Has anyone been able to compile EA utils on Moutain Lion? about ea-utils HOT 9 CLOSED

The new version of varcall requires the GNU scientific library to be installed 
in order to compile.

On UBUNTU  : 

apt-get install libgsl0-dev

On CENTOS/REDHAT:

rpm -i gsl-devel

[deleted comment]

You can just not compile varcall, it's pretty optional.

Thanks! 

I am still trying to find a way of installing the GNU library on the Current 
OSX.

T.

Ha!

Perfect! Worked like a charm!

Thanks,

T.

adding on to this issue - i encountered this same build error on Centos but I 
have gsl-devel installed

[chow@deepseq ea-utils.1.1.2-537]# uname -a
Linux deepseq 2.6.18-348.12.1.el5 #1 SMP Wed Jul 10 05:28:41 EDT 2013 x86_64 
x86_64 x86_64 GNU/Linux
[chow@deepseq ea-utils.1.1.2-537]# yum list gsl-devel
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: centos.sonn.com
 * epel: linux.mirrors.es.net
 * extras: mirrors.serveraxis.net
 * ius: mirror.symnds.com
 * updates: mirror.nwresd.org
Installed Packages
gsl-devel.i386                                                                  
                                  1.13-3.el5                                    
                                                               installed
gsl-devel.x86_64                                                                
                                  1.13-3.el5                                    
                                                               installed
[root@deepseq ea-utils.1.1.2-537]# 

Which Centos?   I have a couple Centos 6 boxes lying around I could test with.  

Or, you can just ignore the output... varcall is somewhat beta-ish, until I'm 
happy with the vcf formatting.   

Is your error exactly the same "missing gsl's random distributon headers" ... 
(odd if gsl is installed). 

its Centos 5.9, the build error is below and is the same whether i build by 
hand or build is invoked by qiime-deploy.  doesnt seem to say missing header, 
it looks like a compile error of varcall 

2014-01-10 15:22:39,164 - lib.util         - ERROR    - Failed to compile 
ea-utils
2014-01-10 15:22:39,164 - lib.util         - DEBUG    - ea-utils make failed, 
return code: 512
2014-01-10 15:22:39,165 - lib.util         - DEBUG    - Output: g++ -O3 -I.  
fastq-lib.cpp -o fastq-mcf fastq-mcf.c
fastq-lib.cpp: In function ‘bool poorqual(int, int, const char*, const 
char*)’:
fastq-lib.cpp:164: warning: converting to ‘int’ from ‘double’
g++ -O3 -I.  fastq-lib.cpp -o fastq-multx fastq-multx.c
fastq-lib.cpp: In function ‘bool poorqual(int, int, const char*, const 
char*)’:
fastq-lib.cpp:164: warning: converting to ‘int’ from ‘double’
g++ -O3 -I.  fastq-lib.cpp -o fastq-join fastq-join.c
fastq-lib.cpp: In function ‘bool poorqual(int, int, const char*, const 
char*)’:
fastq-lib.cpp:164: warning: converting to ‘int’ from ‘double’
g++ -O3 -I.  fastq-lib.cpp gcModel.c -o fastq-stats fastq-stats.cpp
fastq-lib.cpp: In function ‘bool poorqual(int, int, const char*, const 
char*)’:
fastq-lib.cpp:164: warning: converting to ‘int’ from ‘double’
fastq-stats.cpp: In function ‘int main(int, char**)’:
fastq-stats.cpp:473: warning: converting to ‘int’ from ‘double’
fastq-stats.cpp:485: warning: converting to ‘int’ from ‘double’
g++ -O3 -I.  fastq-lib.cpp -o fastq-clipper fastq-clipper.c
fastq-lib.cpp: In function ‘bool poorqual(int, int, const char*, const 
char*)’:
fastq-lib.cpp:164: warning: converting to ‘int’ from ‘double’
cd samtools && make libbam.a
make[1]: Entering directory `/tmp/tmp5IbWj3/ea-utils.1.1.2-537/samtools'
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE 
-D_USE_KNETFILE -D_CURSES_LIB=1 -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[1]: Leaving directory `/tmp/tmp5IbWj3/ea-utils.1.1.2-537/samtools'
g++ -O3 -I.  samtools/*.o -lz -lpthread fastq-lib.cpp sam-stats.cpp -o sam-stats
fastq-lib.cpp: In function ‘bool poorqual(int, int, const char*, const 
char*)’:
fastq-lib.cpp:164: warning: converting to ‘int’ from ‘double’
sam-stats.cpp: In member function ‘void sstats::dostats(std::string, int, 
int, const std::string&, int, int, const std::string&, int, const std::string&, 
const char*, int, int, int)’:
sam-stats.cpp:646: warning: converting to ‘int’ from ‘double’
sam-stats.cpp:656: warning: converting to ‘int’ from ‘double’
sam-stats.cpp: In member function ‘bool sstats::parse_sam(FILE*)’:
sam-stats.cpp:756: warning: converting to ‘int’ from ‘double’
g++ -O3 -I.  fastq-lib.cpp tidx/tidx-lib.cpp -o varcall varcall.cpp -lgsl 
-lgslcblas
fastq-lib.cpp: In function ‘bool poorqual(int, int, const char*, const 
char*)’:
fastq-lib.cpp:164: warning: converting to ‘int’ from ‘double’
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pa
ir.h: In instantiation of ‘std::pair<const std::string&, const 
std::vector<annot, std::allocator<annot> > >’:
tidx/tidx-lib.cpp:34:   instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pa
ir.h:84: error: forming reference to reference type ‘const std::string&’
varcall.cpp: In member function ‘int vcall::mq_rms() const’:
varcall.cpp:112: warning: converting to ‘int’ from ‘double’
varcall.cpp: In member function ‘int vcall::qual_rms() const’:
varcall.cpp:113: warning: converting to ‘int’ from ‘double’
varcall.cpp: In member function ‘void 
VarCallVisitor::VisitX(PileupSummary&)’:
varcall.cpp:1073: warning: converting to ‘int’ from ‘double’
varcall.cpp:1075: warning: converting to ‘int’ from ‘double’
varcall.cpp:1249: warning: converting to ‘int’ from ‘double’
make: *** [varcall] Error 1
2014-01-10 15:22:39,165 - lib.application  - ERROR    - Problem making ea-utils.
2014-01-10 15:22:39,177 - lib.deploy       - ERROR    - Deploy of ea-utils 
failed.