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Old 12-26-2011, 10:38 AM   #1
Junior Member
Location: china

Join Date: May 2010
Posts: 2
Default Can't make Maq

i am installing maq-0.7.1,after ./configure no problem,when i make,some problems appeared,what should i do?
root@ubuntu:~# cd /home/glr/biosoftware/maq-0.7.1
root@ubuntu:/home/glr/biosoftware/maq-0.7.1# ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking if gcc accepts -m64... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
root@ubuntu:/home/glr/biosoftware/maq-0.7.1# make
make all-am
make[1]: 姝e湪杩涘叆鐩綍 `/home/glr/biosoftware/maq-0.7.1'
g++ -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -o maq main.o const.o seq.o bfa.o read.o fasta2bfa.o fastq2bfq.o merge.o match_aux.o match.o sort_mapping.o assemble.o pileup.o mapcheck.o get_pos.o assopt.o aux_utils.o rbcc.o subsnp.o pair_stat.o indel_soa.o maqmap.o maqmap_conv.o altchr.o submap.o rmdup.o simulate.o genran.o indel_pe.o stdaln.o indel_call.o eland2maq.o csmap2ntmap.o break_pair.o glfgen.o -lm -lz
/usr/bin/ld.bfd.real: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.4.3/ when searching for -lstdc++
/usr/bin/ld.bfd.real: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.4.3/libstdc++.a when searching for -lstdc++
/usr/bin/ld.bfd.real: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.4.3/ when searching for -lstdc++
/usr/bin/ld.bfd.real: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.4.3/libstdc++.a when searching for -lstdc++
/usr/bin/ld.bfd.real: cannot find -lstdc++
collect2: ld returned 1 exit status
make[1]: *** [maq] 閿欒 1
make[1]:姝e湪绂诲紑鐩綍 `/home/glr/biosoftware/maq-0.7.1'
make: *** [all] 閿欒 2
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Old 12-30-2011, 08:24 PM   #2
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

Looks like an architecture mismatche problem. Check for similar problems and solutions when installing other software causing the same error ("cannot find -lstdc++")
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