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dpryan79 / bison

Bisulfite alignment on nodes of a cluster
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trying to compile master branch #2

Closed avilella closed 9 years ago

avilella commented 9 years ago

git clone --recursive https://github.com/dpryan79/bison cd bison make

git clone --recursive https://github.com/dpryan79/bison Initialized empty Git repository in /bi/home/rocks-av/bison/.git/ remote: Counting objects: 511, done. remote: Total 511 (delta 0), reused 0 (delta 0), pack-reused 511 Receiving objects: 100% (511/511), 194.40 KiB, done. Resolving deltas: 100% (373/373), done. Submodule 'htslib' (https://github.com/samtools/htslib.git) registered for path 'htslib' Initialized empty Git repository in /bi/home/rocks-av/bison/htslib/.git/ remote: Counting objects: 6404, done. remote: Compressing objects: 100% (39/39), done. remote: Total 6404 (delta 21), reused 0 (delta 0), pack-reused 6365 Receiving objects: 100% (6404/6404), 5.50 MiB | 3.38 MiB/s, done. Resolving deltas: 100% (4134/4134), done. Submodule path 'htslib': checked out '94d13ce0d780780140c913459a5f7ad2e0d680a0' [rocks-av@rocks1 ~]$ cd bison [rocks-av@rocks1 bison]$ make make -C htslib make[1]: Entering directory /bi/home/rocks-av/bison/htslib' gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c In file included from faidx.c:33: htslib/faidx.h:94: error: wrong number of arguments specified for ￃﾢﾀﾘ__deprecated__ￃﾢﾀﾙ attribute make[1]: *** [faidx.o] Error 1 make[1]: Leaving directory/bi/home/rocks-av/bison/htslib' make: *\ [HTSlib] Error 2

Any ideas?

dpryan79 commented 9 years ago

Odd, this is an htslib issue. If you just clone/compile it do you get a similar error?

avilella commented 9 years ago

It compiles fine in my laptop with a newer version of gcc, so I am assuming that's the issue. Can't run it on my laptop, since it's a virtualbox, and I am not sure I can pretend to have 5 nodes on a VM for mpiexec...

On Sun, Jun 28, 2015 at 2:56 PM, Devon Ryan notifications@github.com wrote:

Odd, this is an htslib issue. If you just clone/compile it do you get a similar error?

— Reply to this email directly or view it on GitHub https://github.com/dpryan79/bison/issues/2#issuecomment-116282041.

dpryan79 commented 9 years ago

Yeah, trying to simulate 5 (or even 3) nodes inside a VM doesn't sound like a fruitful thing to do.

Perhaps you can just modify htslib/htslib/hts_defs.h to have the following on line 94:

#define HTS_DEPRECATED(x) __attribute__ ((__deprecated__))

Allegedly some older versions of gcc don't pass a character array to __deprecated__.

dpryan79 commented 9 years ago

I'm going to go ahead and close this issue, since it's really an interaction between an outdated gcc and htslib.