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Ensembl / WiggleTools

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency
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Possible glibc issue when installing WiggleTools #1

Closed lcolladotor closed 10 years ago

lcolladotor commented 10 years ago

Hello,

I tried installing WiggleTools and encountered a couple errors.

First, there seem to be some minor errors when installing kent. I don't think that the error matters much in this case as it's related to preserving the permissions for some files as shown below.

cp -pf gitFiles /home/bst/student/lcollado/software/userApps/scripts/gitFiles
cp: preserving permissions for `/home/bst/student/lcollado/software/userApps/scripts/gitFiles': Operation not supported
cp: preserving ACL for `/home/bst/student/lcollado/software/userApps/scripts/gitFiles': Operation not supported

I later encountered a warning when installing WiggleTools which lead to errors. The key part seems to be:

in statically linked applications requires at runtime the shared libraries from the glibc version used for linking

These seems different to the errors you anticipated about -lssl or -lcrypto. Right? If so, google lead me to http://stackoverflow.com/questions/2725255/create-statically-linked-binary-that-uses-getaddrinfo which doesn't seem to help in this case. Then from http://bytes.com/topic/c/answers/877929-lnk-error-using-dlopen-statically-linked-apps-requires-runtime-shared-lib I checked the environment variable they mention:

22:04 WiggleTools $ echo $LD_LIBRARY_PATH
/hpscc/usr/local/gcc-4.1.2/install/libraries/lib:/opt/gridengine/lib/lx26-amd64:/opt/gridengine/lib/lx26-amd64::/usr/local/atlas/3.9.4/lib:/usr/local/gsl/1.12/lib

Could this be a compiler issue? Do you have any suggestions? I could also double check with the system administrators of our cluster environment.

Thank you! Leonardo

Log

Here's the full log information https://gist.github.com/lcolladotor/9753882

dzerbino commented 10 years ago

Hello Leonardo,

Thanks for your very detailed bug report, it does make my life much easier!

The first error appears towards the end:

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `get_rc_clockskew':
(.text+0xbe): undefined reference to `krb5_rc_default'

This means that linking to the static library /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a leads to an error because it is incomplete (It's not glibc per se, but it is a common library).

Googling around, this seems to be a recurring issue with OpenSSL, possibly linked to the Linux distribution you are using (which one is it?)

My best suggestion would be for you to re-install OpenSSL (http://www.openssl.org/).

Hope this helps,

Daniel

lcolladotor commented 10 years ago

Hi Daniel,

I'm glad that the long bug report was useful. For now, I'll try installing OpenSSL myself.

The linux distribution in our cluster is RedHat 5.4 but uses gcc version 4.1.2. The details are shown below using the commands described at http://www.cyberciti.biz/faq/find-linux-distribution-name-version-number/

10:21 ~ $ cat /etc/*-release
Red Hat Enterprise Linux Server release 5.4 (Tikanga)
Rocks release 5.2 (Chimichanga)
10:21 ~ $ lsb_release -a
LSB Version:    :core-3.1-amd64:core-3.1-ia32:core-3.1-noarch:graphics-3.1-amd64:graphics-3.1-ia32:graphics-3.1-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 5.4 (Tikanga)
Release:    5.4
Codename:   Tikanga
10:21 ~ $ uname -a
Linux compute-0-47.local 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
10:21 ~ $ uname -mrs
Linux 2.6.18-164.el5 x86_64
10:21 ~ $ cat /proc/version
Linux version 2.6.18-164.el5 (mockbuild@x86-003.build.bos.redhat.com) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)) #1 SMP Tue Aug 18 15:51:48 EDT 2009

Also, this is the OpenSSL version installed:

$  openssl version -a
OpenSSL 0.9.8e-fips-rhel5 01 Jul 2008
built on: Mon Jun 29 18:09:33 EDT 2009
platform: linux-x86_64
options:  bn(64,64) md2(int) rc4(ptr,int) des(idx,cisc,16,int) blowfish(ptr2)
compiler: gcc -fPIC -DOPENSSL_PIC -DZLIB -DOPENSSL_THREADS -D_REENTRANT -DDSO_DLFCN -DHAVE_DLFCN_H -DKRB5_MIT -I/usr/kerberos/include -DL_ENDIAN -DTERMIO -Wall -DMD32_REG_T=int -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wa,--noexecstack -DOPENSSL_USE_NEW_FUNCTIONS -fno-strict-aliasing -DOPENSSL_BN_ASM_MONT -DSHA1_ASM -DSHA256_ASM -DSHA512_ASM -DMD5_ASM -DAES_ASM
OPENSSLDIR: "/etc/pki/tls"
engines:  dynamic

Cheers, Leonardo

lcolladotor commented 10 years ago

Hi again,

It seems like I might need to install a local gcc since having a local OpenSSL didn't help.

# Latest (marked in red) at http://www.openssl.org/source/
$ wget http://www.openssl.org/source/openssl-1.0.1f.tar.gz
$ tar -zxvf openssl-1.0.1f.tar.gz
$ cd openssl-1.0.1f
$ ./config --openssldir=/home/bst/student/lcollado/software/localopenssl
$ make
$ make test
$ make install
$ cd /home/bst/student/lcollado/software/localopenssl/bin
$ export PATH=$PWD:$PATH
$ openssl version -a
OpenSSL 1.0.1f 6 Jan 2014
built on: Tue Mar 25 10:49:13 EDT 2014
platform: linux-x86_64
options:  bn(64,64) rc4(8x,int) des(idx,cisc,16,int) idea(int) blowfish(idx)
compiler: gcc -DOPENSSL_THREADS -D_REENTRANT -DDSO_DLFCN -DHAVE_DLFCN_H -Wa,--noexecstack -m64 -DL_ENDIAN -DTERMIO -O3 -Wall -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: "/home/bst/student/lcollado/software/localopenssl"

Attempt at installing WiggleTools

$ 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: 1284, done.
remote: Total 1284 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (1284/1284), 2.33 MiB, done.
Resolving deltas: 100% (742/742), 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: 'finish' may be used uninitialized in this function
bigWiggleReader.c:20: warning: 'start' 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 'seekRegion':
bamReader.c:131: warning: dereferencing type-punned pointer will break strict-aliasing rules
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
plots.c: In function 'updateProfile':
plots.c:31: warning: implicit declaration of function 'round'
plots.c:31: warning: incompatible implicit declaration of built-in function 'round'
plots.c:34: warning: incompatible implicit declaration of built-in function 'round'
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/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libcrypto.a(fips.o): In function `FIPSCHECK_verify':
(.text+0x7fa): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/home/bst/student/lcollado/software/userApps/kent/src/lib/local/jkweb.a(osunix.o): In function `getUser':
/home/bst/student/lcollado/software/userApps/kent/src/lib/osunix.c:524: warning: Using 'getpwuid' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/home/bst/student/lcollado/software/userApps/kent/src/lib/local/jkweb.a(internet.o): In function `internetHostIp':
/home/bst/student/lcollado/software/userApps/kent/src/lib/internet.c:44: warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libcrypto.a(b_sock.o): In function `BIO_gethostbyname':
(.text+0x211): warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libcrypto.a(b_sock.o): In function `BIO_get_port':
(.text+0x4cd): warning: Using 'getservbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `get_rc_clockskew':
(.text+0xbe): undefined reference to `krb5_rc_default'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `get_rc_clockskew':
(.text+0xd0): undefined reference to `krb5_rc_initialize'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `get_rc_clockskew':
(.text+0xf0): undefined reference to `krb5_rc_get_lifespan'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `get_rc_clockskew':
(.text+0x10a): undefined reference to `krb5_rc_destroy'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_validate_times':
(.text+0x13c): undefined reference to `krb5_init_context'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_validate_times':
(.text+0x159): undefined reference to `krb5_timeofday'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_validate_times':
(.text+0x185): undefined reference to `krb5_free_context'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_tgt_is_available':
(.text+0x269): undefined reference to `krb5_init_context'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_tgt_is_available':
(.text+0x286): undefined reference to `krb5_free_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_tgt_is_available':
(.text+0x29d): undefined reference to `krb5_free_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_tgt_is_available':
(.text+0x2af): undefined reference to `krb5_free_context'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_tgt_is_available':
(.text+0x2e8): undefined reference to `krb5_sname_to_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_tgt_is_available':
(.text+0x301): undefined reference to `krb5_cc_default'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_tgt_is_available':
(.text+0x323): undefined reference to `krb5_cc_get_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_tgt_is_available':
(.text+0x34f): undefined reference to `krb5_get_credentials'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_keytab_is_available':
(.text+0x39c): undefined reference to `krb5_init_context'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_keytab_is_available':
(.text+0x3b8): undefined reference to `krb5_kt_resolve'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_keytab_is_available':
(.text+0x3d2): undefined reference to `krb5_kt_close'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_keytab_is_available':
(.text+0x3e6): undefined reference to `krb5_free_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_keytab_is_available':
(.text+0x3f5): undefined reference to `krb5_free_context'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_keytab_is_available':
(.text+0x40d): undefined reference to `krb5_kt_default'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_keytab_is_available':
(.text+0x43e): undefined reference to `krb5_sname_to_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_keytab_is_available':
(.text+0x45a): undefined reference to `krb5_kt_get_entry'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_keytab_is_available':
(.text+0x47a): undefined reference to `krb5_kt_free_entry'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `populate_cksumlens':
(.text+0x8db): undefined reference to `valid_cksumtype'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `populate_cksumlens':
(.text+0x8fe): undefined reference to `krb5_checksum_size'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `populate_cksumlens':
(.text+0x93d): undefined reference to `krb5_checksum_size'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_cget_tkt':
(.text+0x13d5): undefined reference to `krb5_init_context'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_cget_tkt':
(.text+0x140b): undefined reference to `krb5_sname_to_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_cget_tkt':
(.text+0x1459): undefined reference to `krb5_free_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_cget_tkt':
(.text+0x1470): undefined reference to `krb5_free_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_cget_tkt':
(.text+0x148a): undefined reference to `krb5_auth_con_free'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_cget_tkt':
(.text+0x149c): undefined reference to `krb5_free_context'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_cget_tkt':
(.text+0x14f1): undefined reference to `krb5_cc_default'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_cget_tkt':
(.text+0x1511): undefined reference to `krb5_cc_get_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_cget_tkt':
(.text+0x1597): undefined reference to `krb5_get_credentials'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_cget_tkt':
(.text+0x162e): undefined reference to `krb5_mk_req_extended'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1988): undefined reference to `krb5_auth_con_free'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x19b0): undefined reference to `krb5_auth_con_init'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x19e4): undefined reference to `krb5_kt_close'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x19fa): undefined reference to `krb5_free_ticket'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1a10): undefined reference to `krb5_free_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1a5c): undefined reference to `krb5_auth_con_getrcache'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1a90): undefined reference to `krb5_sname_to_principal'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1abe): undefined reference to `krb5_auth_con_setrcache'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1ae7): undefined reference to `krb5_kt_resolve'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1b51): undefined reference to `krb5_principal_compare'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1bf4): undefined reference to `krb5_init_context'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1c38): undefined reference to `krb5_get_server_rcache'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1cc9): undefined reference to `krb5_kt_default'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1d10): undefined reference to `krb5_kt_get_entry'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1d74): undefined reference to `krb5_decrypt_tkt_part'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_sget_tkt':
(.text+0x1dac): undefined reference to `krb5_kt_free_entry'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/libssl.a(kssl.o): In function `kssl_krb5_free_data_contents':
(.text+0x203): undefined reference to `krb5_free_data_contents'
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

Cheers, Leonardo

lcolladotor commented 10 years ago

From reading https://groups.google.com/forum/#!topic/xbps/mTkzFkWfcGo

$ pkg-config openssl --libs --static
-L/usr/kerberos/lib64 -lssl -lcrypto -ldl -lz

Looks like I need the krb5 library

lcolladotor commented 10 years ago

Ok, seems like the solution in this case is to install openssl with krb5 support.

manojsdoshi commented 6 years ago

so how did u manage to do that install openssl with krb5 support

lcolladotor commented 6 years ago

I never installed wiggletools. Our cluster admin did so in the end. Maybe he can tell you how he did it https://jhpce.jhu.edu/contact/

dzerbino commented 6 years ago

Thanks to a change of library dependency, neither the Kent nor the SSL libraries need to be installed, so hopefully most of the problems encountered by Leonardo are no longer a concern.