setComparisons.c compile error

[lcolladotor]

Hello Daniel,

After discussing briefly https://github.com/Ensembl/WiggleTools/issues/1 with our system administrators, they recommended me to use the brand new version of our local cluster they just finished installing. In this version, they have OpenSSL with krb5 support installed system wide, so that resolved https://github.com/Ensembl/WiggleTools/issues/1.

However, I have now encountered a new issue when attempting to install WiggleTools. Basically it's:

setComparisons.c:17:25: error: gsl/gsl_cdf.h: No such file or directory
setComparisons.c: In function ‘TTestReductionPop2’:
setComparisons.c:116: warning: implicit declaration of function ‘gsl_cdf_tdist_Q’
make[1]: *** [setComparisons.o] Error 1
make[1]: Leaving directory `/home/bst/student/lcollado/software/userApps/WiggleTools/src'
make: *** [Wiggletools] Error 2

Have you seen such an error before? How do you recommend proceeding?

Thank you! Leonardo

System info

12:51 WiggleTools $ openssl version -a
OpenSSL 1.0.1e-fips 11 Feb 2013
built on: Tue Jan  7 04:14:47 EST 2014
platform: linux-x86_64
options:  bn(64,64) md2(int) rc4(8x,int) des(idx,cisc,16,int) idea(int) blowfish(idx)
compiler: gcc -fPIC -DOPENSSL_PIC -DZLIB -DOPENSSL_THREADS -D_REENTRANT -DDSO_DLFCN -DHAVE_DLFCN_H -DKRB5_MIT -m64 -DL_ENDIAN -DTERMIO -Wall -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wa,--noexecstack -DPURIFY -DOPENSSL_IA32_SSE2 -DOPENSSL_BN_ASM_MONT -DOPENSSL_BN_ASM_MONT5 -DOPENSSL_BN_ASM_GF2m -DSHA1_ASM -DSHA256_ASM -DSHA512_ASM -DMD5_ASM -DAES_ASM -DVPAES_ASM -DBSAES_ASM -DWHIRLPOOL_ASM -DGHASH_ASM
OPENSSLDIR: "/etc/pki/tls"
engines:  dynamic
12:52 WiggleTools $ cat /etc/*-release
Cluster Manager v6.1
slave
Red Hat Enterprise Linux Server release 6.3 (Santiago)
Red Hat Enterprise Linux Server release 6.3 (Santiago)
12:52 WiggleTools $ lsb_release -a
LSB Version:    :core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 6.3 (Santiago)
Release:    6.3
Codename:   Santiago
12:52 WiggleTools $ uname -a
Linux compute-058 2.6.32-279.el6.x86_64 #1 SMP Wed Jun 13 18:24:36 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
12:52 WiggleTools $ uname -mrs
Linux 2.6.32-279.el6.x86_64 x86_64
12:52 WiggleTools $ cat /proc/version
Linux version 2.6.32-279.el6.x86_64 (mockbuild@x86-008.build.bos.redhat.com) (gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) ) #1 SMP Wed Jun 13 18:24:36 EDT 2012
12:52 WiggleTools $ pkg-config openssl --libs --static
-Wl,-z,relro -lssl -lcrypto -ldl -lz -lgssapi_krb5 -lkrb5 -lcom_err -lk5crypto

Log

Here's the summary of commands used:

$ cd software/
12:47 software $ rm -fr userApps/
12:47 software $ git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git beta src/userApps > userApps.zip
12:47 software $ unzip -d userApps -j userApps.zip
12:47 software $ rm userApps.zip
12:47 software $ cd userApps
12:47 userApps $ make fetchSource
12:47 userApps $ make
12:50 userApps $ export KENT_SRC=$PWD/kent/src
12:50 userApps $ git clone https://github.com/samtools/tabix.git
12:50 userApps $ export TABIX_SRC=$PWD/tabix
12:50 userApps $ cd tabix
12:50 tabix $ make
12:50 tabix $ cd ..
12:50 userApps $ git clone git@github.com:Ensembl/WiggleTools.git
12:51 userApps $ cd WiggleTools/
12:51 WiggleTools $ make
12:51 WiggleTools $ openssl version -a
12:52 WiggleTools $ cat /etc/*-release
12:52 WiggleTools $ lsb_release -a
12:52 WiggleTools $ uname -a
12:52 WiggleTools $ uname -mrs
12:52 WiggleTools $ cat /proc/version
12:52 WiggleTools $ pkg-config openssl --libs --static

The full log is available here https://gist.github.com/lcolladotor/9766383

[dzerbino]

Hello again,

I'm glad things forward (a bit). This would appear to be a missing GNU scientific library (http://www.gnu.org/software/gsl/) which I assumed to be default on other people's computers, but apparently is not. I'll update the documentation shortly.

Regards,

Daniel

[lcolladotor]

Hi Daniel,

The system administrator from our cluster kindly installed gsl-devel in the cluster and it worked a bit more. Now there's another missing dependency which I am posting here just for completeness sake. It's

/usr/bin/ld: cannot find -lz

I'll report back once this dependency is solved.

Cheers, Leonardo

Log

$ cd /home/bst/student/lcollado/software/userApps
$ export KENT_SRC=$PWD/kent/src
$ export TABIX_SRC=$PWD/tabix
$ rm -fr WiggleTools/
$ git clone git@github.com:Ensembl/WiggleTools.git
Initialized empty Git repository in /home/bst/student/lcollado/software/userApps/WiggleTools/.git/
remote: Reusing existing pack: 1287, done.
remote: Total 1287 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (1287/1287), 2.33 MiB, done.
Resolving deltas: 100% (744/744), done.
$ cd WiggleTools/
$ make
cd samtools; make
make[1]: Entering directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools'
make[2]: Entering directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools'
make[3]: Entering directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools'
gcc -c -g -Wall  -O2 -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  -O2 -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  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
make[3]: Leaving directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools'
make[3]: Entering directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools/bcftools'
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
make[3]: Leaving directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools/bcftools'
make[3]: Entering directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools/misc'
make[3]: Nothing to be done for `lib'.
make[3]: Leaving directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools/misc'
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
gcc -c -g -Wall  -O2 -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  -O2 -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  -O2 -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
make[2]: Leaving directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools'
make[2]: Entering directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools/bcftools'
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -Wall  -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L.  -lbcf -lm -lz -lpthread
make[2]: Leaving directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools/bcftools'
make[2]: Entering directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools/misc'
gcc -c -g -Wall  -O2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -Wall  -O2 -o md5sum-lite md5sum-lite.o
gcc -c -g -Wall  -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
gcc -g -Wall  -O2 -c -I.. -o md5fa.o md5fa.c
gcc -g -Wall  -O2 -o md5fa md5.o md5fa.o -lz
gcc -g -Wall  -O2 -o maq2sam-short maq2sam.c -lz
gcc -g -Wall  -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -g -Wall  -O2 -c -I.. -o ace2sam.o ace2sam.c
gcc -g -Wall  -O2 -o ace2sam ace2sam.o -lz
gcc -g -Wall  -O2 -c -I.. -o wgsim.o wgsim.c
gcc -g -Wall  -O2 -o wgsim wgsim.o -lm -lz
gcc -g -Wall  -O2 -c -I.. -o bamcheck.o bamcheck.c
gcc -g -Wall  -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
make[2]: Leaving directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools/misc'
make[1]: Leaving directory `/home/bst/student/lcollado/software/userApps/WiggleTools/samtools'
cd src; make
make[1]: Entering directory `/home/bst/student/lcollado/software/userApps/WiggleTools/src'
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c wiggleIterator.c -o wiggleIterator.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c wigReader.c -o wigReader.o
wigReader.c: In function ‘WiggleReaderSeek’:
wigReader.c:209: warning: assignment discards qualifiers from pointer target type
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c bigWiggleReader.c -o bigWiggleReader.o
bigWiggleReader.c: In function ‘readBigWigBuffer’:
bigWiggleReader.c:20: warning: ‘start’ may be used uninitialized in this function
bigWiggleReader.c:20: warning: ‘finish’ may be used uninitialized in this function
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c multiplexer.c -o multiplexer.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c reducers.c -o reducers.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c bedReader.c -o bedReader.o
bedReader.c: In function ‘BedReaderSeek’:
bedReader.c:77: warning: assignment discards qualifiers from pointer target type
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c bigBedReader.c -o bigBedReader.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c bamReader.c -o bamReader.o
bamReader.c: In function ‘BamReaderSeek’:
bamReader.c:192: warning: assignment discards qualifiers from pointer target type
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c apply.c -o apply.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c bigFileReader.c -o bigFileReader.o
bigFileReader.c: In function ‘BigFileReaderSeek’:
bigFileReader.c:121: warning: assignment discards qualifiers from pointer target type
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c commandParser.c -o commandParser.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c wigWriter.c -o wigWriter.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c statistics.c -o statistics.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c unaryOps.c -o unaryOps.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c multiSet.c -o multiSet.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c setComparisons.c -o setComparisons.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c bufferedReader.c -o bufferedReader.o
bufferedReader.c: In function ‘createBlockData’:
bufferedReader.c:60: warning: assignment from incompatible pointer type
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c vcfReader.c -o vcfReader.o
vcfReader.c: In function ‘VcfReaderSeek’:
vcfReader.c:70: warning: assignment discards qualifiers from pointer target type
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c bcfReader.c -o bcfReader.o
bcfReader.c: In function ‘nextLine’:
bcfReader.c:42: warning: return discards qualifiers from pointer target type
bcfReader.c: In function ‘BcfReaderSeek’:
bcfReader.c:104: warning: assignment discards qualifiers from pointer target type
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c plots.c -o plots.o
mkdir -p ../lib
ar rcs ../lib/libwiggletools.a *.o ../samtools/bam_plcmd.o ../samtools/sample.o ../samtools/bam2bcf.o ../samtools/errmod.o ../samtools/bam2bcf_indel.o
cc -g -Wall -O3 -I../samtools -I/home/bst/student/lcollado/software/userApps/kent/src/inc -I../../tabix -D_PBGZF_USE -c wiggletools.c -o wiggletools.o
mkdir -p ../bin
cc -g -Wall -O3 -L/home/bst/student/lcollado/software/userApps/kent/src/lib/ -L../samtools -L../samtools/bcftools -L../lib -L../../tabix wiggletools.c -static ../lib/libwiggletools.a /home/bst/student/lcollado/software/userApps/kent/src/lib/local/jkweb.a -lbam -lbcf -lz -lpthread -lssl -lcrypto -ldl -lgsl -lm -ltabix -o ../bin/wiggletools
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
make[1]: *** [../bin/wiggletools] Error 1
make[1]: Leaving directory `/home/bst/student/lcollado/software/userApps/WiggleTools/src'
make: *** [Wiggletools] Error 2

Googling the error leads to http://stackoverflow.com/questions/3373995/usr-bin-ld-cannot-find-lz and http://serverfault.com/questions/481859/usr-bin-ld-cannot-find-lz-but-libz-exists

[dzerbino]

Waiting for user's sys admin to install libz, probably solved by now.

Daniel