| 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> |
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