Comments (9)
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 [email protected]
on 4 Mar 2013 at 2:14
- Added labels: Type-Other
- Removed labels: Type-Defect
from ea-utils.
[deleted comment]
from ea-utils.
You can just not compile varcall, it's pretty optional.
Original comment by [email protected]
on 4 Mar 2013 at 2:28
from ea-utils.
Thanks!
I am still trying to find a way of installing the GNU library on the Current
OSX.
T.
Original comment by [email protected]
on 4 Mar 2013 at 2:29
from ea-utils.
Ha!
Perfect! Worked like a charm!
Thanks,
T.
Original comment by [email protected]
on 4 Mar 2013 at 2:45
from ea-utils.
Original comment by [email protected]
on 28 May 2013 at 5:07
- Changed state: WontFix
from ea-utils.
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 [email protected]
on 13 Jan 2014 at 6:23
from ea-utils.
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 [email protected]
on 13 Jan 2014 at 9:44
from ea-utils.
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 [email protected]
on 13 Jan 2014 at 10:08
from ea-utils.
Related Issues (20)
- sam-stats doesn't support -o and -O option HOT 3
- Incorrect total reads when using FIFO HOT 2
- fastq-mcf: invalid adapter file ==> Floating point exception HOT 1
- The gtf2bed script generate bed with wrong chrStart and chrEnd coordinates for plus strand HOT 4
- Limit on the number of files it can handle HOT 1
- fastq-multx when barcode is in header between # and / symbols? HOT 7
- fastq-multx supporting sequence in header HOT 1
- Compilation on Mac HOT 2
- Giant FASTQ support in stats HOT 3
- Wrong number (/ counter / calculation) in summary statistics of fastq-mcf HOT 2
- fastq-mcf not working correctly on ubuntu 14.04 HOT 9
- error message: "fastq-mcf has stopped working" HOT 4
- gtf2bed wrong output. HOT 1
- compilation error because sparsehash/sparse_hash_map is not found HOT 1
- "fastq-mcf has stopped working"
- Patches for porting ea-utils to other POSIX platforms + warnings clean-up HOT 1
- Use fastq-mcf with methylation data HOT 2
- installing ea-utils on windows7 HOT 1
- gsl_randist.h: No such file or directory HOT 1
- Support for detecting fixed-length prefix barcodes for fastq-multx
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from ea-utils.