am no longer able to compile samtools from any version, eg 0.1.18 or 0.1.19. The errors are shown below at the very bottom of the output. The issue seems to be an invalid reference to gzopen64 from the zlib library.

Has anyone run into this problem before? What would you suggest to clean up this mess. We need to recover the samtools binary soon.

Thanks for any help you can supply.

Joe White

$ make
make[1]: Entering directory `/home/whitejo/samtools-0.1.19'
make[2]: Entering directory `/home/whitejo/samtools-0.1.19'
gcc -c -g -Wall -O3 -m64 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
gcc -c -g -Wall -O3 -m64 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -Wall -O3 -m64 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
[.. snip ..]
gcc -c -g -Wall -O3 -m64 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
gcc -c -g -Wall -O3 -m64 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
gcc -g -Wall -O3 -m64 -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
phase.o: In function `loadpos':
/home/whitejo/samtools-0.1.19/phase.c:475: undefined reference to `gzopen64'
bedcov.o: In function `main_bedcov':
/home/whitejo/samtools-0.1.19/bedcov.c:69: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `__bam_get_lines':
/home/whitejo/samtools-0.1.19/bam_import.c:76: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_open':
/home/whitejo/samtools-0.1.19/bam_import.c:472: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_header_read2':
/home/whitejo/samtools-0.1.19/bam_import.c:126: undefined reference to `gzopen64'
libbam.a(bedidx.o):/home/whitejo/samtools-0.1.19/bedidx.c:107: more undefined references to `gzopen64' follow
collect2: ld returned 1 exit status
make[1]: *** [samtools] Error 1
make[1]: Leaving directory `/home/whitejo/samtools-0.1.19'
make: *** [all-recur] Error 1
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Old 05-16-2014, 01:33 PM   #2
Richard Finney
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Location: bethesda

Join Date: Feb 2009
Posts: 700

See previous discussion ...
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Old 09-24-2014, 12:28 PM   #3
Junior Member
Location: Detroit, MI

Join Date: Sep 2014
Posts: 1
Smile How I fixed my gzopen64 issue

1. Download/compile/install zlib 1.2.8 from source
 ./configure && make && make install
2. vim ./Makefile <-- edit the make file
3. replace all -lz with the variable $(ZLIB)
4. Add near the top under LDLIBS=
ZLIB = -I/usr/local/include -L/usr/local/lib -lz
5. save/quit
6. make

Last edited by CloneNum3; 09-24-2014 at 12:31 PM. Reason: install zlib 1.2.8 before other steps
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