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melisanahtar / ea-utils

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Has anyone been able to compile EA utils on Moutain Lion? #13

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
WHen I run make install I get this error: 
2.
3.

What is the expected output? What do you see instead?

++ -O3 -I.  fastq-lib.cpp tidx/tidx-lib.cpp -o varcall varcall.cpp -lgsl 
-lgslcblas
/usr/include/c++/4.2.1/bits/stl_pair.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/include/c++/4.2.1/bits/stl_pair.h:84: error: forming reference to 
reference type ‘const std::string&’
varcall.cpp:33:29: error: gsl/gsl_randist.h: No such file or directory
varcall.cpp: In member function ‘void 
VarCallVisitor::VisitX(PileupSummary&)’:
varcall.cpp:1125: error: ‘gsl_ran_poisson_pdf’ was not declared in this 
scope
varcall.cpp:1167: error: ‘gsl_ran_poisson_pdf’ was not declared in this 
scope
make: *** [varcall] Error 1

What version of the product are you using? On what operating system?
The newer one 1.1.2.537

Please provide any additional information below.

Thanks!

Original issue reported on code.google.com by tiago.h...@gmail.com on 4 Mar 2013 at 2:00

GoogleCodeExporter commented 8 years ago 
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

Original comment by earone...@gmail.com on 4 Mar 2013 at 2:14

GoogleCodeExporter commented 8 years ago 
[deleted comment]
GoogleCodeExporter commented 8 years ago 
You can just not compile varcall, it's pretty optional.

Original comment by earone...@gmail.com on 4 Mar 2013 at 2:28

GoogleCodeExporter commented 8 years ago 
Thanks! 

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

T.

Original comment by tiago.h...@gmail.com on 4 Mar 2013 at 2:29

GoogleCodeExporter commented 8 years ago 
Ha!

Perfect! Worked like a charm!

Thanks,

T.

Original comment by tiago.h...@gmail.com on 4 Mar 2013 at 2:45

GoogleCodeExporter commented 8 years ago

Original comment by earone...@gmail.com on 28 May 2013 at 5:07

GoogleCodeExporter commented 8 years ago 
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]#

Original comment by Adam.Soc...@gmail.com on 13 Jan 2014 at 6:23

GoogleCodeExporter commented 8 years ago 
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).

Original comment by earone...@gmail.com on 13 Jan 2014 at 9:44

GoogleCodeExporter commented 8 years ago 
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.

Original comment by Adam.Soc...@gmail.com on 13 Jan 2014 at 10:08