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Id: 101733
Status: open
Priority: 0/
Queue: Bio-SamTools

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Owner: Nobody in particular
Requestors: shokin [...] carnegiescience.edu
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Subject: bam2bedgraph compile error (Fedora 21, stock gcc, etc.)
Date: Sun, 25 Jan 2015 12:24:10 -0600
To: bug-Bio-SamTools [...] rt.cpan.org
From: Sam Hokin <shokin [...] carnegiescience.edu>
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Hi, Lincoln, I'm getting the following error when trying to compile Bio::SamTools 1.41 directly, or 1.39 via CPAN. I am referencing samtools-0.1.19 as per your README. DIRECT: [root@biogrinder Bio-SamTools-1.41]# ./Build Building Bio-SamTools gcc -I../samtools-0.1.19 -Ic_bin -I/usr/lib64/perl5/CORE -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -o c_bin/bam2bedgraph.o c_bin/bam2bedgraph.c cc1: error: -Wformat-security ignored without -Wformat [-Werror=format-security] cc1: some warnings being treated as errors error building c_bin/bam2bedgraph.o from 'c_bin/bam2bedgraph.c' at /usr/share/perl5/ExtUtils/CBuilder/Base.pm line 177. CPAN: [root@biogrinder src]# cpan install Bio::DB::Bam::SplitAlignmentPart Reading '/root/.cpan/Metadata' Database was generated on Sun, 25 Jan 2015 11:29:02 GMT Running install for module 'Bio::DB::Bam::SplitAlignmentPart' Checksum for /root/.cpan/sources/authors/id/L/LD/LDS/Bio-SamTools-1.39.tar.gz ok Configuring L/LD/LDS/Bio-SamTools-1.39.tar.gz with Build.PL This module requires samtools 0.1.10 or higher (samtools.sourceforge.net). Please enter the location of the bam.h and compiled libbam.a files: /usr/local/src/samtools-0.1.19 Found /usr/local/src/samtools-0.1.19/bam.h and /usr/local/src/samtools-0.1.19/libbam.a. Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-SamTools' version '1.39' LDS/Bio-SamTools-1.39.tar.gz /usr/bin/perl Build.PL -- OK Running Build for L/LD/LDS/Bio-SamTools-1.39.tar.gz Building Bio-SamTools gcc -I/usr/local/src/samtools-0.1.19 -Ic_bin -I/usr/lib64/perl5/CORE -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -o c_bin/bam2bedgraph.o c_bin/bam2bedgraph.c cc1: error: -Wformat-security ignored without -Wformat [-Werror=format-security] cc1: some warnings being treated as errors error building c_bin/bam2bedgraph.o from 'c_bin/bam2bedgraph.c' at /usr/share/perl5/ExtUtils/CBuilder/Base.pm line 177. LDS/Bio-SamTools-1.39.tar.gz ./Build -- NOT OK
From: dan.bolser [...] gmail.com
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Do you have all the right libraries installed? What happens when you issue the gcc command 'manually'?
Subject: Re: [rt.cpan.org #101733] bam2bedgraph compile error (Fedora 21, stock gcc, etc.)
Date: Thu, 20 Aug 2015 07:55:38 -0500
To: bug-Bio-SamTools [...] rt.cpan.org
From: Sam Hokin <shokin [...] carnegiescience.edu>
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You can kill this old one - I somehow managed to get around this problem, don't remember how, though. Probably by reverting some Fedora distro Perl to CPAN-installed Perl. On 08/20/2015 07:27 AM, Dan Bolser via RT wrote: Show quoted text
> <URL: https://rt.cpan.org/Ticket/Display.html?id=101733 > > > Do you have all the right libraries installed? What happens when you issue the gcc command 'manually'? >


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