Code:
Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf) \
&& ./configure --prefix=`pwd` && make install
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for g++... g++
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 g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for library containing cos... none required
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make[1]: Entering directory `/home/rynka/trinity/Inchworm'
Making install in src
make[2]: Entering directory `/home/rynka/trinity/Inchworm/src'
make[3]: Entering directory `/home/rynka/trinity/Inchworm/src'
test -z "/home/rynka/trinity/Inchworm/bin" || mkdir -p -- "/home/rynka/trinity/Inchworm/bin"
/usr/bin/install -c 'inchworm' '/home/rynka/trinity/Inchworm/bin/inchworm'
/usr/bin/install -c 'cigar_tweaker' '/home/rynka/trinity/Inchworm/bin/cigar_tweaker'
/usr/bin/install -c 'pull_reads_with_kmers' '/home/rynka/trinity/Inchworm/bin/pull_reads_with_kmers'
/usr/bin/install -c 'FastaToDeBruijn' '/home/rynka/trinity/Inchworm/bin/FastaToDeBruijn'
/usr/bin/install -c 'fastaToKmerCoverageStats' '/home/rynka/trinity/Inchworm/bin/fastaToKmerCoverageStats'
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/rynka/trinity/Inchworm/src'
make[2]: Leaving directory `/home/rynka/trinity/Inchworm/src'
make[2]: Entering directory `/home/rynka/trinity/Inchworm'
make[3]: Entering directory `/home/rynka/trinity/Inchworm'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/rynka/trinity/Inchworm'
make[2]: Leaving directory `/home/rynka/trinity/Inchworm'
make[1]: Leaving directory `/home/rynka/trinity/Inchworm'
cd Chrysalis && make UNSUPPORTED=yes
make[1]: Entering directory `/home/rynka/trinity/Chrysalis'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/rynka/trinity/Chrysalis'
cd trinity-plugins/rsem && make
make[1]: Entering directory `/home/rynka/trinity/trinity-plugins/rsem-1.2.3'
g++ -Wall -O2 -c -I. parseIt.cpp
In file included from sam/bam.h:52:0,
from SamParser.h:11,
from parseIt.cpp:26:
sam/bgzf.h:29:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make[1]: *** [parseIt.o] Error 1
make[1]: Leaving directory `/home/rynka/trinity/trinity-plugins/rsem-1.2.3'
make: *** [all] Error 2
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